Related LncRNAs
ID	lncRNA Name	Disease	Method	Sample	Expression pattern	Dysfunction type	Description	PMID	Source
EL0002	1700007L15Rik	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Involved in maintaining pluripotency in ESCs.	21874018
EL0005	4930570G19Rik	N/A	knockdown, over-expression	N/A	N/A	interaction	In vitro knockdown of the long non-coding RNA resulted in significant down-regulation of Negr1 mRNA expression, NEGR1 protein levels and neurite length whereas over-expression enhanced Negr1 mRNA expression, NEGR1 protein levels and increased neurite length. The long non-coding RNA, BC048612, and microRNA-203 were determined to be positive and negative regulators of Negr1 gene expression respectively.	26723899
EL0007	5430416N02Rik	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Mouse RNA was found to interact with a number of chromatin binding protein/complexes in mouse embryonic stem cells including PRC1, PRC2, JARID1B, ESET, SUV39H1, SETD8 and CBX1 with the general pattern being interaction with repressors of gene expression.	21874018
EL0009	6430411K18Rik	N/A	N/A	N/A	N/A	interaction	Several additional mirnas are processed from antipeg11 and that these regulate rtl1/peg11 in trans by guiding risc-mediated cleavage of its mrna.	15854907
EL0011	9530018H14Rik	N/A	ChIRP-seq, siRNA-mediated reductions	E 11 mouse embryos	up-regulated	interaction	Mechanistically the LncRNA-HIT siRNA treatments impacted pro-chondrogenic gene expression by reducing H3K27ac or p100 activity, confirming that LncRNA-HIT is essential for chondrogenic differentiation in the limb mesenchyme.	26633036
EL0026	AC058791.1	N/A	strand-specific RNA-seq	single radial glia cells	up-regulated	N/A	regulates cell proliferation	27081004
EL0033	Adapt15	N/A	methylmeth- anesulfonate and cis-platinum, X-irradiation	hamster HA-1 fibroblasts	up-regulated	expression	These rnas may act in concert to protect cells against the damaging effects of oxidative stress.	8638945
EL0033	Adapt15	N/A	RT-PCR, knockdown, MTT assay	N/A	N/A	interaction	Gadd7 regulates the G1/S checkpoint in response to UV irradiation.	23103768
EL0033	Adapt15	N/A	UV radiation, overexpression	Chinese hamster ovary (CHO) cells	up-regulated	expression	Overexpression of gadd7 led to a decrease in cell growth. interestingly, gadd7 cdna does not contain an appreciable open reading frame and does not appear to encode a protein product, but instead may function at the rna level.	8649973
EL0040	AFAP1-AS1	N/A	N/A	hepatocellular carcinoma (HCC) tissues	up-regulated	expression	High AFAP1-AS1 expression was associated with tumor size, TNM stage, vascular invasion, and poor prognosis. Silencing of AFAP1-AS1 significantly reduced cell proliferation, clonal growth, cell migration, and invasion and increased apoptosis in vitro. AFAP1-AS1 silencing markedly reduced tumor growth in a murine allograft model in vivo.	26803513
EL0041	AGAP2-AS1	N/A	RNA seq	human differentiated endothelial cells	up-regulated	expression	We have identified and functionally characterized 3 novel lncRNAs involved in vertebrate and human cardiovascular development, and we provide a comprehensive transcriptomic roadmap that sheds new light on the molecular mechanisms underlying human embryonic development, mesodermal commitment, and cardiovascular specification.	25739401
EL0043	AIRN	N/A	N/A	N/A	N/A	expression	Air rna is required for silencing. the truncated air allele maintains imprinted expression and methylation of the air promoter, but shows complete loss of silencing of the igf2r/slc22a2/slc22a3 gene cluster on the paternal chromosome.	11845212
EL0044	Airn	N/A	N/A	E6.5 epiblast	N/A	locus	Here we show lineage- and temporal-specific regulation of DNA methylation and histone modifications at the Igf2r/Airn locus correlating with differential establishment of imprinted expression during gastrulation. After gastrulation commences, the locus becomes imprinted in the embryonic lineage with the lncRNA Airn expressed from the paternal allele and Igf2r restricted to maternal allele expression.	25918552
EL0044	Airn	N/A	N/A	mouse placenta	up-regulated	interaction	Air accumulates at the Slc22a3 promoter in correlation with localized H3K9 methylation and transcriptional repression. Genetic ablation of G9a results in nonimprinted, biallelic transcription of Slc22a3.	18988810
EL0060	AK133540	N/A	lncRNA microarray	brown adipose tissue (BAT) and white adipose tissue (WAT)	N/A	expression	We found that AK142386 and AK133540 may affect adipogenesis and metabolism. Our data indicate that AK142386 and AK133540 may be involved in BAT and WAT development through their target genes Hoxa3 and Acad10.	25472036
EL0069	alncRNA-EC7	N/A	Depleting	differentiating mouse fetal liver red blood cells	N/A	N/A	alncRNA-EC7, is transcribed from an enhancer and is specifically needed for activation of the neighboring gene encoding BAND 3.	24200680
EL0070	alpha-250 and alpha-280	N/A	Tissue culture transfection and cell-free transcription, Electrophoretic mobility shift experiments	N/A	N/A	interaction	Alpha-250 and alpha-280 stimulate s14 mrna transcription, whereas free ribosomal protein s14 inhibits it.	7867928
EL0072	alpha-MHC antisense transcripts	N/A	Northern blot, RT-PCR	neonatal rat heart	N/A	expression	In the neonatal heart naturally occurring antisense mrna may play a role in the regulation of mhc expression and, therefore, in the control of the energetical and contractile behaviour of the heart.	9632112
EL0073	Alu lncRNAs	N/A	Biochemical assays to probe the network of protein-DNA interactions	mouse B2 RNA and human Alu RNA	N/A	interaction	We conclude that B2 and Alu RNA prevent Pol II from properly engaging the DNA during closed complex formation, resulting in complexes with an altered conformation that are transcriptionally inert. In the absence of its normal contacts with the promoter, Pol II is likely held in these inactive complexes on DNA through interactions with promoter-bound TATA box-binding protein and transcription factor IIB.	19307572
EL0074	Ancr-1	N/A	RNA fluorescent in situ hybridization, cDNA cloning	cortex	N/A	expression	Ancr-1 is involved in diverse organ functions.	15208441
EL0075	antisense TGF beta 3	N/A	N/A	chick heart	N/A	expression	The temporally controlled appearance of rna complementary to tgf beta 3 suggests that this molecule may play a role in the regulation of tgf beta 3 production in the heart.	1511174
EL0080	APOA1-AS	N/A	Chromatin immunoprecipitation (ChIP) analyses, Targeting APOA1-AS with short antisense oligonucleotides	human and monkey liver cells	down-regulated	N/A	acts as a negative transcriptional regulator of APOA1 both in vitro and in vivo. Inhibition of APOA1-AS in cultured cells resulted in the increased expression of APOA1 and two neighboring genes in the APO cluster.	24388749
EL0081	APOLO	N/A	RT-PCR/RT-qPCR	Auxin-controlled development	down-regulated	N/A	The Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport.	25018019	PLNlncRbase
EL0086	ASAR6	N/A	N/A	N/A	N/A	N/A	Disruption of the large non-coding RNA gene ASAR6 results in ate replication, an under-condensed appearance during mitosis, and structural instability of human chromosome 6. Similarly, disruption of the mouse Xist gene in adult somatic cells results in a late replication and instability phenotype on the X chromosome. ASAR6 shares many characteristics with Xist, including random mono-allelic expression and asynchronous replication timing.	22706734
EL0087	ASAR6	N/A	Disruption of ASAR6	N/A	N/A	N/A	Disruption of ASAR6 leads to the formation of bridged chromosomes, micronuclei, and structural instability of chromosome 6	23593023
EL0088	ASCO-RNA	N/A	qRT-PCR	leaves	up-regulated	N/A	Double Atnsr mutants and ASCO overexpressors exhibit an altered ability to form LRs after auxin treatment. Interestingly, auxin induces a major change in AS patterns of many genes, a response largely dependent on NSRs. RNA immunoprecipitation assays demonstrate that AtNSRs interact not only with their alternatively spliced mRNA targets but also with the ASCO-RNA in vivo. The ASCO-RNA displaces an AS target from an NSR-containing complex in vitro. Expression of ASCO-RNA(lnc351) in Arabidopsis affects the splicing patterns of several NSR-regulated mRNA targets. Hence, lncRNA can hijack nuclear AS regulators to modulate AS patterns during development. Plants overexpressing the ASCO-RNA showed changes in isoform distribution of the auxin-related protein (At2G33830). (Bardou et al., 2014) Expression of the lncRNA ASCO-RNA do not promote lateral root growth. The lncRNA does not cause NSR relocalization but alters NSR activity through direct binding to NSRs and displacement of them from their mRNA targets. In other words, ASCO-RNA prevents the effects of NSRs on the regulation of alternative splicing in their transcript targets. ASCO-RNA overexpression in live plants duplicates the morphological effects observed in the nsra/nsrbdouble mutant, i.e., a decreased lateral root density when plants are grown on auxin. (Kornblihtt et al., 2014)	25073154, 25073153	PLNlncRbase
EL0089	asHSFB2a	N/A	qRT-PCR/Southern blot hybridization	gametophyte development	up-regulated	N/A	HSFB2a expression was counteracted by a natural long non-coding antisense RNA, asHSFB2a. In leaves, the antisense RNA gene is only expressed after heat stress and dependent on the activity of HSFA1a/HSFA1b. HSFB2a and asHSFB2a RNAs were also present in the absence of heat stress in the female gametophyte. Transgenic overexpression of HSFB2a resulted in a complete knock down of the asHSFB2a expression. Conversely, asHSFB2a overexpression leads to the absence of HSFB2a RNA. The knockdown of HSFB2a by asHSFB2a correlated with an improved, knockdown of asHSFB2a by HSFB2a overexpression with an impaired biomass production early in vegetative development. In both cases the development of female gametophytes was impaired.	24874772	PLNlncRbase
EL0091	ASL	N/A	RT-PCR	vernalization	down-regulated	N/A	Furthermore, AtRRP6L1 physically associates with the ASL transcript and directly interacts with the FLC locus. We propose that AtRRP6L proteins participate in the maintenance of H3K27me3 at FLC via regulating ASL. Furthermore, AtRRP6Ls might participate in multiple FLC silencing pathways by regulating diverse antisense RNAs derived from the FLC locus.	25211139	PLNlncRbase
EL0095	AT102202	N/A	Microarrays, RT-PCR	cultured human liver (HepG2) hepatocytes treated with epigallocatechin-3-gallate( EGCG)	up-regulated	expression	Using a real-time polymerase chain reaction technique, we confirmed that EGCG down-regulated mRNA expression level of the HMGCR and up-regulated expression of AT102202. After AT102202 knockdown in HepG2, weobserved that the level of HMGCR expression was significantly increased relative to the scrambled small interfering RNA control (P < 0.05).	25563320
EL0096	AT1G04425	N/A	qRT-PCR/RT-PCR	heat and highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, AT1G04425 is downregulated by heat and highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0097	AT1G10682	N/A	qRT-PCR/RT-PCR	heat and highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, AT1G10682 is downregulated by heat and highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0098	AT1G11175	N/A	qRT-PCR/RT-PCR	cold/salt	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G11175 is downregulated by cold stress and upregulated by salt stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0099	AT1G11185	N/A	qRT-PCR/RT-PCR	drought and salt	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, and lncRNA AT1G11185 is upregulated by drought and salt stresses. (details are listed in Appendix S2)	25256571	PLNlncRbase
EL0100	AT1G13448	N/A	qRT-PCR/RT-PCR	cold, highlight and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, and lncRNA AT1G13448 is downregulated by cold/highlight/salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0101	AT1G15002	N/A	qRT-PCR/RT-PCR	heat/cold	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT1G15002 is upregulated by cold/highlight stresses and downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0102	AT1G15175	N/A	qRT-PCR/RT-PCR	cold, heat and highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT1G15175 is downregulated by cold/heat/highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0103	AT1G15405	N/A	qRT-PCR/RT-PCR	highlight/salt	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G15405 is upregulated by salt stress and downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0104	AT1G16635	N/A	qRT-PCR/RT-PCR	cold and highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G16635 is upregulated by cold/highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0105	AT1G18745	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, AT1G18745 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0106	AT1G21529	N/A	qRT-PCR/RT-PCR	heat	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, AT1G21529 is upregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0107	AT1G26208	N/A	qRT-PCR/RT-PCR	heat and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, AT1G26208 is downregulated by heat and salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0108	AT1G26558	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, AT1G26558 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0109	AT1G31935	N/A	qRT-PCR/RT-PCR	heat and highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G31935 is downregulated by heat and highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0110	AT1G34418	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G34418 is downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0111	AT1G43765	N/A	qRT-PCR/RT-PCR	drought	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G43765 is upregulated by drought stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0112	AT1G46554	N/A	qRT-PCR/RT-PCR	drought/heat	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G46554 is upregulated by drought stress and downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0113	AT1G57835	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G57835 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0114	AT1G58590	N/A	qRT-PCR/RT-PCR	heat and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G58590 is downregulated by heat and salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0115	AT1G64618	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G64618 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0116	AT1G67105	N/A	qRT-PCR/RT-PCR	drought and highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G67105 is upregulated by drought and highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0117	AT1G67365	N/A	qRT-PCR/RT-PCR	drought, heat and salt	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G67365 is upregulated by drought, heat and salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0118	AT1G69252	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G69252 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0119	AT1G70518	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G70518 is downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0120	AT1G74205	N/A	qRT-PCR/RT-PCR	cold, drought and heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT1G74205 is downregulated by cold/drought/heat stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0121	At1NC018710	N/A	qRT-PCR/RNA-seq	roots	up-regulated	N/A	Figure 3. Expression Profiles of lincRNAs in Different Arabidopsis Plant Organs and in Response to Biotic and Abiotic Stresses.	23136377	PLNlncRbase
EL0122	AT1TU075330	N/A	qRT-PCR	light	up-regulated	N/A	Our qRT-PCR results confirmed that some lncNATs were significantly regulated by light and their expression profiles were also consistent with the results from ATH NAT arrays (Figure 2 C-F, Supplemental Figure 8 and Supplemental Table 3).	24402519	PLNlncRbase
EL0123	AT1TU099900	N/A	qRT-PCR	light	up-regulated	N/A	Our qRT-PCR results confirmed that some lncNATs were significantly regulated by light and their expression profiles were also consistent with the results from ATH NAT arrays (Figure 2 C-F, Supplemental Figure 8 and Supplemental Table 3).	24402519	PLNlncRbase
EL0124	AT2G01422	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G01422 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0125	AT2G06002	N/A	qRT-PCR/RT-PCR	cold, drought, heat, highlight and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G06002 is downregulated by cold/drought/heat/highlight/salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0126	AT2G09795	N/A	qRT-PCR/RT-PCR	heat and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G09795 is downregulated by heat and salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0127	AT2G14878	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G14878 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0128	AT2G15292	N/A	qRT-PCR/RT-PCR	heat and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G15292 is downregulated by heat and salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0129	AT2G15555	N/A	qRT-PCR/RT-PCR	drought and highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G15555 is upregulated by drought and highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0130	AT2G18735	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G18735 is downregulated by heat stress and upregulated by drought and highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0131	AT2G26355	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G26355 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0132	AT2G31585	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G31585 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0133	AT2G32315	N/A	qRT-PCR/RT-PCR	drought	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G32315 is upregulated by drought stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0134	AT2G32795	N/A	qRT-PCR/RT-PCR	cold and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G32795 is downregulated by cold/salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0135	AT2G41178	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G41178 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0136	AT2G41312	N/A	qRT-PCR/RT-PCR	cold and heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G41312 is downregulated by cold and heat stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0137	AT2G42388	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G42388 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0138	AT2G42485	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G42485 is downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0139	AT2G43375	N/A	qRT-PCR/RT-PCR	highlight/salt	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G43375 is upregulated by highlight stress and downregulated by salt stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0140	AT2G44798	N/A	qRT-PCR/RT-PCR	drought and highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G44798 is upregulated by drought and highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0141	AT2G44995	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G44995 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0142	AT2G45023	N/A	qRT-PCR/RT-PCR	drought, heat and highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G45023 is downregulated by drought/heat/highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0143	AT2G45245	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G45245 is downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0144	AT2G46192	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT2G46192 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0145	At2NC044550	N/A	qRT-PCR/RNA-seq	leaves	up-regulated	N/A	Figure 3. Expression Profiles of lincRNAs in Different Arabidopsis Plant Organs and in Response to Biotic and Abiotic Stresses.	23136377	PLNlncRbase
EL0146	AT2TU076050	N/A	qRT-PCR	hypocotyls	up-regulated	N/A	The majority of light-regulated NAT pairs at the two time points were different suggesting amplification of light signal and utilization of specific NAT pairs in short and long term light response. For example, SPA1, which encodes a light signaling repressor, was up-regulated more than eight times after 1h of light treatment in cotyledons. Its concordant antisense transcript, AT2TU076050, was also up-regulated more than four times at the same time point and in the same organ. Neither showed such strong induction at the other time point or organs.	24402519	PLNlncRbase
EL0147	AT2TU077810	N/A	qRT-PCR	hypocotyls	up-regulated	N/A	Our qRT-PCR results confirmed that some lncNATs were significantly regulated by light and their expression profiles were also consistent with the results from ATH NAT arrays (Figure 2 C-F, Supplemental Figure 8 and Supplemental Table 3).	24402519	PLNlncRbase
EL0148	AT3G04485	N/A	qRT-PCR/RT-PCR	drought, heat and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G04485 is downregulated by drought/heat/salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0149	AT3G06125	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G06125 is downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0150	AT3G07215	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G07215 is downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0151	AT3G13277	N/A	qRT-PCR/RT-PCR	highlight/cold	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G13277 is upregulated by highlight stress and downregulated by cold and heat stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0152	AT3G27884	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G27884 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0153	AT3G27990	N/A	qRT-PCR/RT-PCR	heat and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G27990 is downregulated by heat and salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0154	AT3G29644	N/A	qRT-PCR/RT-PCR	highlight and salt	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G29644 is upregulated by highlight and salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0155	AT3G44798	N/A	qRT-PCR/RT-PCR	salt	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G44798 is upregulated by salt stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0156	AT3G45638	N/A	qRT-PCR/RT-PCR	cold	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G45638 is upregulated by cold stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0157	AT3G48115	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G48115 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0158	AT3G52072	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions,and lncRNA AT3G52072 is downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0159	AT3G52742	N/A	qRT-PCR/RT-PCR	cold, drought and highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT3G52742 is upregulated by cold/drought/highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0160	AT3G52748	N/A	qRT-PCR/RT-PCR	salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT3G52748 is downregulated by salt stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0161	AT3G54366	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT3G54366 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0162	AT3G57157	N/A	qRT-PCR/RT-PCR	heat/highlight	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT3G57157 is upregulated by highlight stress and downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0163	AT3G59765	N/A	qRT-PCR/RT-PCR	drought, heat, highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT3G59765 is downregulated by drought/heat/highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0164	AT3G60972	N/A	qRT-PCR/RT-PCR	drought	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT3G60972 is upregulated by drought stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0165	AT3G61198	N/A	qRT-PCR/RT-PCR	cold	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT3G61198 is downregulated by cold stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0166	AT3TU028510	N/A	qRT-PCR	hypocotyls	up-regulated	N/A	The majority of light-regulated NAT pairs at the two time points were different suggesting amplification of light signal and utilization of specific NAT pairs in short and long term light response. For example, SPA1, which encodes a light signaling repressor, was up-regulated more than eight times after 1 h of light treatment in cotyledons. Its concordant antisense transcript, AT2TU076050,was also up-regulated more than four times at the same time point and in the same organ. Neither showed such strong induction at the other time point or organs. Another example is HYH, a homolog of HY5, and its concordant NAT, AT3TU028510. At 1h, both HYH and AT3TU028510 were significantly induced in hypocotyls only; they were further induced at 6h in roots as well as hypocotyls.	24402519	PLNlncRbase
EL0167	AT3TU075200	N/A	qRT-PCR	hypocotyls	up-regulated	N/A	Genes coding for transcription factors were significantly over-represented after 1h of white light, whereas metabolism-related genes were over-represented after 6h of white light. For example, an mRNA coding the phototropic-responsive NPH3 family protein, AT3G49970, was specifically down-regulated in hypocotyls after 1h light accompanied by its up-regulated lncNAT, AT3TU075200.	24402519	PLNlncRbase
EL0168	At4	N/A	RT-PCR	roots	up-regulated	N/A	Loss of At4 lead to increased shoot Pi content and an increase in the shoot: root Pi ratio under low Pi conditions suggesting At4 affects Pi distribution and plant growth. (Shin et al., 2006) In Arabidopsis, the induced expression of ncRNAs of the IPS1/At4 family during phosphate starvation responses results in the accumulation of the PHO2 mRNA,a target of miR399 (micro-RNA 399). showed that a conserved motif of 23 nt in this ncRNA family is complementary to miR399 but has critical mismatches at positions. Therefore, IPS1/At4 RNAs are not cleaved by miR399 but instead sequester miR399 to inhibit its effect on PHO2 mRNA, in a mechanism known as target mimicry. PHO2 RNA encodes an E2 ubiquitin conjugase-related protein that negatively affects shoot phosphate content and remobilization in an unknown mechanism. (Au et al., 2011) The Arabidopsis pho1 mutant is impaired in its ability to load Pi into the xylem and therefore to translocate Pi to the shoot. At4 transcripts were abundant in pho1 plants receiving both low-Pi and high-Pi fertilizer. These results were observed in two independent experiments. Thus, the At4 transcript is not down-regulated in response to Pi in the pho1 mutant, suggesting that down-regulation is dependent on the translocation of Pi to the shoot. (Burleigh et al., 1999) At4 was designated as the TPSI1/Mt4 family because of their common characteristics. They are up-regulated by P limitation and rapidly down-regulated by supply of P or colonization of mycorrhizal fungi. This fact indicates the possibility that they have an important role on the strategies for low P adaptation, although their physiological function is not still clarified. (Jun et al., 2003)	16460506, 21525783, 9880366	PLNlncRbase
EL0169	At4-1	N/A	Northern blot/RT-PCR	roots	up-regulated	N/A	We also tested the effects of overexpressing a close IPS1 paralog, At4. As with IPS1I, At4 overexpression also resulted in decreased shoot Pi accumulation (Supplementary Fig. 4a online). This finding suggests redundancy between IPS1 and At4 and possibly among the other IPS1 family members, all of which are responsive to Pi starvation and contain a region of miR-399 complementarity (Supplementary Fig. 1). (Franco-Zorrilla et al., 2007) The second regulatory mechanism of lncRNAs in plants might work as a decoy of miRNAs, these kind of lncRNAs exert their functions by binding miRNAs in a target mimicry mechanism to sequestrate the miRNAs’ regulation roles on their target genes, such as lncRNAs IPS1 and at4. IPS1 is complementary to miR399, but contains a mismatch loop which makes it uncleavable when miR399 binding. It is induced by phosphate starvation in plants, and then allows the increased expression of miR399 targets including PHO2, consequently alters shoot phosphate content. IPS1 has many family members in a number of plant species, including At4, At4-1, At4-2 and At4-3 in Arabidopsis thaliana. At4 appears to be functionally redundant with IPS1, overexpression of one of them could result in the same phenotypic change as that when overexpressing both At4 and IPS1. (Zhang et al., 2013)	17643101, 23726911	PLNlncRbase
EL0170	At4-2	N/A	Northern blot/RT-PCR	roots	up-regulated	N/A	We also tested the effects of overexpressing a close IPS1 paralog, At4. As with IPS1I, At4 overexpression also resulted in decreased shoot Pi accumulation (Supplementary Fig. 4a online). This finding suggests redundancy between IPS1 and At4 and possibly among the other IPS1 family members, all of which are responsive to Pi starvation and contain a region of miR-399 complementarity (Supplementary Fig. 1). (Franco-Zorrilla et al., 2007) The second regulatory mechanism of lncRNAs in plants might work as a decoy of miRNAs, these kind of lncRNAs exert their functions by binding miRNAs in a target mimicry mechanism to sequestrate the miRNAs’ regulation roles on their target genes, such as lncRNAs IPS1 and at4. IPS1 is complementary to miR399, but contains a mismatch loop which makes it uncleavable when miR399 binding. It is induced by phosphate starvation in plants, and then allows the increased expression of miR399 targets including PHO2, consequently alters shoot phosphate content. IPS1 has many family members in a number of plant species, including At4, At4-1, At4-2 and At4-3 in Arabidopsis thaliana. At4 appears to be functionally redundant with IPS1, overexpression of one of them could result in the same phenotypic change as that when overexpressing both At4 and IPS1. (Zhang et al., 2013)	17643101, 23726911	PLNlncRbase
EL0171	At4-3	N/A	Northern blot/RT-PCR	roots	up-regulated	N/A	We also tested the effects of overexpressing a close IPS1 paralog, At4. As with IPS1I, At4 overexpression also resulted in decreased shoot Pi accumulation (Supplementary Fig. 4a online). This finding suggests redundancy between IPS1 and At4 and possibly among the other IPS1 family members, all of which are responsive to Pi starvation and contain a region of miR-399 complementarity (Supplementary Fig. 1). (Franco-Zorrilla et al., 2007) The second regulatory mechanism of lncRNAs in plants might work as a decoy of miRNAs, these kind of lncRNAs exert their functions by binding miRNAs in a target mimicry mechanism to sequestrate the miRNAs’ regulation roles on their target genes, such as lncRNAs IPS1 and at4. IPS1 is complementary to miR399, but contains a mismatch loop which makes it uncleavable when miR399 binding. It is induced by phosphate starvation in plants, and then allows the increased expression of miR399 targets including PHO2, consequently alters shoot phosphate content. IPS1 has many family members in a number of plant species, including At4, At4-1, At4-2 and At4-3 in Arabidopsis thaliana. At4 appears to be functionally redundant with IPS1, overexpression of one of them could result in the same phenotypic change as that when overexpressing both At4 and IPS1. (Zhang et al., 2013)	17643101, 23726911	PLNlncRbase
EL0172	AT4G01533	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G01533 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0173	AT4G01593	N/A	qRT-PCR/RT-PCR	cold, heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G01593 is downregulated by cold and heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0174	AT4G02005	N/A	qRT-PCR/RT-PCR	salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G02005 is downregulated by salt stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0175	AT4G03811	N/A	qRT-PCR/RT-PCR	salt	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G03811 is upregulated by salt stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0176	AT4G06701	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G06701 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0177	AT4G08035	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G08035 is downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0178	AT4G13495	N/A	qRT-PCR/RT-PCR	heat, highlight, salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G13495 is downregulated by heat/highlight/salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0179	AT4G14548	N/A	qRT-PCR/RT-PCR	drought, salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G14548 is downregulated by drought and salt stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0180	AT4G15242	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G15242 is upregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0181	AT4G20362	N/A	qRT-PCR	hypocotyls	down-regulated	N/A	We also found 766 light-responsive discordant NAT pairs (Figure 3B&E and Supplemental Figure9). Here, the large number of light-responsive, discordant NAT pairs that were identified suggested a potentially widespread occurrence of negative regulation by NATs.	24402519	PLNlncRbase
EL0182	AT4G30975	N/A	qRT-PCR/RT-PCR	salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G30975 is downregulated by salt stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0183	AT4G36648	N/A	qRT-PCR/RT-PCR	heat	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G36648 is downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0184	AT4G38932	N/A	qRT-PCR/RT-PCR	salt/cold and higlight	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G38932 is upregulated by salt stress and downregulated by cold/highlight stresses .(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0185	AT4G40065	N/A	qRT-PCR/RT-PCR	heat/highlight	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT4G40065 is upregulated by highlight stress and downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0186	At4NC047210	N/A	qRT-PCR/RNA-seq	flowers	up-regulated	N/A	Figure 3. Expression Profiles of lincRNAs in Different Arabidopsis Plant Organs and in Response to Biotic and Abiotic Stresses.	23136377	PLNlncRbase
EL0187	AT4TU030900	N/A	qRT-PCR	hypocotyls	up-regulated	N/A	Our qRT-PCR results confirmed that some lncNATs were significantly regulated by light and their expression profiles were also consistent with the results from ATH NAT arrays (Figure 2 C-F, Supplemental Figure 8 and Supplemental Table 3).	24402519	PLNlncRbase
EL0188	AT4TU034830	N/A	qRT-PCR	hypocotyls	up-regulated	N/A	Our qRT-PCR results confirmed that some lncNATs were significantly regulated by light and their expression profiles were also consistent with the results from ATH NAT arrays (Figure 2 C-F, Supplemental Figure 8 and Supplemental Table 3).	24402519	PLNlncRbase
EL0189	AT5G01175	N/A	qRT-PCR/RT-PCR	cold	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G01175 is upregulated by cold stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0190	AT5G03285	N/A	qRT-PCR/RT-PCR	cold/heat	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G03285 is upregulated by heat stress and downregulated by cold.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0191	AT5G06165	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G06165 is upregulated highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0192	AT5G07322	N/A	qRT-PCR/RT-PCR	drought, highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G07322 is downregulated by drought/highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0193	AT5G15022	N/A	qRT-PCR/RT-PCR	highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G15022 is upregulated highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0194	AT5G23410	N/A	qRT-PCR/RT-PCR	heat/drought	down-regulated/up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G23410 is upregulated by drought stress and downregulated by heat stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0195	AT5G24735	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G24735 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0196	AT5G40316	N/A	qRT-PCR/RT-PCR	highlight, salt	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G40316 is upregulated by highlight/salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0197	AT5G43403	N/A	qRT-PCR/RT-PCR	drought, highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G43403 is upregulated by drought/highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0198	AT5G43725	N/A	qRT-PCR/RT-PCR	heat, salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G43725 is downregulated by heat/salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0199	AT5G44569	N/A	qRT-PCR/RT-PCR	drought/salt	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G44569 is upregulated by drought/salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0200	AT5G48412	N/A	qRT-PCR/RT-PCR	highlight	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G48412 is downregulated by highlight stress.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0201	AT5G50190	N/A	qRT-PCR/RT-PCR	drought, highlight, salt	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT5G50190 is upregulated by drought/highlight/salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0202	At5NC025190	N/A	qRT-PCR/RNA-seq	drought and ABA	up-regulated	N/A	The expression of four representative lincRNAs by qRT-PCR (see Supplemental Figure 12 online). All of the four lincRNAs showed similar induction pattern during drought stress or ABA treatment.	23136377	PLNlncRbase
EL0203	At5NC029980	N/A	qRT-PCR/RNA-seq	drought and ABA	up-regulated	N/A	The expression of four representative lincRNAs by qRT-PCR (see Supplemental Figure 12 online). All of the four lincRNAs showed similar induction pattern during drought stress or ABA treatment.	23136377	PLNlncRbase
EL0204	At5NC055270	N/A	qRT-PCR/RNA-seq	drought and ABA	up-regulated	N/A	The expression of four representative lincRNAs by qRT-PCR (see Supplemental Figure 12 online). All of the four lincRNAs showed similar induction pattern during drought stress or ABA treatment.	23136377	PLNlncRbase
EL0205	At5NC056820	N/A	qRT-PCR/RNA-seq	flowers	up-regulated	N/A	Detection and experimental verification of At5NC056820, a predicted lincRNA. Expression levels are given with SD bars (n = 3). Note that At5NC056820 was highly induced by elf18 and moderately induced by ABA and drought treatment.	23136377	PLNlncRbase
EL0206	AT5TU062110	N/A	qRT-PCR	hypocotyls	up-regulated	N/A	Our qRT-PCR results confirmed that some lncNATs were significantly regulated by light and their expression profiles were also consistent with the results from ATH NAT arrays (Figure 2 C-F, Supplemental Figure 8 and Supplemental Table 3).	24402519	PLNlncRbase
EL0207	AtCR20-1	N/A	microarray, qRT-PCR	cytokinins/phosphate starvation	down-regulated/up-regulated	N/A	AtCR20-1 is regulated by biotic (down-regulated by cytokinins) and abiotic (up-regulated by phosphate starvation) signals. AtGUT15 and AtCR20-1 comprise two members of a family of genes that lack a long ORF.	11706161	PLNlncRbase
EL0208	AtGUT15	N/A	microarray, qRT-PCR	seeds	up-regulated	N/A	AtGUT15 is regulated by biotic (down-regulated by cytokinins) and abiotic (up-regulated by phosphate starvation) signals. AtGUT15 and AtCR20-1 comprise two members of a family of genes that lack a long ORF.	11706161	PLNlncRbase
EL0211	AtR18	N/A	RT-PCR	hypoxic stress	down-regulated	N/A	A specific Pol III-derived ncRNA (AtR18) responded negatively to hypoxic stress and this regulation was evidently different from that of U6 snRNA. Specifically, AtR18 was not processed into a smaller fragment and no small open reading frames (sORFs) were included.	24252906	PLNlncRbase
EL0212	AtR18	N/A	RT-PCR	hypoxic stress	down-regulated	N/A	AtR18, transcribed by RNA polymerase III (Pol III), were identified by efficient in vitro transcription in tobacco nuclear extracts.	24914100	PLNlncRbase
EL0213	AtR8	N/A	RT-PCR	roots and cytosol of cultured cells	down-regulated	N/A	A root-specific AtR8 RNA was found in Arabidopsis. AtR8 RNA was observed in the plant roots and cytosol of cultured cells. The RNA was not processed into a smaller fragment and no short open reading frame was included. AtR8 RNA are transcribed by Pol III and not by Pol II. The expression of the AtR8 RNA responded negatively to hypoxic stress, and this regulation evidently differed from that of U6 snRNA. AtR8 RNA expression respond to hypoxic stress. The AtR8 RNA levels gradually declined under the hypoxic conditions.	22336715	PLNlncRbase
EL0214	AtR8	N/A	RT-PCR	hypoxic stress	down-regulated	N/A	AtR8, transcribed by RNA polymerase III (Pol III), were identified by efficient in vitro transcription in tobacco nuclear extracts.	24914100	PLNlncRbase
EL0222	B2 SINE RNA	N/A	electrophoretic mobility shift assays	plasmids	N/A	interaction	In vitro B2 RNA assembles into preinitiation complexes on promoter DNA via its interaction with the polymerase, thus rendering the complexes inactive.	17307818
EL0222	B2 SINE RNA	N/A	N/A	N/A	N/A	epigenetics	miR-468-mediated suppression of LSH leads to aberrant methylation of LINE1 and SINE B2.	19959559	LncRNADisease
EL0223	B4GALT1-AS1	N/A	cap analysis of gene expression (CAGE)	normal and malignant tissues	N/A	interaction	We identified at 5'-end of B4GALT1 a 1.454 kb sequence forming a transcription regulatory region, referred to by us as the TR1-PE1, had all characteristics of a bidirectional promoter directing the transcription of B4GALT1 in a divergent manner along with its long non-coding RNA (lncRNA) antisense counterpart B4GALT1-AS1. The five lncRNA B4GALT1-AS1 transcripts showed significant complementarity with B4GALT1 mRNA.	26315939
EL0234	Bc1	N/A	Biochemical experiments	nerve cells	N/A	interaction	Bc1-mediated repression targets translation at the level of initiation. specifically, bc1 rna inhibited formation of the 48s preinitiation complex	12451124
EL0234	Bc1	N/A	eliminate the BC1 RNA gene	N/A	N/A	expression	The lack of bc1 rna appears to reduce exploratory activity.	12944471
EL0234	Bc1	N/A	N/A	N/A	N/A	interaction	Competition experiments using variants of bc1 and bc200 rnas demonstrated that the central adenosine-rich region of both rnas mediates binding to pabp.	12162957
EL0234	Bc1	N/A	N/A	controls and knockout mice	N/A	expression	The neuron-specific non-messenger bc1 rna contributes to the aptive modulation of behaviour.	15302134
EL0234	Bc1	N/A	N/A	rabbit reticulocyte lysate system, HeLa cells	N/A	interaction	In vivo, all bc1 rna appears to be complexed with pabp. nevertheless, in the micro-environment of dendritic spines of neuronal cells, bc1 rnps or bc200 rnps might mediate regulatory functions by differential interactions with locally limited pabp and/or directly or indirectly, with other translation initiation factors.	16154588
EL0234	Bc1	N/A	Western-blot	Oocytes	N/A	interaction	Interactions of this domain with eukaryotic initiation factor 4A and poly(A) binding protein mediate repression;BC1 RNA modulates translation-dependent processes in neurons and germs cells by directly interacting with translation initiation factors.	16330711
EL0236	BcMF11	N/A	RT-PCR	pollen development	up-regulated	N/A	A 828-bp full-length cDNA of BcMF11, a novel pollen-specific non-coding mRNA-like gene from Chinese cabbage. Antisense RNA transgenic plants displayed decreasing expression of BcMF11 and showed distinct morphological defects. Pollen germination test in vitro and in vivo of the transgenic plants suggested that inhibition of BcMF11 decreased pollen germination efficiency and delayed the pollen tubes’ extension in the style. Under scanning electron microscopy, many shrunken and collapsed pollen grains were detected in the antisense BcMF11 transgenic Chinese cabbage. Further cytological observation revealed abnormal pollen development process in transgenic plants, including delayed degradation of tapetum, asynchronous separation of microspore, and aborted development of pollen grain. These results suggest that BcMF11, as a non-coding RNA, plays an essential role in pollen development and male fertility. RT-PCR and Northern blotting analyses showed that BcMF11 was transcribed at most stages of pollen development. These results suggested that the BcMF11 is a novel non-coding RNA involved in pollen development of Chinese cabbage. (Song et al., 2013) The BcMF11 cDNA has a total length of 828 bp with poly (A) tail. Analysis of the sequence demonstrated that BcMF11 is a novel non-coding RNA which has no prominent open reading frame (ORF) or coding capacity. Transcription analysis indicated that BcMF11 is a novel pollen-specific ncRNA and may be involved in the pollen development of Chinese cabbage. BcMF11 was expressed in developing flower buds, flowers and anthers at a high level, but was not detected in roots, stems, leaves, pistils and developing siliques. Identical expression patterns were also showed in RT-PCR analysis. This indicated BcMF11 is a pollen-preferential expressed gene in Chinese cabbage. (Song et al., 2007)	23064614, 17207554	PLNlncRbase
EL0237	BCYRN1	N/A	BC200 truncations and RNase footprinting assays, pull-down assays	N/A	N/A	interaction	Tests performed to assess whether BC200 interferes with RHAU helicase activity have demonstrated the ability of BC200 to act as an acceptor of unwound quadruplexes via a cytosine-rich region near the 3'-end of the RNA. RHAU may direct BC200 to bind and exert regulatory functions at quadruplex-containing RNA or DNA sequences.	26740632
EL0237	BCYRN1	N/A	N/A	N/A	N/A	interaction	Competition experiments using variants of bc1 and bc200 rnas demonstrated that the central adenosine-rich region of both rnas mediates binding to pabp.	12162957
EL0237	BCYRN1	N/A	N/A	rabbit reticulocyte lysate system, HeLa cells	N/A	interaction	In vivo, all bc1 rna appears to be complexed with pabp. nevertheless, in the micro-environment of dendritic spines of neuronal cells, bc1 rnps or bc200 rnps might mediate regulatory functions by differential interactions with locally limited pabp and/or directly or indirectly, with other translation initiation factors.	16154588
EL0237	BCYRN1	N/A	N/A	N/A	N/A	expression	In normal aging, BC200 levels in cortical areas were reduced by >60% between the ages of 49 and 86. In contrast, BC200 RNA was significantly up-regulated in AD brains, in comparison with age-matched normal brains.	17553964	LncRNADisease
EL0237	BCYRN1	N/A	N/A	N/A	N/A	interaction	A protein that binds bc200 rna in vivo is immunoreactive with antibodies against srp9.	9605471
EL0237	BCYRN1	N/A	transgenic	transgenic mice	N/A	expression	when all upstream regions of the G22 gene were removed, expression was completely abolished, despite the presence of intact internal RNA polymerase III promoter elements	17175535
EL0241	bft	N/A	N/A	N/A	N/A	expression	Bft acts downstream of cut and tramtrack to implement correct bristle morphogenesis.	12019237
EL0247	Borg	N/A	In situ hybridization,RT-PCR	N/A	N/A	expression	Nuclear localization of BORG was mediated through a novel RNA motif consisting of the pentamer sequence AGCCC with sequence restrictions at positions -8 (T or A) and -3 (G or C) relative to the first nucleotide of the pentamer.	24732794
EL0247	Borg	N/A	N/A	C2C12 mouse myoblast cell line	N/A	expression	The transcript of borg lacks any extensive open reading frames and contains a cluster of multiple interspersed repetitive sequences in its middle part.	9642273
EL0249	BRCA1	N/A	knockdown	human fibroblast cells	N/A	expression	Gene expression analysis after RNAi treatment targeted against DDSR1 revealed 119 genes that show differential expression.	26697398
EL0249	BRCA1	N/A	microarray, qRT-PCR	N/A	N/A	interaction	Loss of DDSR1 impairs cell proliferation and DDR signaling and reduces DNA repair capacity by homologous recombination (HR). The HR defect in the absence of DDSR1 is marked by aberrant accumulation of BRCA1 and RAP80 at DSB sites.	26411689
EL0262	C730029A08Rik	N/A	knockdown	N/A	N/A	interaction	Blnc1 promotes brown and beige adipocyte differentiation and function	25002143
EL0263	C730036E19Rik	N/A	knockdown	mouse liver	up-regulated	expression	These data support a model in which lncLSTR regulates a TDP-43/FXR/apoC2-dependent pathway to maintain systemic lipid homeostasis.	25738460
EL0270	CARs	N/A	sequencing, Northern hybridization, ChRIP, qPCR, RACE, siRNA transfection	human fibroblast (HF) cells	N/A	N/A	regulates gene expression of neighboring genes through modulating the chromatin structure in cis.	20404130
EL0284	CCLS96.1	N/A	RT-PCR/Northern blot	flower buds	up-regulated	N/A	A 1.8-kb transcript was observed not only in male flower buds but also in female flower buds. The hybridization signal of CCLS96.1 in the Northern blot analysis was so week that semi-quantitative RT-PCR was performed to analyze the expression patterns of CCLS96.1. CCLS96.1 was expressed also in male and female leaves.In the male plant, the expression of CCLS96.1 in flower buds was 2.67-to 3.42-fold higher than that in leaves. In contrast, in the female plant, the expression of CCLS96.1 in flower buds was 0.06-to 0.19-fold less than that in leaves. This suggests that the CCLS96.1 homologs play some role in the male flower bud. CCLS96.1 was also expressed in both male and female leaves. CCLS96.1 homologs are expressed in leaves and buds. The CCLS96.1 homologs play some role in the male flower bud. (Sugiyama et al., 2003) CCLS96.1 expressed in both genders in leaves and flowers, yet it is expressed 3-fold higher in male flowers than in female flowers, and 4-8-fold higher in female leaves than in male leaves suggestive that CCLS96.1 plays a role in male flowers and perhaps female leaves, a mode of action has yet to be ascertained. (Rymarquis et al., 2008)	14686583, 18448381	PLNlncRbase
EL0286	CCND1 promoter-derived lncRNAs	N/A	N/A	N/A	N/A	expression	Biogenesis, metabolism, and functions of lncRNAs are otherwise interconnected with known pathogenic mechanisms	23791884	LncRNADisease
EL0289	CDKN2B-AS1	N/A	N/A	N/A	N/A	mutation	Recent studies showed that single nucleotide polymorphisms (rs3217992, A>G;rs1063192, C>T) mapping in the vicinity of ANRIL are linked to a wide spectrum of conditions, including cardiovascular disease, ischemic stroke, type 2 diabetes, frailty and Alzheimer's disease.	17459456	LncRNADisease
EL0290	CDR1-AS	N/A	N/A	mouse brain	N/A	N/A	acts as a miR-7 sponge	23446346
EL0290	CDR1-AS	N/A	sequence and computationally analysis, knockdown	N/A	N/A	N/A	CDR1as is a miRNA antagonist with a miRNA-binding capacity ten times higher than any other known transcript.	23446348
EL0297	cis-NATPHO1;2	N/A	qRT-PCR	Phosphate homeostasis	up-regulated	N/A	PHOSPHATE1;2 (PHO1;2), a gene involved in phosphate loading into the xylem in rice, and its associated cis-NATPHO1;2 are both controlled by promoters active in the vascular cylinder of roots and leaves. While the PHO1;2 promoter is unresponsive to the plant phosphate status, the cis-NATPHO1;2 promoter is strongly upregulated under phosphate deficiency.	24096344	PLNlncRbase
EL0299	COLDAIR	N/A	RT-PCR	vernalization	down-regulated	N/A	COLDAIR, an intronic long ncRNA of the FLC. COLDAIR is required for the vernalization-mediated epigenetic repression of FLC. COLDAIR physically associates with a component of PRC2 and targets PRC2 to FLC. Our results show that COLDAIR is required for establishing stable repressive chromatin at FLC through its interaction with PRC2. COLDAIR is required for proper repression of FLC during the course of vernalization. COLDAIR is necessary for the recruitment of CLF to FLC chromatin. (Heo et al., 2011) COLDAIR lncRNAs transcribed from the first intron of FLC are also transiently induced by the cold. The CLF subunit of PHD–PRC2 associates with COLDAIR, leading to the enrichment of this complex on FLC chromatin in the cold. A partial deletion of the COLDAIR promoter or knockdown of COLDAIR expression compromises FLC silencing. Thus, COLDAIR is required for FLC silencing by vernalization. (He et al., 2012) COLDAIR, provided the evidence that the lncRNA plays a crucial role in the regulation of flowering time by recruiting a chromatin remodeling complex to the proper target, FLC, for stable silencing by vernalization. COLDAIR, is transcribed from the first intron of FLC and its expression is increased by cold. COLDAIR physically interacts with PRC2 and is required for the enrichment of PRC2 at FLC chromatin by vernalization. Reduced COLDAIR expression by RNAi compromises the vernalization response. The interaction between COLDAIR and PRC2 increases transiently only during the cold exposure but COLDAIR is necessary for the stable maintenance of silenced FLC after cold. (Kim et al., 2012) COLDAIR play a role in the intragenerational repression of FLC. COLDAIR is an lncRNA that is expressed in the sense direction from the first intron of FLC. COLDAIR is induced during cold exposure and associates with PRC2. Its knockdown leads to a decrease in epigenetic silencing, less H3K27me3, implicating it as a required component in the recruitment of PRC2. (Jones et al., 2014) A sense intronic lncRNA named COLDAIR, participate in different phases of the cold-induced repression and the stable silencing of FLC by PRC2. Cold-induced COOLAIR-like and COLDAIR-like lncRNAs could be involved, respectively, in the initial downregulation of DAM genes and the function of PRC2 complexes. (Ríos et al., 2014) In Arabidopsis the COLDAIR lncRNA-triggered chromatin silencing of a central floral repressor known as FLC, involves H3K27me3, but not cytosine methylation. In response to a prolonged cold exposure, COLDAIR expression is induced from the first intron of FLC, and subsequently, this lncRNA recruits a PRC2-like complex to FLC chromatin to deposit H3K27me3, leading to FLC silencing. (He et al., 2013) A long intronic noncoding RNA, named COLD ASSISTED INTRONIC NONCODING RNA (COLDAIR), was shown to be required for the vernalization-mediated epigenetic repression of FLC. COLDAIR physically associates with CLF, suggesting that COLDAIR establishes stable repressive chromatin at FLC through recruiting PRC2 in H3K27me3 deposition. (Yao et al., 2011) In Arabidopsis, the floral repressor FLOWERING LOCUS C (FLC), a master regulator of flowering, is stably suppressed by prolonged exposure to cold, which promotes the enrichment of tri-methylated histone H3K27me3 at FLC locus. This process is mediated by the interaction of a long intronic noncoding RNA (named COLDAIR) to the FLC locus via recruitment of PRC2. (Pignatta et al., 2012) A long intronic noncoding RNA (COLD ASSISTED INTRONIC NONCODING RNA, COLDAIR) is also required for the stable repression of FLC after cold. COLDAIR is transcribed from the first intron of FLC during vernalization and it targets PRC2 to the FLC chromatin. (Justyna et al., 2012) The COLDAIR sense transcript is produced from within FLC intron 1, and plays a role in FLC silencing via recruitment of Polycomb repressing complex 2 (PRC2) to FLC during vernalization. The establishment of H3K27 trimethylation to silence FLC in vernalization requires COLDAIR. (Shin et al., 2014) long noncoding RNA called COLDAIR shown to be important in regulating vernalization responses in Arabidopsis. (Moghe et al., 2012) In mediating transcriptional regulation, histone modification can also involve ncRNAs such as COLDAIR, a cold-inducible long ncRNA that increases H3K27me3 marks at chromatin of the floral repressor FLC through recruitment of polycomb repressive complex 2. (Zhang et al., 2013) Two noncoding RNAs have now been implicated in vernalization induced recruitment of PHD-PRC2. One of these, termed COLDAIR, is a long (about 1 kb) noncoding sense RNA produced from sequences within the large first intron of FLC. Expression of COLDAIR is cold-induced and several observations suggest that it is functionally important for FLC silencing. In particular, transgenes with deletions that removed part or all of the COLDAIR gene showed fairly normal downregulation during cold treatments but regained activity when plants were returned to warm conditions. (Müller et al., 2011)	21127216, 22658650, 22078062, 24808013, 24917873, 23000433, 25211139, 23132786, 23838953, 21876724	PLNlncRbase
EL0300	COOLAIR	N/A	N/A	N/A	N/A	interaction	N/A	23641115
EL0300	COOLAIR	N/A	N/A	N/A	N/A	interaction	N/A	24799695
EL0300	COOLAIR	N/A	RT-PCR	vernalization	up-regulated	N/A	longnpcRNA,COOLAIR (cold induced long antisense intragenic RNA), is cold induced FLC antisense transcripts, and has an early role in the epigenetic silencing of FLC and to silence FLC transcription transiently. COOLAIR suggested to function in early cold induced silencing of FLC transcription; COOLAIR promoter could silence some reporter genes. Suggests COOLAIR may function through transcriptional interference, although a function for the transcripts has not been tested. (Swiezewski et al., 2009) COOLAIR is expressed at A.thaliana FLOWERING LOCUS C(FLC) in response to winter temperatures. Its contribution to cold-induced silencing of FLC was proposed but its functional and evolutionary significance remain unclear. COOLAIR has been shown to participate in FLC downregulation by the autonomous pathway but its function in the cold-induced silencing of FLC is still unclear. Evolutionary conservation of COOLAIR and its seasonal expression in perennial A.alpina supports a significant role for this asRNA in repression of FLC gene expression during vernalization. The COLDAIR lncRNA transcribed from it were previously shown to be required for stable silencing of FLC in A.thaliana. (Castaings et al., 2014) COOLAIR comprises the Class I and II polyadenylated antisense FLC transcripts, and has been proposed to trigger vernalization-mediated FLC silencing by a co-transcriptional mechanism. A recent study using FLC mutants with insertional T-DNAs that can block the full-length transcription and separate the sense and antisense transcription, has revealed that elimination of COOLAIR transcription does not impair FLC silencing by vernalization. Thus, COOLAIR is not essential for FLC silencing. Of note, it is likely that COOLAIR might participate in vernalization-mediated FLC silencing via a co-transcriptional mechanism involving an overlapping transcription of sense and antisense transcripts. (He et al., 2012) COOLAIR is now used to describe the FLC antisense transcript generally, both in warm-and cold-treated plants. COOLAIR transcription is generally positively correlated with sense transcription in a range of flowering mutants that both upregulate (late-flowering mutants) and downregulate (early-flowering mutants) FLC expression. COOLAIR might modulate FLC expression. When vernalized for longer, COOLAIR expression and FLC mRNA decrease over time and remain stably silenced after return to the warm. The involvement of COOLAIR and COLDAIR in regulating FLC during vernalization. (Ietswaart et al., 2012) COOLAIR, produced at Arabidopsis FLOWERING LOCUS C (FLC). COOLAIR initiates just downstream of the major sense transcript poly(A) site and terminates either early or extends into the FLC promoter region. We now show that splicing of COOLAIR is functionally important. Since reduced use of the COOLAIR proximal poly(A) site disrupted transcriptional repression of FLC，we reasoned that reduced splicing efficiency of the COOLAIR class Ii intron, necessary to generate the exon containing that poly(A) site, might be an important factor in the increased expression of FLC in prp8. (Marquardt et al., 2014) COOLAIR is an antisense RNA that is transcribed in response to cold treatment. COOLAIR is alternatively polyadenylated at the 3' end, resulting in a proximal poly(A)site or a distal ploy(A) site. to reduce the H3K4me2 level at the FLC locus, leading to a transition from an active chromatin state to a repressive state. The reduction of H3K4me2 might benefit the H3K27me3 modification; thus, COOLAIR acts as an in direct recruiter of PRC2. However,how FLD is activated using the proximal site of COOLAIR remains unknown. (He et al., 2013) Two non coding RNAs(ncRNA) are involved in FLC repression. Early FLC silencing is mediated by COOLAIR (cold induced long antisense intragenic RNA), a cold-induced FLC antisense transcript expressed early during vernalization. (Bergonzi et al., 2012)	20010688, 25030056, 22658650, 22785023, 24725596, 24312106	PLNlncRbase
EL0304	CRG	N/A	In situ hybridization, Northern blotting, Western blotting, RACE, RT-PCR and quantitative RT-PCR	N/A	N/A	interaction	CRG deficiency led to reduced locomotor activity and a defective climbing ability-phenotypes that are often seen in CASK mutant.	23074190
EL0306	Crxos	N/A	RT-PCR and RNA in situ hybridization	retina	N/A	interaction	We overexpressed another nat, crxos, in mouse adult retina using adeno-associated viral vectors and we observed a significant decrease in the expression levels of the corresponding sense gene, crx.	15703187
EL0313	CU1NC165	N/A	hub-based and module-based methods	stress treatment	N/A	N/A	CU1NC165 is response to salicylic acid stimulus, osmotic stress, salt stress, jasmonic acid stimulus, wounding, water deprivation,oxidative stress.(to see table S5 for details)	25799544	PLNlncRbase
EL0314	CU1NC272	N/A	hub-based and module-based methods	stress treatment	N/A	N/A	For example, one of the cucumber lincRNAs (CU1NC272) targeted by csa-miRNA396b is presented (Fig. 4).	25799544	PLNlncRbase
EL0315	CU1NC333	N/A	hub-based and module-based methods	stress treatment	N/A	N/A	CU1NC333 is response to osmotic stress, water, salicylic acid stimulus.(to see table S5 for details)	25799544	PLNlncRbase
EL0316	CU1NC355	N/A	hub-based and module-based methods	stress treatment	N/A	N/A	CU1NC355 is response to fungus stress, salt stress, oxidative stress, osmotic stress.(to see table S5 for details)	25799544	PLNlncRbase
EL0317	CU2NC636	N/A	hub-based and module-based methods	stress treatment	N/A	N/A	CU2NC636 is response to salt stress, osmotic stress, jasmonic acid stimulus, oxidative stress, water deprivation, wounding.(to see table S5 for details)	25799544	PLNlncRbase
EL0318	CU3NC1105	N/A	hub-based and module-based methods	stress treatment	N/A	N/A	CU3NC1105 is response to water deprivation, wounding, water.(to see table S5 for details)	25799544	PLNlncRbase
EL0319	CX3CL1	N/A	RT-PCR, Southern blot and fluorescence in situ hybridization analyses	activated CD4+ T cells	N/A	expression	Ntt has no open reading frame larger than 270 bp. it is transcribed in a select subset of cd4+ t-cell clones propagated in vitro.	9027504
EL0324	CYP707A1	N/A	Northern blot/RT-PCR/Microarray	ABA treatment	up-regulated	N/A	Fig. 3E shows a fSAT of an ABA-inducible gene, CYP707A1 (At4g19230) encoding ABA 8'-hydroxylase (Kushiro et al. 2004, Saito et al. 2004) and the novel ABA-inducible antisense TUs. The presence of novel ABA-inducible antisense TU was confirmed by real-time RT-PCR and Northern analyses using strand-specific RNA probes (Figs. 3F, 3G); The RD29A and CYP707A1 lancRNAs that were simultaneously accumulated with sense mRNAs, were accumulated by drought- and ABA treatments(Plant Cell Physiol.2008, 49, 1135–1149.).	18625610	PLNlncRbase
EL0328	Dalir	N/A	N/A	neuroblastoma cells	up-regulated	expression	Dali is transcribed downstream of the Pou3f3 transcription factor gene and its depletion disrupts the differentiation of neuroblastoma cells. Locally, Dali transcript regulates transcription of the Pou3f3 locus. Distally, it preferentially targets active promoters and regulates expression of neural differentiation genes, in part through physical association with the POU3F3 protein.	25415054
EL0329	DANCR	N/A	knockdown	Synovium-derived mesenchymal stem cells (SMSCs)	N/A	interaction	N/A	26514989
EL0329	DANCR	N/A	microarray, quantitative real-time reverse transcription plus the polymerase chain reaction, overexpression	human dental pulp cells	down-regulated	interaction	N/A	26646542
EL0337	DHFR upstream transcripts	N/A	N/A	N/A	N/A	expression	The dhfr minor transcript may function in vivo (in cis) to regulate the transcriptional activity of the major (core) promoter.	12461786
EL0338	DHRS4-AS1	N/A	gene duplication	N/A	N/A	N/A	AS1DHRS4 not only mediates deacetylation of histone H3 and demethylation of H3K4 in cis for the DHRS4 gene, but also interacts physically in trans with the epigenetic modifiers H3K9- and H3K27-specific histone methyltransferases G9a and EZH2, targeting the promoters of the downstream DHRS4L2 and DHRS4L1 genes to induce local repressive H3K9me2 and H3K27me3 histone modifications.	22891334
EL0339	DIO3OS	N/A	RT-PCR	N/A	N/A	locus	The dio3 gene may lie within the structure of the antisense gene, a complex arrangement often observed in imprinted loci.	14962667
EL0340	Dio3os	N/A	RT-PCR	N/A	N/A	locus	The dio3 gene may lie within the structure of the antisense gene, a complex arrangement often observed in imprinted loci.	14962667
EL0343	DLEU1	N/A	N/A	N/A	N/A	expression	The nondeleted allele of the car and est70/leu1 genes was expressed in b-cll specimens, including those with monoallelic loss	11264177
EL0347	Dlx1as	N/A	Biochemical analysis	midgestation mouse brain	N/A	expression	Antisense dlx-1 and -6 have their highest expression in the svz.	9415433
EL0347	Dlx1as	N/A	compared between freshly-isolated and cultured dental mesenchymal cells	mouse dental mesenchymal cells	down-regulated in dental mesenchymal cells; up-regulated in odontogenic dental mesenchymal tissue	N/A	loss of odontogenic potential	26986487
EL0347	Dlx1as	N/A	RNA-seq, RNA CaptureSeq, and ChIP-seq	adult mouse subventricular zone neural stem cell lineage	N/A	expression	shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells.	23583100
EL0347	Dlx1as	N/A	RT-PCR	N/A	N/A	interaction	Mice devoid of Dlx1as RNA are viable and fertile, and display a mild skeletal and neurological phenotype reminiscent of a Dlx1 gain-of function phenotype, suggesting a role for this non-coding antisense RNA in modulating Dlx1 transcript levels and stability.	23415800
EL0349	DLX6-AS1	N/A	N/A	N/A	N/A	locus	the Evf-2 ncRNA activates transcriptional activity by directly influencing Dlx-2 activity	16705037
EL0351	DMRT2	N/A	a light-switching pyrene probe	living human cell	N/A	N/A	N/A	20679250
EL0359	dutA	N/A	Disruption of the dutA gene	N/A	N/A	N/A	Duta rna functions without being translated into protein. disruption of the duta gene did not cause phenotypic changes, suggesting that the function of duta is redundant.	8127653
EL0369	EMX2OS	N/A	N/A	endometrium	N/A	interaction	A biological function for emx2os, presumably to regulate emx2.	12573261
EL0370	Emx2os	N/A	N/A	endometrium	N/A	interaction	A biological function for emx2os, presumably to regulate emx2.	12573261
EL0372	enod40	N/A	RT-PCR	Nodule formation	up-regulated	N/A	The absence of conserved sORFs in Brassicales enod40 sequences (A.thaliana, Thlaspi caerulescens and Brassica napus)could be related to the fact that, in contrast to the majority of angiosperms, these species in natural environment do not form effective symbiotic mycorrhizal associations with fungi. Mycorrhizal symbioses are probable evolutionary predecessors of nitrogen-fixing nodule symbioses, and enod40 seems to be involved in both.	17452360	PLNlncRbase
EL0373	enod40	N/A	RT-PCR	roots	up-regulated	N/A	The absence of conserved sORFs in Brassicales enod40 sequences (A.thaliana, Thlaspi caerulescensand Brassica napus)could be related to the fact that, in contrast to the majority of angiosperms, these species in natural environment do not form effective symbiotic mycorrhizal associations with fungi. Mycorrhizal symbioses are probable evolutionary predecessors of nitrogen-fixing nodule symbioses, and enod40 seems to be involved in both.	17452360	PLNlncRbase
EL0374	enod40	N/A	RT-PCR	Nodule formation	up-regulated	N/A	enod40 (BI452209) was isolated from a fungus extraradical mycelium during arbuscular mycorrhizal symbiosis with the plant.	17452360	PLNlncRbase
EL0375	ENOD40	N/A	Southern and PCR Analysis	Nodule formation	up-regulated	N/A	Cytokinin Induces ENOD Gene Expression in Uninoculated Roots. Earlier research had demonstrated that purified Nod factor induced the expression of ENOD40 in uninoculated vetch roots (see ref. 12). A similar response has been found for Glycine soja and alfalfa; ENOD40 transcripts were detected by RNA transfer blot analysis as early as 6 h after treatment (ref. 34; data not shown). Early nodulin genes are characteristically expressed during nodule morphogenesis.	11038545	PLNlncRbase
EL0376	ENOD40	N/A	a yeast three-hybrid screening, Immunolocalization	N/A	N/A	interaction	Enod40, a short open reading frame-containing mrna, induces cytoplasmic localization of a nuclear rna binding protein in medicago truncatula.	15037734
EL0377	ENOD40	N/A	RT-PCR	lateral root development	up-regulated	N/A	ENOD40 transcripts are also detected at very early stages of lateral root development, in the dividing pericycle cells of the root stele that give rise to the lateral root primordia. In sections of nodules at this stage of development, the ENOD40 transcripts are localized in dividing cells of the root pericycle and in the forming connecting vascular bundle.The ENOD40 gene is expressed in the differentiating tissues of emerging lateral roots. Expression during nodule and lateral root development. ENOD40 is proven to be an important gene not only because it is involved in nodule development from very early stages, but also because it could serve as a tool in gaining access to mechanisms involved in the determination of other developmental processes in the plant. Furthermore, due to its differential expression in adventitious and acropetal lateral roots, ENOD40 gene could serve as a molecular marker in studies of lateral root initiation.	8605294	PLNlncRbase
EL0378	ENOD40	N/A	RT-PCR	Nodule formation	down-regulated	N/A	The expression of ENOD40 in Sesbania rostrata, an annual legume endemic to the Sahel region of West Africa and one of the few legume species that can be nodulated on stems as well as on roots.	9620265	PLNlncRbase
EL0379	enod40	N/A	RT-PCR	roots	up-regulated	N/A	The absence of conserved sORFs in Brassicales enod40 sequences (A.thaliana, Thlaspi caerulescens and Brassica napus)could be related to the fact that, in contrast to the majority of angiosperms, these species in natural environment do not form effective symbiotic mycorrhizal associations with fungi.Mycorrhizal symbioses are probable evolutionary predecessors of nitrogen-fixing nodule symbioses, and enod40 seems to be involved in both.	17452360	PLNlncRbase
EL0380	ENOD40	N/A	RT-PCR	roots	up-regulated	N/A	ENOD40, which are activated during early stages of Rhizobium-induced nodulation, are also induced during AM formation. These observations, together with the ancient nature of AM formation, suggest that some of the plant processes leading to nodulation may have evolved from those already established for fungal endosymbiosis. ENOD40, is also not very attractive for Nod factor signal transduction studies since it is activated in the root pericycle and it is unknown whether Nod factors are transported to this tissue. Furthermore, this gene can be activated by chitin fragments. Hence, this gene might be activated by fungal cell wall fragments, which makes it unclear whether its expression is of physiological meaning.	10.1046/j.1365-313x.1998.00228.x	PLNlncRbase
EL0381	ENOD40	N/A	RT-PCR	roots	up-regulated	N/A	ENOD40, an early nodulin gene, is expressed following inoculation with Rhizobium meliloti or by adding R.meliloti-produced nodulation (Nod) factors or the plant hormone cytokinin to uninoculated roots. It is detectable in the root pericycle opposite the nodule primordium even before the appearance of infection threads, and is also found later on, associated with vascular strands in mature nodules. Comparison of the enod40 sequence isolated from several legumes and one non-legume did not reveal any conserved large ORF. Instead, a conserved region was found which may allow the production of a particularly stable cytoplasmic RNA. Therefore it has been proposed that enod40 encodes an RNA with regulatory function. In addition ENOD40 also shows a very short ORF of only 10–13 amino acids, but the 34-untranslated region appears to have important functions as a riboregulator.	9847177	PLNlncRbase
EL0382	ENOD40	N/A	RT-PCR	stem, lateral root primordia, embryonic tissue	up-regulated	N/A	ENOD40 still able to interact with mycorrhizal fungi. Furthermore, no phenotypic aberrations correlated to the presence of e40-mum1. ENOD40 expression is also observed in the stem, lateral root primordia, and in embryonic tissue, it is likely that ENOD40 is also involved in nonsymbiotic processes.	14522083	PLNlncRbase
EL0383	enod40	N/A	Northern blot/Southern blot	Nodule formation	down-regulated	N/A	The alb1 is a symbiotic mutant of lotus japonicus that form empty nodules, mature alb1 nodules exhibied very weak or no expression of enod40 in the peripheral cells of the undeveloped nodule vascular bundle. ENOD40 may play a role in the differentiation of nodule vascular bundles. Expression of enod40 in alb1 nodules is restricted to early stages of nodule initiation. Nodule initiation on alb1 root is accompanied by the expression of enod40 in the same spatial pattern as and at a level comparable to, those in the wild type nodules. (Imaizumi-Anraku et al., 2000) Knock-down of ENOD40 leads to severe suppression of nodule primordium initiation but does not affect early bacterial infection events, thus clearly indicating that ENOD40 is required for nodule primordium formation as well as for subsequent nodule rganogenesis. knockdown of two ENOD40s in L.japonicus caused strong inhibition of nodulation. (Kumagai et al., 2006) In situ localization of LjENOD40 genes transcripts in Lotus japonicus(Gifu B-129) root nodules, young seed pods, and embryos. ENOD40, an early nodulin gene, has been postulated to play a significant role in legume root nodule ontogenesis. High levels of ENOD40 gene transcripts were found in nonsymbiotic tissues such as stems, fully developed flowers, green seed pods, and hypocotyls. lower level of transcripts was observed in leaves, roots, and cotyledons. In mature nodules, transcripts of both ENOD40 genes accumulate in the nodule vascular system; in young seed pods strong signal is observed in the ovule, particularly in the phloem and epithelium, as well as in globular stage embryos. ENOD40 genes are indirectly triggered by Nod factors via an effect on the levels of common plant hormones such as auxin. The expression of ENOD40 in developing embryos, as well as in ovule tissues, of L.japonicus adds further proof to the suggestion that the ENOD40 gene is a plant gene involved in organogenesis. (Flemetakis et al., 2000)	11129043, 16816411, 10975655	PLNlncRbase
EL0384	enod40	N/A	RT-PCR	Nodule formation	up-regulated	N/A	enod40 is not an inducer of cell division per se, but other factors likely present only in the inner cortex are required to complete cell cycle activation. Stable constitutive expression of enod40 in transgenic plants resulted in a large proportion of dividing root cortical cells when grown under nitrogen-limited conditions Translation was observed in epidermal and outer cortical cells of intact roots. As well as accelerated nodulation. Further suggesting that our transient assay is related to the biological activity of enod40 in the root ortex. enod40 action in alfalfa roots. enod40 regulation in nodule organogenesis. (Sousa et al., 2001) Enod40 is a key regulatory gene expressed early during nodule organogenesis. Enod40 is one of the first molecular markers expressed at the onset of nodule organogenesis in the root pericycle and cortex. Enod40 has been proposed as one of the key regulatory genes involved in a signal transduction pathway activated during nodule initiation. (Jiménez-Zurdo et al., 2000) MsENOD40 transcripts can be detected within 24h after Rhizobium meliloti infection and are found not only in the root pericycle cells and nodule primordia as reported for both soybean and pea ENOD40, but also in cells typically classed as meristems: the distal ends of nodules and developing lateral roots, the margins of young leaf primordia, and the procambial cells of the stem and root.In 10-day-old nodules, MsENOD40 transcripts were restricted to the nodule meristem and to cells surrounding the vascular bundle (not shown). In mature (21-day or older) nodules, MsENOD40 transcripts were localized to the cells of the meristem and immediately adjacent to it, with the intensity of label decreasing in the invasion zone and older parts of the nodule. (Asad et al., 1994) Early nodulin genes are characteristically expressed during nodule morphogenesis. MsENOD40 would be expressed in mycorrhizal roots. because transcripts for these genes accumulate in the bacteria-free nodules elicited by R.Meliloti exopolysaccharide (exo) mutants or in alfalfa roots treated with auxin transport inhibitors. MsENOD40 transcripts accumulated in the cells of the pericycle and to a more limited extent in the epidermis and inner cortical cells, especially those containing immature arbuscules. Forming arbuscular mycorrhizae and Rhizobium-induced nodules.we show that mycorrhizae resemble nodules at the molecular level in that these two early nodulin genes are expressed. We also show that cytokinin induces both MsENOD2 and MsENOD40 expression in uninoculated roots,indicating this plant hormone may be part of the mechanism of signal transduction. (van et al., 1997)	11113209, 10656590, 10.1007/BF01276808, 11038545	PLNlncRbase
EL0385	enod40	N/A	RT-PCR	nodule initiation	up-regulated	N/A	enod40, expressed in spontaneous nodules nodule-related organs developed in the absence of Rhizobium on certain alfalfa plants during nitrogen limitation. This indicates that enod40 expression is associated to the nodule developmental program independently of any infection process. Interestingly, an enod40 homolog was recently found in tobacco whose expression increases auxin tolerance of tobacco protoplasts. enod40 is involved in the initiation of root nodule organogenesis. enod40 expression induced dedifferentiation and division of cortical cells under nitrogen-limiting conditions. Our results suggest that this early nodulin gene is involved in the initiation of nodule development. (Charon et al., 1997) enod40, has a regulatory function in nodule initiation. enod40 is highly conserved among leguminous plants and it has also been identied in the non-legumes tobacco, rice and maize. In the legume roots, it is expressed in the early stages of the interaction, specically in the pericycle adjacent to the protoxylem pole and well before the initiation of cortical cell divisions that lead to nodule formation. Furthermore, it is induced by NFs and chitin pentamers and the phytohormone cytokinin. (Girard et al., 2003) ENOD40 was identified as a candidate for such a plant factor with a regulatory role during nodulation. ENOD40 Bright Yellow-2 (BY-2) tobacco cell suspensions. ENOD40 action can be counteracted by an ethylene perception blocker, indicating that ethylene is a negative regulator of elongation growth in 35S:NtENOD40 cells, and that the NtENOD40-induced response is mediated by alteration of ethylene biosynthesis kinetics. (Ruttink et al., 2006)	11038563, 12930950, 12930950	PLNlncRbase
EL0386	enod40	N/A	RT-PCR	stems	up-regulated	N/A	Studies on rice enod40 suggest that legume and non-legume enod40 genes may share some common functions in differentiation and/or functions of vascular bundles, where rice enod40 is mostly accumulated. (Girard et al., 2003) Expression of OsENOD40 was detected only in stems. OsENOD40 is expressed only at the early stages of the development of lateral vascular bundles that conjoin the emerging leaf, and its expression is down-regulated after the onset of leaf expansion. OsENOD40 expression is restricted to lateral (large) vascular bundles only. (Kouchi et al., 1999)	12930950, 10363365	PLNlncRbase
EL0387	enod40	N/A	RT-PCR	Nodule formation	up-regulated	N/A	The over expression of enod40 in M.truncatula plants infected by Sinorhizobium melilotiresulted in fast nodulation of these transgenic plants. Altered levels of enod40 expression considerably affect nodule induction by S.meliloti. During this symbiotic interaction, overexpression of enod40 resulted in accelerated nodulation and enhanced root growth of transgenic plants. Those plants in which silencing of enod40 gene expression was detected exhibited reduced nodulation capacity. (Charon et al., 1999) Mycorrhizal colonization is regulated by enod40, an early nodulin gene known to be involved in the nodule symbiosis of legumes with nitrogen-fixing bacteria. Medicago truncatula plants overexpressing enod40 exhibited stimulated mycorrhizal colonization in comparison with control plants. Overexpression of enod40 promoted fungal growth in the root cortex and increased the frequency of arbuscule formation. enod40 might be a plant regulatory gene involved in the control of the mycorrhizal symbiosis. Overexpression of enod40 Promotes Development of Arbuscules. M.truncatula plants overexpressing enod40 exhibited accelerated mycorrhizal colonization.This paper shows that alteration in the transcript level of the enod40 gene has an effect on the growth of mycorrhizal fungi in the root and on the development of cells containing arbuscules. (Staehelin et al., 2001) ENOD40 expression was detected in cells surrounding the giant cells but not within the giant cells. ENOD40 up-regulation in giant cells and their surrounding cells. overexpressing ENOD40, increased initiation of nodule primordia was observed at early timepoints, which was accompanied by a proliferation response close to the root tip . ENOD40 induction is a limiting step in primordium formation, ENOD40 could play a role in transport of compounds. The early nodulin gene ENOD40 involved in primordium formation and the cell cycle gene CCS52a required for cell differentiation and endoreduplication, are expressed in galls of the host plant. (Favery et al., 2002) Overexpression of enod40 in Medicago truncatula results in a considerable increase of cortical cell divisions when plants are subjected to nitrogen-limiting conditions. Interestingly, such plants infected by Sinorhizobium meliloti nodulate faster and exhibit increased sensitivity to the Nod signals upon treatment with purified Nod factors or inoculation with S.meliloti mutants. In mature nodules, enod40 is expressed in the pericycle of the vascular bundles but also in several non-symbiotic tissues. (Girard et al., 2003) ENOD40 transcripts are required for correct subcellular localization of RNP particles in legume plants.Transgenic Medicago truncatula overexpressing enod40 exhibited accelerated nodulation, whereas plants with reduced amounts of enod40 transcripts formed only a few and modified nodule-like tructures.Mtenod40 was expressed in nodules at a high level, to a lesser extent in stems and roots,and was not detected in leaves. (Campalans et al., 2004) Under nitrogenlimiting conditions overexpression of Medicago truncatula (a model leguminous plant) enod40 (Mtenod40) induces cortical cell division in Medicago roots. These experiments also showed that transient expression of either region 1 carrying box I or a 3'sequence (region 2) spanning box II evoked a response similar to that evoked by the complete gene in alfalfa (Medicago sativa) roots. (Sousa et al., 2011) Transgenic Medicago truncatula plants overexpressing or silenced for ENOD40 exhibited accelerated nodulation or form only a few and modified nodule-like structures, respectively, suggesting that MtENOD40 regulates nodule development. The ENOD40 npcRNA was shown to re-localize a nuclear-speckle RBP from the nucleus to the cytoplasm in Medicago truncatula. Plant RBPs have been also implicated in RNA-mediated chromatin silencing in the FLC locus through interaction with specific antisense transcripts. (Charon et al., 2010)	10521525, 11752473, 12437298, 12930950, 15037734, 11113209, 11113209	PLNlncRbase
EL0388	ENOD40-1	N/A	RT-PCR	Nodule formation	up-regulated	N/A	GmENOD40 has a complex expression pattern during development of determinate soybean nodules. At early stages of development transcription is induced in dividing root cortical cells, the nodule primordium and the pericycle of the root vascular bundle. In mature soybean nodules, the gene is expressed in the uninfected cells of the central tissue and in the pericycle of the nodule vascular bundles. The GmENOD40 in the nodule vascular bundle requires the presence of intracellular bacteria or infection threads. GmENOD40 was localized in soybean roots at different time points after inoculation with B.japonicum USDA110 to determine where and when the gene is expressed during nodule formation. GmENOD40 gene expression in empty soybean nodule, which formed by B.japonicum mutant 3160. These nodules contain neither intracellular bacteria nor infection thresds. These empty nodules contain at the distal part a central vascular bundle. (Yang et al., 1993) ENOD40 expression was seen in dividing subepidermal cortical cells. ENOD40 expression in response to bacterial inoculation is first detectable in the pericycle of the central vascular system. ENOD40 expression in the pericycle can also be induced by nod signal addition in the absence of bacterial inoculation. ENOD40 express in soybean roots in response to various lipo-chitin signal molecules. (Minami et al., 1996) ENOD40 peptides are involved in the control of sucrose use in nitrogen-fixing nodules. Suggests that ENOD40 peptides may contribute to the control of photosynthate use in plants, which is consistent within situ hybridization studies that revealed that ENOD40 transcripts predominantly occur in the vascular bundles of mature soybean nodules. suggesting a role in the regulation of sucrose utilization in nodules. (Rohrig et al., 2002) The plant gene ENOD40 is one of the earliest nodulin genes specifically induced by nodulation factor-secreting rhizobia and appears to play an important role in root nodule organogenesis. ENOD40 is expressed at an early stage of root nodule organogenesis and has been postulated to play a central regulatory role in the Rhizobium-legume interaction. ENOD40 encoded peptides bind to SuSy suggest that these short translation products are involved in the control of sucrose utilization in nitrogen-fixing nodules. In addition to the two small peptides, the secondary structure of ENOD40 mRNA has been shown to be a key element in the signaling process underlying nodule organogenesis. Modification of sucrose synthase with ENOD40 peptide A activates sucrose cleavage activity whereas the synthesis activity of the enzyme is unaffected. The results are discussed in relation to the role of sucrose synthase in the control of sucrose utilization in nitrogen-fixing nodules. (Röhrig et al., 2004)	8220464, 8758977, 11842184, 15541370	PLNlncRbase
EL0389	enod40-1	N/A	RT-PCR	Nodule formation	up-regulated	N/A	LjENOD40-1 is highly expressed in the developing vascular bundles. In 21-day-old nodules, LjENOD40-1 gene transcripts accumulate in the vascular tissue surrounding the nodule. Additionally, in green young pods, LjENOD40-1 is up-regulated in the ovules and very strong hybridization signal is observed in the phloem tissue and epithelium cells. High expression was also observed at the globular stage embryo. In mature 21-day-old nodules LjENOD40-1 is highly expressed in vascular tissues of nodule. (Flemetakis et al., 2000) LjENOD40-1 is abundantly induced in very early stages of bacterial infection or Nod factor application, LjENOD40-1 is predominant in responding to Nod factors at the early stages of nodule formation. (Kumagai et al., 2006)	10975655, 16816411	PLNlncRbase
EL0390	enod40-2	N/A	RT-PCR	Nodule formation	up-regulated	N/A	LjENOD40-2 expression failed to be enhanced in nodule primordia induced by Nod factors, LjENOD40-2 showed a high level of expression in nodule primordia induced by rhizobia and in nodules. The results indicate that LjENOD40-2 is not a pseudogene, and has a role in nodule formation.	15937327	PLNlncRbase
EL0491	FAS-AS1	N/A	a culture model of human erythropoiesis	erythroblasts derived from CD34(+) hematopoietic stem cell progenitor cells of healthy donors	up-regulated	N/A	Fas-antisense 1 (Fas-AS1 or Saf) was induced during differentiation Fas-antisense 1 (Fas-AS1 or Saf) was induced during differentiation through the activity of essential erythroid transcription factors GATA-1 and KLF1	27067490
EL0491	FAS-AS1	N/A	orientation-specific RT-PCR and northern blot analysis	Jurkat cells	N/A	interaction	Saf might protect t lymphocytes from fas-mediated apoptosis by blocking the binding of fasl or its agonistic fas antibody.	15829500
EL0501	Firre	N/A	knockdown	mouse embryonic stem cells	N/A	epigenetics	Firre is X-linked and expressed from a macrosatellite repeat locus associated with a cluster of CTCF and cohesin binding sites, and is preferentially located adjacent to the nucleolus. Knockdown of Firre disrupts perinucleolar targeting and H3K27me3 levels in mouse fibroblasts, demonstrating a role in maintenance of an important epigenetic feature of the inactive X chromosome.	25887447
EL0501	Firre	N/A	weighted gene coexpression network analysis	mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs)	up-regulated	expression	Firre, a lncRNA highly enriched in the nucleoplasm and previously reported to mediate chromosomal contacts in ESCs, controls a network of genes related to RNA processing.	26048247
EL0503	FLC	N/A	N/A	N/A	N/A	interaction	The degradation of FRI (FRIGIDA) is accompanied by an increase in the levels of the long noncoding RNA ColdAIR, which reduces the level of histone H3Lys4 trimethylation (H3K4me3) in FLOWERING LOCUS C chromatin to promote flowering.	25538183
EL0513	frq antisense RNAs	N/A	N/A	wild-type strain, mutant strains	N/A	expression	These data provide an unexpected link between antisense rna and circadian timing and provide a new example of a eukaryotic cellular process regulated by naturally occurring antisense rna.	12607002
EL0514	FTX	N/A	N/A	N/A	Up-regulated	interaction	mutation cuasesalteration of transcript levels within the X-inactivation center and particularly important decreases in Xist RNA levels	21118898
EL0517	G730013B05Rik	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Involved in maintaining pluripotency in ESCs.	21874018
EL0522	GAL10	N/A	N/A	N/A	N/A	interaction	The GAL lncRNAs could also promote transcriptional activation of the targeted GAL protein-coding genes. Interestingly, these lncRNAs help determine how quickly the GAL genes can be induced in response to galactose, without altering final steady-state transcript levels.	24563719
EL0526	GAS5	N/A	knockdown	human glioma cells	down-regulated	interaction	The introduction of Gas5 by plasmid transfection increased the expression of tumor suppressor Bcl-2-modifying factor (bmf) and Plexin C1 via directly targeting and reducing the expression of miR-222. Downregulated expression of miR-222 inhibited U87 and U251 cell proliferation and promoted the apoptosis by upregulating bmf. Gas5 combined with the knockdown of miR-222 resulted in the smallest tumor volumes and the longest survivals of nude mice in vivo.	26364613
EL0526	GAS5	N/A	N/A	N/A	Up-regulated	expression	nonprotein-coding RNA GAS5 in the inhibition of T-cell proliferation	20421347
EL0530	GATA3-AS1	N/A	N/A	CD4+ T-cell	N/A	N/A	N/A	23870669
EL0532	Gfra1	N/A	global expression profiling as responsive to glial cell-derived	Spermatogonial stem cells (SSCs)	up-regulated	N/A	an antisense transcript of the GDNF receptor alpha1	26962690
EL0537	Gm15050	N/A	lncRNA microarray	brown adipose tissue (BAT) and white adipose tissue (WAT)	N/A	expression	We found that AK142386 and AK133540 may affect adipogenesis and metabolism. Our data indicate that AK142386 and AK133540 may be involved in BAT and WAT development through their target genes Hoxa3 and Acad10.	25472036
EL0538	Gm15577	N/A	Microarray analysis, RT-qPCR	neuronal specific Nbs1-deficient (Nbs1(CNS-del)) mouse model	N/A	interaction	N/A	26705043
EL0540	Gm2694	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Involved in maintaining pluripotency in ESCs.	21874018
EL0541	Gm30731	N/A	knockdown	neural stem cell (NSC) in the embryonic and postnatal brain	N/A	Interaction	In NSCs, Pnky and PTBP1 regulate the expression and alternative splicing of a core set of transcripts that relates to the cellular phenotype. These data thus unveil Pnky as a conserved lncRNA that interacts with a key RNA processing factor and regulates neurogenesis from embryonic and postnatal NSC populations.	25800779
EL0545	GNG12-AS1	N/A	multiple small interfering RNAs (siRNAs) to silence GNG12-AS1	N/A	N/A	N/A	GNG12-AS1 transcripts alters MET signalling and cell migration	26832224
EL0546	GRMZM2G010274_T01	N/A	RT-PCR/RNA-seq	pollens	N/A	N/A	Two of the lncRNAs (GRMZM2G010274_T01 and GRMZM2G518002_T01) showed additional isoforms in some of the tissues that may reflect tissue-specific splicing variants.	24576388	PLNlncRbase
EL0547	GRMZM2G088590_T04	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	GRMZM2G088590_T04 which was down-regulated in root stressed for 5 h, was up-regulated in roots stressed for 10h as determined by qRT-PCR.	24892290	PLNlncRbase
EL0548	GRMZM2G420571_T01	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	GRMZM2G420571_T01 is precursor sequences of MIR172c, GRMZM2G420571_T01 was an intragenic lncRNA, showed up-regulation in drought-stress leaves in comparison with RNA-seq.	24892290	PLNlncRbase
EL0549	GRMZM2G518002_T01	N/A	RT-PCR/RNA-seq	leaves	N/A	N/A	Two of the lncRNAs (GRMZM2G010274_T01 and GRMZM2G518002_T02) showed additional isoforms in some of the tissues that may reflect tissue-specific splicing variants.	24576388	PLNlncRbase
EL0550	GRMZM2G580571_T01	N/A	RT-PCR/RNA-seq	roots and shoot apical meristem	N/A	N/A	The B1 locus in maize identified a region located more than 100 kb upstream of the coding required sequence, GRMZM2G580571_T01 in the regulatory region of B1, which was previously identified as for B' paramutation.	24576388	PLNlncRbase
EL0554	GUT15	N/A	qRT-PCR/RT-PCR	heat and salt	down-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G18440 is downregulated by heat and salt stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL0555	H19	N/A	deletion of the H19 transcription	N/A	N/A	expression	The homozygous mutant animals are viable and fertile and display an overgrowth phenotype of 8% compared with wild-type littermates.	9203585
EL0555	H19	N/A	genetic complementation approach	H19 KO myoblast cells	N/A	interaction	Ectopic expression of the mouse 91H RNA can up-regulate Igf2 expression in trans	22662250
EL0555	H19	N/A	knockdown, overexpression	N/A	N/A	interaction	H19 modulates let-7 availability by acting as a molecular sponge. H19 depletion causes precocious muscle differentiation, a phenotype recapitulated by let-7 overexpression.	24055342
EL0556	H19	N/A	ChIP-seq analysis	fetal liver cells	N/A	interaction	Long noncoding RNA H19 inhibits the proliferation of fetal liver cells and the Wnt signaling pathway.	26801864
EL0556	H19	N/A	knockdown	N/A	N/A	interaction	H19 knockdown activates SAHH, leading to increased DNMT3B-mediated methylation of an lncRNA-encoding gene Nctc1 within the Igf2-H19-Nctc1 locus. Methylation changes at numerous gene loci consistent with SAHH modulation by H19.	26687445
EL0556	H19	N/A	knockdown	gallbladder cancer cell, GBC-SD and NOZ cells	up-regulated	interaction	H19/miR-194-5p/AKT2 axis regulatory network might modulate cell proliferation in GBC. H19 elevation was significantly associated with tumor size. Cell proliferation decreased significantly after knockdown of H19 in GBC-SD and NOZ cells and after knockdown of AKT2 in NOZ cells. the S phase were significantly decreased after knockdown of H19 in NOZ cells but significantly elevated after overexpression of H19 in GBC-SD cells.	26803515
EL0556	H19	N/A	lncRNA microarray	human bone marrow mesenchymal stem cells (MSCs)	up-regulated	expression	The results showed that the two up-regulated lncRNAs are likely to play important roles in osteogenic differentiation process。	25634249
EL0556	H19	N/A	LncRNA microarray	Dermal papilla (DP) cells	up-regulated	expression	RP11-766N7.3, H19 and HOTAIR are specific lncRNAs that were aberrantly expressed in DP cells and played an important role in regulating Wnt signaling	25285630
EL0556	H19	N/A	N/A	undifferentiated multipotent mesenchymal C2C12 cells	N/A	expression	H19 operates as a molecular scaffold that facilitates effective association of KSRP with myogenin and otherlabile transcripts, and we propose that H19 works with KSRP to optimize an AKT-regulated posttranscriptional switch that controls myogenic differentiation.	25385579
EL0556	H19	N/A	N/A	intestinal epithelial cell	up-regulated	N/A	controlling the intestinal epithelial barrier function by serving as a precursor for microRNA 675 (miR-675	26884465
EL0556	H19	N/A	N/A	N/A	N/A	interaction	Human h19 rna contains four attachment sites for the oncofetal igf-ii mrna-binding protein (imp)	10875929
EL0556	H19	N/A	N/A	N/A	N/A	expression	Down-regulation of the IGF-2/H19 locus during normal and malignant hematopoiesis is independent of the imprinting pattern.	15645136	LncRNADisease
EL0556	H19	N/A	N/A	N/A	N/A	N/A	N/A	18587395
EL0556	H19	N/A	overexpression, knockdown	N/A	up-regulated	interaction	The novel pathway H19/miR-675/TGF-β1/Smad2/HDAC regulates osteogenic differentiation of hMSCs and may serve as a potential target for enhancing bone formation in vivo.	26417995
EL0556	H19	N/A	RIP assays combined with luciferase reporter assays	osteogenesis in hMSCs	up-regulated	N/A	lncRNA H19 modulates Wnt/β-catenin pathway	26853553
EL0556	H19	N/A	RNA interference	human K562 leukemia cells	N/A	interaction	Imp-3 protein associates with igf-ii leader-3 and leader-4 mrnas and h19 rna	15753088
EL0556	H19	N/A	transfect	two embryonal tumour cell lines, RD and G401	N/A	expression	Two embryonal tumour cell lines, rd and g401, showed growth retardation and morphological changes when transfected with an h19 expression construct.	7692308
EL0560	Halr1	N/A	knockdown	mouse embryonic stem cells	N/A	interaction	Depletion of linc-HOXA1 RNA at its site of transcription increased transcription of the Hoxa1 gene cis to the chromosome and that exposure of cells to retinoic acid can disrupt this interaction.	23723417
EL0560	Halr1	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Involved in maintaining pluripotency in ESCs.	21874018
EL0563	HBB	N/A	N/A	N/A	N/A	expression	The human beta-globin locus is divided into three differentially activated chromatin subdomains. large transcripts precisely delineate the active domains at key cell cycle points associated with chromatin transitions and remodeling.	10882078
EL0563	HBB	N/A	N/A	N/A	N/A	interaction	Intergenic transcripts of the beta-globin gene cluster are specifically upregulated in dicer-deficient cells.	16227618
EL0563	HBB	N/A	nuclear run-on analysis, in situ hybridization analysis	erythroid cell lines, nonerythroid cell lines, erythroid tissue	N/A	expression	The plasmid colocalizes with the endogenous beta-globin locus providing insight into the mechanism of transinduction.	9334315
EL0566	HELLPAR	N/A	N/A	N/A	N/A	mutation	We identified a novel long intergenic noncoding RNA (lincRNA) transcript of 205,012 bases with (peri)nuclear expression in the extravillous trophoblast using strand-specific RT-PCR complemented with RACE and FISH.	23093777	LncRNADisease
EL0568	HID1	N/A	qRT-PCR	seedling photomorphogenesis	down-regulated	N/A	HID1(HIDDEN TREASURE 1), that modulates red-light-mediated seedling photomorphogenesis in Arabidopsis. Knocking down HID1 led to increased levels of PIF3 mRNA, which in turn correlated directly with the elongated hypocotyl phenotype observed in the hid1 mutant seedlings grown under cR. We further demonstrated that HID1 is a chromatin-bound RNA and functions as a direct repressor of PIF3 transcription in cR. Thus, to our knowledge, HID1 appears to be the first lncRNA identified as being involved in the precise control of light-mediated seedling development. HID1 was expressed ubiquitously throughout the Arabidopsis development processes.	24982146	PLNlncRbase
EL0569	HIF1A-AS1	N/A	Real‑time polymerase chain reaction (PCR), western blot analysis, lncRNA PCR arrays and chromatin immunoprecipitation	human bone marrow stromal cells	down-regulated	interaction	HIF1α‑AS1 is an essential mediator of osteoblast differentiation.	26460121
EL0574	Hm629797	N/A	ChOP (Chromatin oligo affinity precipitation)	mouse spermatogonial Gc1-Spg cells	up-regulated	expression	Our findings in the Gc1-Spg cell line also correlate with the results from analysis of mouse testicular tissue which further highlights the in vivo physiological significance of mrhl RNA in the context of gene regulation during mammalian spermatogenesis.	25584904
EL0574	Hm629797	N/A	N/A	N/A	N/A	locus	This meiotically active locus happens to be flanked by a transcribed region encoding a non-protein-coding rna polymerase ii transcript and the previously characterized repair site.	15169920
EL0576	Hog	N/A	qRT-PCR, ChIP on chip	cecal buds	N/A	interaction	N/A	24075990
EL0578	HOTAIR	N/A	Illumina microarrays and confirmed by RT-PCR	Abdominal and gluteal adipose tissue aspirates obtained from 35 subjects	N/A	interaction	Ectopic expression of HOTAIR in abdominal preadipocytes produced an increase in differentiation as reflected by a higher percentage of differentiated cells, and increased expression of key adipogenic genes including PPARγ and LPL	24862299
EL0578	HOTAIR	N/A	knockdown	urothelial bladder cancer (UBC), urine (Ues)	up-regulated	interaction	Knockdown of HOTAIR in UBC cell lines reduces in vitro migration and invasion.	26800519
EL0578	HOTAIR	N/A	knock-down	human cardiomyocytes	N/A	expression	up-regulation of HOTAIR could suppress the expression of CaV1.2 in human cardiomyocytes. However, HOTAIR knock-down promoted CaV1.2 expression in human cardiomyocytes. enforced expression of CaV1.2 increased the calcium level in cardiomyocytes overexpressing HOTAIR. These results for the first time demonstrate that HOTAIR inhibited the intracellular Ca2+ via regulation of CaV1.2 in human cardiomyocytes.	26255135
EL0578	HOTAIR	N/A	knockdown, Luciferase assays	80 clinical colon cancer tissues	up-regulated	interaction	N/A	26962687
EL0578	HOTAIR	N/A	LncRNA microarray	Dermal papilla (DP) cells	up-regulated	expression	RP11-766N7.3, H19 and HOTAIR are specific lncRNAs that were aberrantly expressed in DP cells and played an important role in regulating Wnt signaling	25285630
EL0578	HOTAIR	N/A	N/A	breast cancer cells	N/A	interaction	Silencing of HBXIP, Hotair, or LSD1 was sufficient to block c-Myc-enhanced cancer cell growth in vitro and in vivo. Taken together, our results support a model in which the HBXIP/Hotair/LSD1 complex serves as a critical effector of c-Myc in activating transcription of its target genes, illuminating long-standing questions on how c-Myc drives carcinogenesis.	26719542
EL0578	HOTAIR	N/A	N/A	N/A	N/A	N/A	serve as scaffolds by providing binding surface	20616235
EL0578	HOTAIR	N/A	RT-PCR,Conventional ChIP and ChIP-chip ,In situ hybridization,RNA interference	N/A	N/A	N/A	We identified a 2.2 kilobase ncRNA residing in the HOXC locus, termed HOTAIR, which represses transcription in trans across 40 kilobases of the HOXD locus. HOTAIR interacts with Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance;	17604720
EL0579	Hotair	N/A	N/A	N/A	N/A	N/A	regulate HOXD genes in trans via the recruitment of Polycomb Repressive Complex 2 (PRC2), followed by the trimethylation of lysine 27 of histone H3.	21637793
EL0580	HOTAIRM1	N/A	sucrose gradient analysis	N/A	up-regulated	expression	Knockdown of HOTAIRM1 quantitatively blunted RA-induced expression of HOXA1 and HOXA4 during the myeloid differentiation of NB4 cells, and selectively attenuated induction of transcripts for the myeloid differentiation genes CD11b and CD18, but did not noticeably impact the more distal HOXA genes.	19144990
EL0581	Hotairm1	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Found to interact with a number of of chromatin binding proteins/complexes in mouse embryonic stem cells including PRC1, PRC2 and CBX1.	21874018
EL0582	HOTTIP	N/A	Strand-specific RT-PCR, RNA-FISH, RNA Interference, overexpression, RNA Immunoprecipitation, RNA chromatography	Primary human fibroblasts	N/A	N/A	driving histone H3 lysine 4 trimethylation and gene transcription	21423168
EL0584	HOXA11-AS	N/A	N/A	N/A	N/A	interaction	Hoxa11 antisense functions by transcriptional interference, repressing hoxa11 expression by competing for transcription of the common gene, rather than by sense/antisense interaction.	12050232
EL0584	HOXA11-AS	N/A	serial section and whole-mount in situ hybridizations	N/A	N/A	expression	In the developing limbs, the sense and antisense transcripts showed complementary expression patterns	7789268
EL0585	Hoxa11os	N/A	N/A	N/A	N/A	interaction	attempts to block hoxa11 function by transfection of the murine uterus with hoxa11 antisense oligonucleotides failed to interrupt normal uterine function, suggesting that hoxa11 antisense does not regulate hoxa11 mrna by formulation of sense/antisense duplexes.	12050232
EL0587	HOXA-AS	N/A	PCR	heart, lung, liver, kidney, colon, placenta, muscle, and brain	N/A	expression	This noncoding transcription is regulated by the retinoic acid morphogen and follows the colinear activation pattern of the cluster. Opening of the cluster at sites of activation of intergenic transcripts is accompanied by changes in histone modifications and a loss of interaction with Polycomb group (PcG) repressive complexes.	17185360
EL0590	HOXA-AS3	N/A	RNA-seq, qRT-PCR	three different brain regions (cortex, white matter, and cerebellum) of human postmortem tissue	N/A	N/A	Thus, these 5 lncRNAs may be applicable as references for accurate normalisation of lncRNA profiling in multiple brain regions during long PMI, enabling the generation of highly reproducible datasets in lncRNA studies of the human brain.	25528156
EL0591	Hoxd3as	N/A	RNA blot analysis, in situ hybridization	hind brain, liver	N/A	expression	The earliest antisense expression was detected at 10.5 days p.c. in cdna libraries. at 12.5 days p.c., sense and antisense transcripts colocalized in the liver.	7710686
EL0593	Hsromega	N/A	Fluorescence RNA, In situ immunocytochemical staining	N/A	N/A	interaction	The hsromega-n transcripts play essential structural and functional roles in organizing and establishing the hnrnp-containing omega speckles and thus regulate the trafficking and availability of hnrnps and other related rna binding proteins in the cell nucleus.	10984439
EL0593	Hsromega	N/A	in situ hybridization	nonstressed cells	N/A	expression	Transcripts appear abruptly at the time that the zygotic genome becomes transcriptionally active, shortly before the formation of the cellular blastoderm.	1704862
EL0593	Hsromega	N/A	RNA in situ hybridization	somatic cyst cells	N/A	interaction	These results further support a significant role of the noncoding hsromega-n transcripts in basic cellular activities, namely regulation of the availability of hnrnps in active (chromatin bound) and inactive (in omega speckles) compartments.	11910129
EL0594	HSUR1	N/A	Microarray and Northern analyses	N/A	N/A	interaction	An unexpected role for the hsurs in regulating a remarkably defined and physiologically relevant set of host targets involved in the activation of virally transformed t cells during latency.	15916956
EL0594	HSUR1	N/A	N/A	T cells	N/A	Interaction	HSURs 1 and 2 interact with the predicted miRNAs in virally transformed T cells.	20558719
EL0595	HSUR2	N/A	Microarray and Northern analyses	N/A	N/A	interaction	An unexpected role for the hsurs in regulating a remarkably defined and physiologically relevant set of host targets involved in the activation of virally transformed t cells during latency.	15916956
EL0595	HSUR2	N/A	N/A	T cells	N/A	Interaction	HSURs 1 and 2 interact with the predicted miRNAs in virally transformed T cells.	20558719
EL0598	Huc1	N/A	N/A	mesodermal tissues	N/A	expression	Mouse huc1 and huc2 act as potent enhancers capable of driving expression of an h19 reporter gene in a range of mesodermal tissues.	11874916
EL0599	Huc2	N/A	N/A	mesodermal tissues	N/A	expression	Mouse huc1 and huc2 act as potent enhancers capable of driving expression of an h19 reporter gene in a range of mesodermal tissues.	11874916
EL0602	HvCesA6	N/A	Strand-specific RT-PCR	Cell-wall synthesis	down-regulated	N/A	The increases in abundance of the CesA6 antisense transcript and the 21-nt and 24-nt siRNAs derived from the transcript are coincident with the down-regulation of primary wall CesAs, several Csl genes, and GT8 glycosyl transferase genes, and are correlated with the reduction in rates of cellulose and (1→3),(1→4)-β-D-glucan synthesis. The expression of individual members of the CesA/Csl superfamily and glycosyl transferases share common regulatory control points, and siRNAs from natural cis-antisense pairs derived from the CesA/Csl superfamily could function in this global regulation of cell-wall synthesis.	19075248	PLNlncRbase
EL0603	HvISP1	N/A	qRT-PCR	phosphate balance	up-regulated	N/A	HvIPS1 plays a distinct role in the regulation of the low-affinity Pi transporters. The expression of HvIPS1 is highly correlated with the expression of HvPHT1;3 and HvPHT1;6 in the four barley genotypes tested under low-P conditions (Figs. 4 and 6), suggesting that HvIPS1 plays a unique role in Pi remobilization. (Huang et al., 2011) The expression patterns of other members of the TPSI1/Mt4 family in monocots were also investigated. The induced expressions of OsIPS1, HvIPS1, ZmIPS2 and TalIPS2 were stronger than those of OsIPS2, HvIPS2 ZmIPS1 and TalIPS1 in roots after 4 or 10 d of Pi starvation, whereas higher induced expressions of OsIPS2, HvIPS1, ZmIPS1 and TalIPS1 were detected in shoots. (HOU et al., 2005)	21606317	PLNlncRbase
EL0608	IGF2-AS	N/A	RNA-seq, qRT-PCR	three different brain regions (cortex, white matter, and cerebellum) of human postmortem tissue	N/A	N/A	Thus, these 5 lncRNAs may be applicable as references for accurate normalisation of lncRNA profiling in multiple brain regions during long PMI, enabling the generation of highly reproducible datasets in lncRNA studies of the human brain.	25528156
EL0609	IL7R	N/A	human lncRNA microarray assays	N/A	down-regulated	N/A	lnc-IL7R was capable of diminishing the LPS-induced inflammatory response	24723426
EL0610	ILF3	N/A	overexpression	human fibroblast cells	down-regulated	interaction	Overexpression of SALNR delayed cellular senescence in fibroblast cells. Ras-induced stress promotes NF90 nucleolus translocation and suppresses its ability to suppress senescence-associated miRNA biogenesis, which could be rescued by SALNR overexpression.	26487301
EL0612	IPO5P1	N/A	microarray, RT-qPCR	human monocyte-derived macrophages (MDMs) incubated in conditions causing activation toward M(IFN-γ + LPS) or M(IL-4) phenotypes.	up-regulated	expression	Knockdown of TCONS_00019715 following the activation of THP-1 cellls using IFN-γ and LPS diminished the expression of M(IFN-γ + LPS) markers, and elevated the expression of M(IL-4) markers.	26796525
EL0613	IPS1	N/A	Northern blot/qRT-PCR	phosphate balance	up-regulated	N/A	Arabidopsis thaliana(AtIPS1) that is induced by Pi starvation, and studied the effect of cytokinin on its expression in response to Pi deprivation. AtIPS1 belongs to the TPSI1/Mt4 family, the members of which are induced by Pi starvation, and the RNAs of which contain only short, non-conserved open reading frames. AtIPS1 is induced by Pi starvation and expression in the root. The induction of AtIPS1 expression under Pi starvation is reversible. AtIPS1:GUS responsiveness to Pi starvationin roots is repressed by cytokinins. However, cytokinins did not repress the increase in root-hair number and length induced by Pi starvation, a response dependent on local Pi concentration rather than on whole-plant Pi status. Our results raise the possibility that cytokinins may be involved in the negative modulation of long-distance, systemically controlled Pi starvation responses, which are dependent on whole-plant Pi status. (Ana et al., 2002) The lncRNA, INDUCED BY PHOSPHATE STARVATIONA (IPS1), is a noncoding transcript that is intimately associated with the function of miRNA399. Under phosphate starvation, the expression PHO2, a target of miRNA399, is up-regulated due to increased binding and sequestering of miRNA399 by IPS1. IPS1 contains complementary sequences to the phosphate (Pi) starvation-induced miRNA399 and thus can compete with PHO2 transcripts for the binding of miRNA399. However, IPS1 is not cleaved by the miRNA because the paring with miRNA is interrupted by a mismatched loop at the expected miRNA cleavage site. (Kim et al., 2011) The effect of miR-399 on PHO2 mRNA was greatly suppressed by simultaneous IPS1 overexpression,suggesting that IPS1 antagonizes the effects of miR-399. In agreement with previous reports on the negative effect of PHO2 on shoot Pi content9-12, the shoot Pi content of IPS1-overexpressing plants was lower than that in their counterparts lacking IPS1 overexpression. And IPS1 contains a motif with sequence complementarity to the phosphate (Pi) starvation-induced miRNA miR-399，IPS1 over expression results in increased accumulation of the miR-399 target PHO2 mRNA and, concomitantly, in reduced shoot Pi content. (Franco-Zorrilla et al., 2007) Induced by Phosphate Starvation1(IPS1), which can bind to ath-miR399 with a three-nucleotide bulge between the 5'end 10th and 11th positions of ath-miR399. Such pairing abolished the cleavage effect of ath-miR399 on IPS1; thus, IPS1 can serve as a decoy for ath-miR399 to interfere with the binding of ath-miR399 to its other targets. (Wu et al., 2013) Under phosphate starvation, transcript levels of the natural target of miR399, PHO2, are increased because of the binding and sequestering of miR399 by IPS1. IPS1 contains a centrally bulged miR399-binding site (called 'target mimic’) that prevents IPS1 cleavage by miR399 and apparently inhibits recycling of the miR399 effector complex. (Brosnan et al., 2009) Induced by Phosphate Starvation 1 (IPS1) with a binding site for miR-399, a phosphate starvation-induced miRNA. However,miR-399 binding does not induce degradation of the IPS1 transcript due to mismatched nucleotides in the binding site, but rather results in sequestration of miR-399 from other target transcripts. Thus, IPS1 can effectively function as a sponge in hibiting the number of miR-399 molecules available for regulating its target PHO2 mRNA. The Arabidopsis thaliana pho2 mutant is aphosphate over-accumulator. This mutant carries a mutation in the PHO2 gene,encoding a ubiquitin-conjugating enzyme(UBC24), that leads to a reduction in full-length transcripts. In response to phosphate starvation, IPS1 RNAs are induced. The latter can sequester miR-399 resulting in stabilization and increased accumulation of PHO2 and, concomitantly, in reduced shoot phosphate content. (Kartha et al., 2014)	22104407, 17643101, 23429259, 19447594, 24523727	PLNlncRbase
EL0614	IPS1	N/A	Northern blot/RT-PCR	phosphate balance	up-regulated	N/A	IPS1 has complementarity to miR-399, but contains a mismatch loop that renders it uncleavable when miR-399 binds. Since target cleavage is the usual plant miRNA pathway the non-cleavable nature of IPS1 acts to sequester the miRNA; Competing endogenous RNA (ceRNA). IPS1 carries out target mimicry to sequester miR-399 and attenuate its effects allowing increased expression of miR-399 targets including PHO2.	17643101	PLNlncRbase
EL0615	IPS1	N/A	Northern blot/qRT-PCR	phosphate balance	up-regulated	N/A	The effect of miR-399 on PHO2: GFP was suppressed by simultaneous expression of IPS1, and a mutant form of IPS1 with reduced complementarity to miR-399 did not affect miR-399-mediated silencing of PHO2: GFP. Finally, we reconstituted the interaction between IPS1, miR-399 and PHO2 in a system in which complementary and compensatory mutations were introduced in all three components.	17643101	PLNlncRbase
EL0616	IPS1	N/A	Northern blot/qRT-PCR	phosphate balance	up-regulated	N/A	IPS1 RNA is not cleaved but instead sequesters miR-399. Thus, IPS1 overexpression results in increased accumulation of the miR-399 target PHO2 mRNA and, concomitantly, in reduced shoot Pi content5–8. Engineering of IPS1 to be cleavable abolishes its inhibitory activity on miR-399.	17643101	PLNlncRbase
EL0617	IPS1	N/A	Northern blot/qRT-PCR	phosphate balance	up-regulated	N/A	IPS1 RNA is not cleaved but instead sequesters miR-399. Thus, IPS1 overexpression results in increased accumulation of the miR-399 target PHO2 mRNA and, concomitantly, in reduced shoot Pi content5–8. Engineering of IPS1 to be cleavable abolishes its inhibitory activity on miR-399.	17643101	PLNlncRbase
EL0621	JPX	N/A	knockdown, FISH, Quantitative RT-PCR, Allele-specific RT-PCR, Luciferase assay	ES cell lines	N/A	interaction	Jpx as an Xist activator	21029862
EL0625	KCNIP4-IT1	N/A	N/A	cerebellum	N/A	expression	Like noncoding rnas, the porcine and human sequences have no common conserved open reading frame and share stretches of high homology interrupted by stretches with almost no homology.	12515386
EL0626	KCNIP4-IT1	N/A	N/A	cerebellum	N/A	expression	Like noncoding rnas, the porcine and human sequences have no common conserved open reading frame and share stretches of high homology interrupted by stretches with almost no homology.	12515386
EL0627	KCNQ1DN	N/A	N/A	N/A	N/A	epigenetics	Continuously hypermethylated upon aging.	22067257	LncRNADisease
EL0628	KCNQ1OT1	N/A	CHIP, PCR, knockdown, RNA-guided chromatin conformation capture method	N/A	N/A	interaction	The 5' region of Kcnq1ot1 RNA orchestrates a long-range intrachromosomal loop between KvDMR1 and the Kcnq1 promoter that is required for maintenance of imprinting.PRC2 (polycomb repressive complex 2), which participates in the allelic repression of Kcnq1, is also recruited by Kcnq1ot1 RNA via EZH2.	24395636
EL0628	KCNQ1OT1	N/A	ChIP,PCR,FISH,immuno-FISH	human placenta	N/A	interaction	The bidirectional silencing property of Kcnq1ot1 maps to a highly conserved repeat motif within the silencing domain, which directs transcriptional silencing by interaction with chromatin, resulting in histone H3 lysine 9 trimethylation.	18299392
EL0628	KCNQ1OT1	N/A	Chromatin RNA Immunoprecipitation and RNA Immunoprecipitation,ImmunoDNA FISH,Chromatin Oligo-Affinity Precipitation	placenta and liver	N/A	interaction	our data describe a mechanism whereby Kcnq1ot1 establishes lineage-specific transcriptional silencing patterns through recruitment of chromatin remodeling complexes and maintenance of these patterns through subsequent cell divisions occurs via targeting the associated regions to the perinucleolar compartment.	18951091
EL0629	Kcnq1ot1	N/A	N/A	a knockout mouse with a deletion encompassing an 890-bp silencing domain (Delta890) downstream of the Kcnq1ot1 promoter	N/A	N/A	Kcnq1ot1 RNA might mediate the silencing of ubiquitously imprinted genes by maintaining allele-specific methylation through its interactions with Dnmt1	20573698
EL0629	Kcnq1ot1	N/A	N/A	N/A	N/A	N/A	silence mulitple genes	21345374
EL0629	Kcnq1ot1	N/A	N/A	an embryonic stem (ES) cell	N/A	N/A	t Kcnq1ot1 silencing extends nearly 300 kb further than previously reported and led us to examine other transcripts between IC1 and IC2	21576366
EL0629	Kcnq1ot1	N/A	RNA/DNA FISH	mouse embryo and placenta	N/A	epigenetics	The paternally expressed long noncoding RNA (ncRNA) Kcnq1ot1 regulates epigenetic gene silencing in an imprinted gene cluster in cis over a distance of 400 kb in the mouse embryo, whereas the silenced region extends over 780 kb in the placenta. Gene silencing by the Kcnq1ot1 RNA involves repressive histone modifications, including H3K9me2 and H3K27me3, which are partly brought about by the G9a and Ezh2 histone methyltransferases.	19144718
EL0630	Khps1	N/A	N/A	N/A	N/A	interaction	Khps1 activates SPHK1 expression by recruiting the histone acetyltransferase p300/CBP to the SPHK1 promoter, which leads to local changes of the chromatin structure that ensures E2F1 binding and enhances transcription.	26590717
EL0631	Khps1a	N/A	N/A	N/A	N/A	expression	Overexpression of two fragments of khps1 caused demethylation of cg sites in the t-dmr. furthermore, this rna-directed demethylation was associated with dna methylation at three cc(a/t)gg sites in the t-dmr.	15325271
EL0632	KIR antisense lncRNA	N/A	N/A	Human NK cells	N/A	interaction	Overexpression of MZF-1 in developing NK cells led to decreased KIR expression, consistent with a role for the KIR antisense lncRNA in silencing KIR gene expression early in development.	23863987
EL0636	Ks-1	N/A	RT-PCR, cDNA cloning, fluorescent in situ hybridization	honeybee brain	N/A	N/A	Ks-1 encodes a novel class of noncoding nuclear rna and is possibly involved in the regulation of neural functions.	12088150
EL0641	LDMAR	N/A	RT-PCR	normal pollen development	up-regulated	N/A	Long-day-specific male-fertility-associated RNA (LDMAR), regulates PSMS in rice. We found that sufficient amount of the LDMAR transcript is required for normal pollen development of plants grown under long-day conditions. LDMAR is required for male fertility under long day conditions. The spontaneous G→C mutation causing a SNP between 58N and 58S altered the RNA secondary structure of this region. This alteration eventually brought about heritable increased methylation in the promoter region of LDMAR, thus reducing the level of transcription specifically under long-day conditions. Such a reduced level of LDMAR results in premature PCD in anther development under long days, thus causing male sterility. (Ding et al., 2012) Photoperiod-sensitive male sterility (PSMS) is a valuable germplasm for hybrid rice breeding. Recently, we cloned pms3, a locus controlling PSMS, which encodes a long non-coding RNA called LDMAR required for normal male fertility of the rice plant under long-day conditions.Increased methylation in the promoter of LDMAR in the PSMS rice (Nongken 58S) relative to the wild-type (Nongken 58) reduced expression of LDMAR leading to male sterility under long-day conditions.all in all, reduced the expression of this lncRNA, resulting in male sterility under long-day conditions. LDMAR required for normal male fertility of the rice plant under long-day conditions. Reduction of LDMAR in Nongken 58S changed the critical day length for fertility recovery and delayed the fertility recovery under short-day conditions. This result added to our understanding of the molecular mechanism for PSMS. (Ding et al., 2012) A long non-coding RNA (lncRNA) named LDMAR. A sufficient amount of LDMAR is required for male fertility under long-day conditions. A spontaneous G-C mutation causing a SNP between NK58 and NK58S, eventually brings about heritable increased methylation in the promoter region of LDMAR, which reduces the level of LDMAR expression. This then results in premature programmed cell death (PCD) in anther development under long days, and hence male sterility. In addition, RNA-dependent DNA methylation (RdDM) is involved in the regulation of PGMS. Promoter siRNA of LDMAR derived from AK11270 is associated with the DNA methylation level of LDMAR, which reduces the expression level of LDMAR, and therefore male sterility in Nonken 58S under long-day conditions. (Wang et al., 2013)	22308482, 23024213, 23596452	PLNlncRbase
EL0643	LeENOD40	N/A	RT-PCR	vascular tissue	up-regulated	N/A	LeENOD40 is expressed in vascular tissue, expression of LeENOD40 in tomato is found in flowers and germinated seeds. Furthermore, it is active in vascular tissues of stems, young leaves (data not shown) and roots. In an early stage of lateral root development the lateral root primordium is flanked by regions of the vascular bundle where LeENOD40::GUS is expressed, whereas in the region where the primordium is located ENOD40 expression is low. LeENOD40::GUS is also expressed in a specific manner during flower development. LeENOD40 expression marks the time of pollination of the stigma. LeENOD40 expression also occurs in the petals after pollination. And based on our observations, we suggest that LeENOD40 could have a role in reducing ethylene production or in reducing local effects of ethylene production.	14508686	PLNlncRbase
EL0651	LINC00261	N/A	RNA-seq, knockdown	human endoderm and pancreatic cells	N/A	Interaction	DEANR1 contributes to endoderm differentiation by positively regulating expression of the endoderm factor FOXA2. Mechanistically, DEANR1 facilitates FOXA2 activation by facilitating SMAD2/3 recruitment to the FOXA2 promoter.	25843708
EL0656	LINC00461	N/A	In Situ Hybridization, RT-PCR, knockdown	Visc-2 knockout mice	N/A	expression	Despite a neurodevelopmental expression pattern of Visc-2 that is highly localized to the cortex and sites of neurogenesis, anomalies in neither cytoarchitecture nor neuroproliferation were identified in knockout mice. These results are important because they contribute to a growing body of evidence that lncRNA loci contribute on average far less to brain and biological functions than protein-coding loci.	25209608
EL0665	LINC00663	N/A	RT-PCR and qPCR methods	various cancer cell lines	N/A	expression	LINC00663 was shown to be differentially expressed in various human tissues and cancer cell lines. LINC00663 undergoes alternative splicing and the novel exonic region alters its secondary structure and its interactions with potential targeting miRNAs.	26743782
EL0705	LINC01613	N/A	RT-PCR	lungs of IPF (idiopathic pulmonary fibrosis) patients	down-regulated	expression	while knock-down of the lncRNA n341773 increased collagen expression in lung fibroblasts.	26269497
EL0711	LINC02	N/A	qRT-PCR	lint-fuzz/linted-fuzzless	up-regulated	N/A	Specifically, the expression of one lncRNA (LINC02) was highlighted, the expression of which might in part underlie the development of lint and fuzz fibres. This lncRNA produced significantly higher transcription levels in lint-fuzz/linted-fuzzless cottons than in lintless-fuzzless cottons (P < 0.05).	25919642	PLNlncRbase
EL0712	linc1242	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Involved in maintaining pluripotency in ESCs.	21874018
EL0713	linc1257	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Found to interact with a number of chromatin binding proteins/complexes in mESCs including PRC1, PRC2, JARID1B, SUV39H1, SETD8 and CBX1, with the general pattern being interaction with repressors of gene expression.	21874018
EL0714	linc1368	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Involved in maintaining pluripotency in ESCs.	21874018
EL0722	Linc-rbe	N/A	N/A	cultured primary hippocampal neurons from adult rat	up-regulated	expression	AtRA-mediated transcriptional upregulation of endogenous expression of a novel long intergenic noncoding RNA-rat brain expressed (LINC-RBE) in cultured primary hippocampal neurons from adult rat.	26572536
EL0722	Linc-rbe	N/A	RT-PCR and RNA in situ hybridization	rat brain	N/A	expression	The expression pattern of the LINC-RBE showed distinct association with the specific neuro-anatomical regions, cell types and sub-cellular compartments of the rat brain in an age-related manner. Thus, its expression increased from immature stage to adulthood and declined further in old age.	26363523
EL0723	LincR-Ccr2-5'AS	N/A	N/A	T cell samples	N/A	N/A	LincR-Ccr2-5'AS, together with GATA-3, was an essential component of a regulatory circuit in gene expression specific to the TH2 subset of helper T cells and was important for the migration of TH2 cells.	24056746
EL0724	lincRNA1039	N/A	RT-qPCR	drought and cold	up-regulated	N/A	A total of 504 lincRNAs were identified (see Supplementary Table S9 at JXB online), and eight were subjected to experimental validation by quantitative real-time polymerase chain reaction (RT-qPCR). As shown in Fig. 6, the expression patterns indicated by the sequencing and RT-qPCR results of drought-responsive lincRNAs were consistent, in a conclusion, those lncRNAs response to drought stress. Drought-induced lincRNA1039 is also up-regulated by cold stress.	24948679	PLNlncRbase
EL0725	lincRNA1085	N/A	RT-qPCR	drought	down-regulated	N/A	A total of 504 lincRNAs were identified (see Supplementary Table S9 at JXB online), and eight were subjected to experimental validation by quantitative real-time polymerase chain reaction (RT-qPCR). As shown in Fig. 6, the expression patterns indicated by the sequencing and RT-qPCR results of drought-responsive lincRNAs were consistent, in a conclusion, those lncRNAs response to drought stress.	24948679	PLNlncRbase
EL0726	lincRNA1128	N/A	RT-qPCR	drought and cold	N/A	N/A	lincRNA1128 regulated ptc-miR482a.1 as target mimics and inhibit its function. Ptc-miR482a.1 has been investigated previously and regulates specific disease-resistance proteins in P.trichocarpa. This miRNA is known to be responsive to four abiotic stresses (cold, heat, salt, and dehydration) in Populus.	24948679	PLNlncRbase
EL0727	lincRNA1310	N/A	RT-qPCR	stress treatments	N/A	N/A	LincRNA1310 is a target of ptc-miR476a.	24948679	PLNlncRbase
EL0728	lincRNA1534	N/A	RT-qPCR	drought	up-regulated	N/A	A total of 504 lincRNAs were identified (see Supplementary Table S9 at JXB online), and eight were subjected to experimental validation by quantitative real-time polymerase chain reaction (RT-qPCR). As shown in Fig. 6, the expression patterns indicated by the sequencing and RT-qPCR results of drought-responsive lincRNAs were consistent, in a conclusion, those lncRNAs response to drought stress.	24948679	PLNlncRbase
EL0729	lincRNA1828	N/A	RT-qPCR	drought and cold	N/A	N/A	lincRNA1828 regulated ptc-miR482a.1 as target mimics and inhibit its function. Ptc-miR482a.1 has been investigated previously and regulates specific disease-resistance proteins in P.trichocarpa. This miRNA is known to be responsive to four abiotic stresses (cold, heat, salt, and dehydration) in Populus.	24948679	PLNlncRbase
EL0730	lincRNA20	N/A	RT-qPCR	drought and cold	up-regulated	N/A	Drought-responsive lincRNA20 adsorbed ptc-miR476, which is a specific family in Populus. lincRNA20 is also specific to Populus, and may thus represent a Populus-specific regulatory mechanism.	24948679	PLNlncRbase
EL0731	lincRNA2085	N/A	RT-qPCR	drought	up-regulated	N/A	A total of 504 lincRNAs were identified (see Supplementary Table S9 at JXB online), and eight were subjected to experimental validation by quantitative real-time polymerase chain reaction (RT-qPCR). As shown in Fig. 6, the expression patterns indicated by the sequencing and RT-qPCR results of drought-responsive lincRNAs were consistent, in a conclusion, those lncRNAs response to drought stress.	24948679	PLNlncRbase
EL0732	lincRNA2131	N/A	RT-qPCR	drought	up-regulated	N/A	A total of 504 lincRNAs were identified (see Supplementary Table S9 at JXB online), and eight were subjected to experimental validation by quantitative real-time polymerase chain reaction (RT-qPCR). As shown in Fig. 6, the expression patterns indicated by the sequencing and RT-qPCR results of drought-responsive lincRNAs were consistent, in a conclusion, those lncRNAs response to drought stress.	24948679	PLNlncRbase
EL0733	lincRNA2198	N/A	RT-qPCR	drought	up-regulated	N/A	A total of 504 lincRNAs were identified (see Supplementary Table S9 at JXB online), and eight were subjected to experimental validation by quantitative real-time polymerase chain reaction (RT-qPCR). As shown in Fig. 6, the expression patterns indicated by the sequencing and RT-qPCR results of drought-responsive lincRNAs were consistent, in a conclusion, those lncRNAs response to drought stress.	24948679	PLNlncRbase
EL0734	lincRNA262	N/A	RT-qPCR	stress treatments	N/A	N/A	LincRNA262 is the target and target mimic of ptc-miR156c.	24948679	PLNlncRbase
EL0735	lincRNA2623	N/A	RT-qPCR	stress treatments	N/A	N/A	lincRNA2623 regulated ptc-miR482a.1 as target mimics and inhibit its function. Ptc-miR482a.1 has been investigated previously and regulates specific disease-resistance proteins in P.trichocarpa. This miRNA is known to be responsive to four abiotic stresses (cold, heat, salt, and dehydration) in Populus.	24948679	PLNlncRbase
EL0736	lincRNA2752	N/A	RT-qPCR	drought	up-regulated	N/A	Drought-responsive lincRNA2752 is a target mimic of ptc-miR169, and could reduce the expression of ptc-miR169. MiR169 is known to regulate the NF-YA transcription factor in plants, which is important in drought stress regulation. This network may be involved in the lincRNA2752-regulation of drought tolerance through miR169 and NF-YA. However, the specific regulatory mechanism requires further investigation, and knock out and over-expression of the lincRNA genes in P.trichocarpa should be performed to increase our understanding of the regulatory mechanisms.	24948679	PLNlncRbase
EL0737	lincRNA2962	N/A	RT-qPCR	drought	up-regulated	N/A	A total of 504 lincRNAs were identified (see Supplementary Table S9 at JXB online), and eight were subjected to experimental validation by quantitative real-time polymerase chain reaction (RT-qPCR). As shown in Fig. 6, the expression patterns indicated by the sequencing and RT-qPCR results of drought-responsive lincRNAs were consistent, in a conclusion, those lncRNAs response to drought stress. Drought-induced lincRNA2962 is also down-regulated by cold stress.	24948679	PLNlncRbase
EL0738	lincRNA3241	N/A	RT-qPCR	drought	up-regulated	N/A	A total of 504 lincRNAs were identified (see Supplementary Table S9 at JXB online), and eight were subjected to experimental validation by quantitative real-time polymerase chain reaction (RT-qPCR). As shown in Fig. 6, the expression patterns indicated by the sequencing and RT-qPCR results of drought-responsive lincRNAs were consistent, in a conclusion, those lncRNAs response to drought stress. LincRNA3241 is down-regulated by water and cold stress.	24948679	PLNlncRbase
EL0747	LINC-ROR	N/A	knockdown	wild-type and NRF2 knockdown mammary stem cells	N/A	expression	NRF2 knockdown or ROR overexpression leads to increased stem cell self-renewal in mammary stem cells	25231996
EL0748	LINC-RSAS	N/A	RT-PCR, in situ RNA hybridization	rat brain	N/A	expression	N/A	26750132
EL0751	LL34	N/A	N/A	lung and foregut endoderm	N/A	interaction	Two lncRNAs, LL18/NANCI (Nkx2.1-associated noncoding intergenic RNA) and LL34, play distinct roles in endoderm development by controlling expression of critical developmental transcription factors and pathways, including retinoic acid signaling	24939938
EL0754	lnc-168	N/A	qRT-PCR	heat and salt	down-regulated	N/A	lnc-508 was down-regulated by heat and cold, while lnc-168 was down-regulated by heat and salt in Arabidopsis.	10.3389/fpls.2015.00267	PLNlncRbase
EL0755	lnc-173	N/A	qRT-PCR/RT-PCR	high light	up-regulated	N/A	lnc-173 and lnc-225,which are potentially regulated by high light and PIF transcription factors.	25256571	PLNlncRbase
EL0756	lnc-225	N/A	qRT-PCR/RT-PCR	high light	up-regulated	N/A	lnc-173 and lnc-225,which are potentially regulated by high light and PIF transcription factors.	25256571	PLNlncRbase
EL0757	lnc-31	N/A	Transcriptome analysis	mdx muscles	up-regulated	N/A	controlling the differentiation commitment of precursor myoblasts	25512605
EL0759	lnc-508	N/A	qRT-PCR	heat and cold	down-regulated	N/A	lnc-508 was down-regulated by heat and cold, while lnc-168 was down-regulated by heat and salt in Arabidopsis.	10.3389/fpls.2015.00267	PLNlncRbase
EL0775	lncLGR	N/A	lncLGR knockdown enhances GCK expression	fasted mice	up-regulated	N/A	lncLGR knockdown enhances GCK expression and glycogen storage lncLGR knockdown enhances GCK expression and glycogen storage	26904944
EL0780	lncRNA1329	N/A	RNA-Seq/qRT–PCR	fruit ripening	down-regulated	N/A	To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6).	25948705	PLNlncRbase
EL0781	lncRNA1459	N/A	RNA-Seq/qRT–PCR	fruit ripening	down-regulated	N/A	Moreover, down-regulation of the expression of some novel intergenic lncRNAs (lncRNA1459 and lncRNA1840) in wild-type tomato fruit induced an obvious delay of fruit ripening.	25948705	PLNlncRbase
EL0782	lncRNA1471	N/A	RNA-Seq/qRT–PCR	fruit ripening	down-regulated	N/A	To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6).	25948705	PLNlncRbase
EL0783	lncRNA1785	N/A	RNA-Seq/qRT–PCR	fruit ripening	down-regulated	N/A	To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6).	25948705	PLNlncRbase
EL0784	lncRNA1840	N/A	RNA-Seq/qRT–PCR	fruit ripening	down-regulated	N/A	Moreover, down-regulation of the expression of some novel intergenic lncRNAs (lncRNA1459 and lncRNA1840) in wild-type tomato fruit induced an obvious delay of fruit ripening.	25948705	PLNlncRbase
EL0785	lncRNA2.7	N/A	RT-PCR	human immunodeficiency virus-1 (HIV-1)	up-regulated	expression	stabilizes Complex I, reduced ROS production and inhibited EC apoptosis	20036157
EL0786	lncRNA246	N/A	psRNATarget/psRobot	phosphate homeostasis	N/A	N/A	LncRNA246 was the eTM of slymiR399, a miRNA that plays an important role in regulating phosphate homeostasis.	25948705	PLNlncRbase
EL0787	lncRNA2943	N/A	RNA-Seq/qRT–PCR	fruit ripening	up-regulated	N/A	To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6).	25948705	PLNlncRbase
EL0788	LncRNA-314	N/A	N/A	cultivar tomato Heinz1706 and its wild relative LA1589	N/A	N/A	N/A	26494192
EL0789	lncRNA3294	N/A	psRNATarget/psRobot	drought	N/A	N/A	In addition, lncRNA3294 was the target of sly-miR169 that is engaged in drought tolerance of tomato.	25948705	PLNlncRbase
EL0790	lncRNA3613	N/A	psRNATarget/psRobot	N/A	N/A	N/A	LncRNA3613 was the target of sly-miR5304 that has been only identified in solanaceous plants.	25948705	PLNlncRbase
EL0792	lncRNA496	N/A	RNA-Seq/qRT–PCR	fruit ripening	up-regulated	N/A	To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6).	25948705	PLNlncRbase
EL0793	lncRNA504	N/A	psRNATarget/psRobot	plant immunity	N/A	N/A	Of these three miRNA targets, lncRNA504 was the target of slymiR6024 that was involved in plant immunity.	25948705	PLNlncRbase
EL0794	lncRNA506	N/A	RNA-Seq/qRT–PCR	fruit ripening	up-regulated	N/A	To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6).	25948705	PLNlncRbase
EL0795	lncRNA864	N/A	RNA-Seq/qRT–PCR	fruit ripening	up-regulated	N/A	To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6).	25948705	PLNlncRbase
EL0796	lncRNA950	N/A	RNA-Seq/qRT–PCR	fruit ripening	up-regulated	N/A	To investigate whether these differentially expressed lncRNAs are engaged in fruit ripening, 10 of them were arbitrarily selected, five from a highly up-regulated group and five from a down-regulated group. The differences in their expression levels observed by RNA-Seq were experimentally validated by qRT–PCR (Fig. 6).	25948705	PLNlncRbase
EL0801	lncRNA-HSVIII	N/A	N/A	spermatocytes	N/A	N/A	upstream and downstream regions of the lncRNA-HSVIII sequence significantly increased Prss42/Tessp-2 promoter activity	27111572
EL0803	lncRNA-Rel	N/A	microarray, qRT-PCR	bone marrow-derived macrophages (BMDMs)	N/A	expression	Many identified LPS-regulated lncRNAs, such as lncRNA-Nfkb2 and lncRNA-Rel, locate near to immune response protein-coding genes.	25652569
EL0804	lncRNA-αGT	N/A	loss of function experiments	N/A	N/A	N/A	promotes full activation of adult gene expression in the chicken α-globin domain. by promoting an active chromatin structure.	24196393
EL0812	LOC100129973	N/A	microarray, qRT-PCR	in the serum and FGF-2 starvation-induced apoptosis of VECs	up-regulated	N/A	lncRNA LOC100129973 upregulated the expression of two apoptosis repressors gene	26887505
EL0815	LOC100288798	N/A	RT-qPCR and RNA-seq	haploid KBM7 cells	N/A	expression	Expression analysis from RNA-seq data shows significant deregulation of 41 protein-coding genes upon LOC100288798 truncation.	26662309
EL0817	LOC101211037	N/A	Northern blot	cotyledons	down-regulated	N/A	The expression of the CR20 gene responded strongly to exogenous cytokinins in excised cotyledons of cucumber, and the level of expression changed in association with phenomena that have been to postulated to involve cytokinins, such as aging of leaves, greening, and responses to wounding. The level of the CR20 transcript decreased during the early phase of greening and soon after the wounding of cotyledons. The levels were much lower in young leaves than in mature or senescent leaves. Cytokinins are thought to control greening and aging of leaves and to mediate responses to wounding. (Teramoto et al., 1996) The CR20 RNA is a product of a cytokinin responsive gene that is repressed in response to cytokinins (plant hormones) or stress conditions and was first isolated from cucumber and later reported in several other plant species. (Szymański et al., 2002)	8980532, 12049667	PLNlncRbase
EL0820	LOC103643717	N/A	qRT-PCR/RNA-seq	leaves	down-regulated	N/A	This lncRNA was downregulated in drought-stress leaves(see Table S2 for details).	24892290	PLNlncRbase
EL0822	LOC105246506	N/A	combined full-length mESC transcriptome genomic mapping data with chromatin immunoprecipitation genomic location maps of the key mESC transcription factors	mouse embryonic stem cells (mESCs)	N/A	Interaction	potential roles in pluripotency	20026622
EL0822	LOC105246506	N/A	in vitro knowdown, qRT-PCR	mESC (mouse embryonic stem cells), MSC (mice mesenchymal stem cells)	up-regulated	interaction	AK141205 positively promoted CXCL13 expression via acetylation of H4 histone in the promoter region;In summary, we report a completely novel role of AK141205/CXCL13 as a regulator of OGP-induced osteogenic differentiation of SMCs. Our finding provides a potential therapeutic targeting of AK141205 for enhancing disease-treatment effect of SMCs. (PMID:26321662). When overexpressed, AK141205 led to an increase in Oct4 mRNA and to a corresponding up-regulation of endodermal markers, in addition to initiating meso- and ectodermal differentiation. (PMID:20026622).	26321662; 20026622
EL0826	LOC105435934	N/A	RT-PCR	cotyledons	up-regulated	N/A	The CsM10 gene was not expressed in the root tissues, but was expressed in the cotyledons. Originating in cucumber floral buds isolated by differential display and differential hybridization. The CsM10 transcript levels in the apical tissues varied with different seedling developmental stages. CsM10 expression does not depend on phytohormones. CsM10 is related to male sex differentiation in the cucumber. (Jeongki et al., 2005) CsM10 was isolated using differential display reverse transcription PCR, which showed differential expression patterns in different tissues, seedling developmental stages and photoperiods. CsM10 habours a 179 bp sequence with high sequence homology to a family of abiotic stress-associated ncRNAs known as the CR20-GUT15-Related (CGR) family, suggesting a role in the regulation of gene expression. (Au et al., 2011)	21525783	PLNlncRbase
EL0832	LOC548136	N/A	RT-PCR	Nodule formation	up-regulated	N/A	The polycistronic nature of enod40 mRNA was recently demonstrated biochemically, with in vitro translation in wheat germ extracts resulting in the de novo synthesis of two peptides of 12 and 24 amino acid residues, subsequently immunoprecipitated by antipeptide antibodies. Additionally, these peptides were shown to specifically bind sucrose synthase (SuSy), thus implicating them in the regulation of SuSy activity and/or its intracellular targeting.	12930950	PLNlncRbase
EL0834	LpENOD40	N/A	RT-PCR	stems	down-regulated	N/A	The LpENOD40 transcript encodes a putative dodecapeptide, similar to that identified in ENOD40s from leguminous plants and other dicots, and also to ENOD40s from monocots. high level of LpENOD40 gene transcript was found expressed in stem tissue. lower level was detected in leaves and only a very low expression in flowers of perennial ryegrass. No LpENOD40 transcript was detected in roots.	12872490	PLNlncRbase
EL0853	MALAT1	N/A	Depletion of MALAT1 or overexpression	N/A	N/A	N/A	MALAT1 regulates AS by modulating the levels of active SR	20797886
EL0853	MALAT1	N/A	knockdown, siRNA	human fetal osteoblastic cell line hFOB 1.19	up-regulated	expression	RANKL, binding to its receptor RANK, inhibited cell proliferation via MALAT1 upregulation in osteoblast cells in vitro.	25817340
EL0853	MALAT1	N/A	N/A	N/A	N/A	expression	Biogenesis, metabolism, and functions of lncRNAs are otherwise interconnected with known pathogenic mechanisms	23791884	LncRNADisease
EL0853	MALAT1	N/A	nuclear magnetic resonance and Förster resonance energy transfer	N/A	N/A	mutation	An m(6)A site in the lncRNA metastasis associated lung adenocarcinoma transcript 1 (MALAT1) was recently shown to induce a local change in structure that increases the accessibility of a U5-tract for recognition and binding by heterogeneous nuclear ribonucleoprotein C (HNRNPC). This m(6)A-dependent regulation of protein binding through a change in RNA structure, termed "m(6)A-switch", affects transcriptome-wide mRNA abundance and alternative splicing. The m(6)A-modified hairpin has a predisposed conformation that resembles the hairpin conformation in the RNA-HNRNPC complex more closely than the unmodified hairpin.	26343757
EL0853	MALAT1	N/A	TaqMan gene expression assays, QPCR	human TK6 (p53 positive) and WTK1 (p53 negative) cells	up-regulated	interaction	The lncRNA MALAT1 and SOX2OT were induced in both TK6 and WTK1 cells	23698766
EL0854	Malat1	N/A	compared between freshly-isolated and cultured dental mesenchymal cells	mouse dental mesenchymal cells	down-regulated in dental mesenchymal cells; up-regulated in odontogenic dental mesenchymal tissue	N/A	loss of odontogenic potential	26986487
EL0854	Malat1	N/A	knock-down, DNA microarray analysis	hippocampal neurons	Up-regulated	regulation	modulates the recruitment of SR family pre-mRNA-splicing factors	20729808
EL0854	Malat1	N/A	Northern blot,knockdown,RNA-seq	a Malat1 loss-of-function genetic model	N/A	interaction	Malat1 is not essential for mouse pre- and postnatal development. However, among a small number of genes that were dysregulated in adult Malat1 knockout mice, many were Malat1 neighboring genes, thus indicating a potential cis-regulatory role of Malat1 gene transcription. a potential cis-regulatory role of Malat1 gene transcription.	22840402
EL0857	MAR	N/A	RT-PCR	flower and leaf development	up-regulated	N/A	MAR(multiple-function-associated mlncRNA) could be involved in multiple complex networks in P.ginseng. The transcripts of MAR could be detected in all tissues analyzed at various levels with the highest in flowers, followed by leaves. It indicates the importance of MAR in flower and leaf development under normal growth conditions.	25040236	PLNlncRbase
EL0858	Maternal somatic nucleus RNAs	N/A	N/A	N/A	N/A	expression	The degree of excision inhibition correlates with the copy number of the maternal internal eliminated sequences (iess), but each ies shows a characteristic inhibition efficiency.	9819394
EL0860	Mdrl	N/A	knockdown	N/A	N/A	interaction	MDRL affects the processing of miR-484 primary transcript in nucleus and regulates the mitochondrial network by targeting miR-361 and miR-484. MDRL inhibits mitochondrial fission and apoptosis by downregulating miR-361, which in turn relieves inhibition of miR-484 processing by miR-361.	25057983
EL0861	MEG3	N/A	RT-qPCR	macrophages	N/A	interaction	Knockdown of MEG3 in macrophages resulted in induction of autophagy and enhanced eradication of intracellular M. bovis BCG.	26757825
EL0861	MEG3	N/A	The luciferase reporter assay and RIP assay	EPCs of subjects with MetS	up-regulated	N/A	Pioglitazone up-regulated MEG3 expression to protect EPCs via decreasing miR-140-5p expression and increasing HDAC7 expression in MetS	26898430
EL0862	Meg3	N/A	compared between freshly-isolated and cultured dental mesenchymal cells	mouse dental mesenchymal cells	down-regulated in dental mesenchymal cells; up-regulated in odontogenic dental mesenchymal tissue	N/A	loss of odontogenic potential	26986487
EL0862	Meg3	N/A	Northern blot hybridizations	N/A	N/A	expression	None of the atg codons of these orfs is in the context of a strong kozak consensus sequence for initiation of translation, suggesting that gtl2 might function as an rna. primary gtl2 transcripts are differently processed in various cell types during development.	9626496
EL0863	MEG8	N/A	N/A	rat brain	N/A	expression	Despite the finding that bsr rna appears to be conserved only among the rattus species, the specific expression pattern of bsr rna suggests that it might have some role in the rat cns.	10095072
EL0863	MEG8	N/A	N/A	N/A	N/A	locus	This host gene, which encodes a previously reported noncoding rna, bsr, spans tandemly repeated 0.9-kilobase units including the snorna-containing intron.	11346658
EL0865	MHM	N/A	expression analysis and retroviral-mediated mis-expression,Northern blot,Whole mount in situ hybridization	chicken embryo	N/A	N/A	MHM has a role in chicken normal embryonic development, including gonadal sex differentiation.	22546690
EL0866	MHM-lncRNA	N/A	N/A	N/A	N/A	expression	The mhm region is transcribed only in the female from the particular strand into heterogeneous, high molecular-mass, non-coding rna, which is accumulated at the site of transcription, adjacent to the dmrt1 locus, in the nucleus.	11321370
EL0869	MIAT	N/A	knockdown,cross-link RNA precipitation analysis	neuroblastoma cell line Neuro2A	down-regulated	interaction	Gomafu indirectly modulates the function of the splicing factors SF1 and Celf3 by sequestering these proteins into separate nuclear bodies.	25145264
EL0869	MIAT	N/A	RT-PCR, knockdown	cataractous lens epithelial cells, plasma fraction of whole blood and aqueous humor of cataract patients	up-regulated	interaction	MIAT knockdown could affect the proliferation, apoptosis and migration of Human lens epithelial cells (HLECs) upon oxidative stress. MIAT knockdown could repress tumour necrosis factor-α-induced abnormal proliferation and migration of HLECs, suggesting a potential role of MIAT in PCO-related pathological process. MIAT acted as a ceRNA, and formed a feedback loop with Akt and miR-150-5p to regulate HLEC function.	26818536
EL0869	MIAT	N/A	TaqMan gene expression assays, QPCR	human TK6 (p53 positive) and WTK1 (p53 negative) cells	up-regulated	expression	The MIAT and PIWIL1 were upregulated in WTK1 cells.	23698766
EL0870	Miat	N/A	combined full-length mESC transcriptome genomic mapping data with chromatin immunoprecipitation genomic location maps of the key mESC transcription factors	mouse embryonic stem cells (mESCs)	N/A	Interaction	potential roles in pluripotency	20026622
EL0870	Miat	N/A	IRES-GFP fusion approach	mouse retinal cell	up-regulated	regulation	regulating mammalian retinal cell fate specification	20459797
EL0871	MIAT	N/A	Northern blot analysis and RNase H treatment, In situ hybridization, Immunoprecipitation and RT-PCR	E5 embryonic chicken brain	N/A	N/A	The tandem UACUAAC Gomafu RNA repeats bind to the SF1 splicing factor with a higher affinity than the divergent branch point sequence in mammals, which affects the kinetics of the splicing reaction in vitro.	21463453
EL0875	Mir124a-1hg	N/A	SAGE, in situ hybridization	developing retina	N/A	expression	Multiple transcripts that were evolutionarily conserved that did not appear to encode open reading frames of more than 100 amino acids in length ("noncoding rnas") were found to be dynamically and specifically expressed in developing and mature retinal cell types.	15226823
EL0880	MIR31HG	N/A	N/A	and in human Duchenne muscular dystrophy (DMD) myoblasts	up-regulated	N/A	controlling the differentiation commitment of precursor myoblasts	25512605
EL0886	mlncR1	N/A	qRT-PCR	leaves	up-regulated	N/A	mlncR1 is abundant in leaves. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type A mlncRNAs, including mlncR1, mlncR2 and mlncR15, showed less than 2-fold changes between any two time-points. These mlncRNAs appears to be not responsive to cold.	22233149	PLNlncRbase
EL0887	mlncR1	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment. mlncR1 and mlncR4 at the time-point of 36-h treatment; mlncR5, mlncR10, mlncR11 and mlncR13 at the time-points of 24- and 36-h treatments; mlncR6 at the time-points of 12-, 36- and 48-h treatments; and mlncR2 at all four points of time. It suggests that the majority of mlncRNAs were down-regulated after MeJA treatment.	25601000	PLNlncRbase
EL0888	mlncR10	N/A	qRT-PCR	leaves	up-regulated	N/A	mlncR10 is abundant in leaves, response to cold stress. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment. The highest level was reached, for most type C mlncRNAs, At 1 h after stress, or in a few cases, at 5 (mlncR30) or 10 hours (mlncR10).	22233149	PLNlncRbase
EL0889	mlncR10	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment. mlncR1 and mlncR4 at the time-point of 36-h treatment; mlncR5, mlncR10, mlncR11 and mlncR13 at the time-points of 24- and 36-h treatments; mlncR6 at the time-points of 12-, 36- and 48-h treatments; and mlncR2 at all four points of time. It suggests that the majority of mlncRNAs were down-regulated after MeJA treatment.	25601000	PLNlncRbase
EL0890	mlncR11	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment. mlncR1 and mlncR4 at the time-point of 36-h treatment; mlncR5, mlncR10, mlncR11 and mlncR13 at the time-points of 24- and 36-h treatments; mlncR6 at the time-points of 12-, 36- and 48-h treatments; and mlncR2 at all four points of time. It suggests that the majority of mlncRNAs were down-regulated after MeJA treatment.	25601000	PLNlncRbase
EL0891	mlncR12	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0892	mlncR13	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0893	mlncR13	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment. mlncR1 and mlncR4 at the time-point of 36-h treatment; mlncR5, mlncR10, mlncR11 and mlncR13 at the time-points of 24- and 36-h treatments; mlncR6 at the time-points of 12-, 36- and 48-h treatments; and mlncR2 at all four points of time. It suggests that the majority of mlncRNAs were down-regulated after MeJA treatment.	25601000	PLNlncRbase
EL0894	mlncR14	N/A	qRT-PCR	leaves and roots	up-regulated	N/A	Higher in leaves and roots than stems and flowers. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0895	mlncR14	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment.	25601000	PLNlncRbase
EL0896	mlncR15	N/A	qRT-PCR	leaves and stems	up-regulated	N/A	mlncR15 exhibit high expression in leaves and stems compared with that in flowers and roots. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type A mlncRNAs, including mlncR1, mlncR2 and mlncR15, showed less than 2-fold changes between any two time-points. These mlncRNAs appears to be not responsive to cold.	22233149	PLNlncRbase
EL0897	mlncR15	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	This lncRNA is response to MeJA treatment in S. miltiorrhiza. (to see Fig 7 for details).	25601000	PLNlncRbase
EL0898	mlncR16	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0899	mlncR16	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment.	25601000	PLNlncRbase
EL0900	mlncR17	N/A	qRT-PCR	roots	up-regulated	N/A	mlncR17 is expressed mainly in roots. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type B, such as mlncR17 and mlncR21, exhibited an immediate decrease after treatment for 1 hour. The decrease continued for at least 10 hours and then some of them, such as mlncR21, showed a trend of recovering to the level in untreated tissues.	22233149	PLNlncRbase
EL0901	mlncR17	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment.	25601000	PLNlncRbase
EL0902	mlncR18	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0903	mlncR18	N/A	qRT-PCR	methyl jasmonate	down-regulated/up-regulated	N/A	Interestingly, the expression of mlncR18 fluctuated from time-point to time-point. It was significantly down-regulated at the time-point of 24-h treatment, while up-regulated at the time-point of 36-h treatment. These results suggest the significance of mlncRNAs in response to MeJA treatment in S. miltiorrhiza.	25601000	PLNlncRbase
EL0904	mlncR19	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0905	mlncR2	N/A	qRT-PCR	leaves and roots	up-regulated	N/A	Higher in leaves and roots than stems and flowers. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type A mlncRNAs, including mlncR1, mlncR2 and mlncR15, showed less than 2-fold changes between any two time-points. These mlncRNAs appears to be not responsive to cold.	22233149	PLNlncRbase
EL0906	mlncR2	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment. mlncR1 and mlncR4 at the time-point of 36-h treatment; mlncR5, mlncR10, mlncR11 and mlncR13 at the time-points of 24- and 36-h treatments; mlncR6 at the time-points of 12-, 36- and 48-h treatments; and mlncR2 at all four points of time. It suggests that the majority of mlncRNAs were down-regulated after MeJA treatment.	25601000	PLNlncRbase
EL0907	mlncR20	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0908	mlncR21	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type B, such as mlncR17 and mlncR21, exhibited an immediate decrease after treatment for 1 hour. The decrease continued for at least 10 hours and then some of them, such as mlncR21, showed a trend of recovering to the level in untreated tissues.	22233149	PLNlncRbase
EL0909	mlncR22	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to dehydration stress, mlncRNAs can also be roughly classified into 3 groups (Figure 9). The level of group I mlncRNAs, such as mlncR22, kept constant within the first 10 hours of dehydration stress and then increased at 24 hours, showing a relatively slow response. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0910	mlncR23	N/A	qRT-PCR	roots	up-regulated	N/A	mlncR23 is abundant in leaves. Based on the expression patterns in response to dehydration stress, mlncRNAs can also be roughly classified into 3 groups (Figure 9). Group III consists of 6 mlncRNAs, including mlncR6, mlncR8, mlncR23, mlncR24, mlncR28 and mlncR30. Expression of mlncRNAs in this group was induced at 1 hour of stress and then immediately downregulated to far below the level in untreated tissues. It is similar to the pattern of type C mlncRNAs in response to cold stress. mlncR23 showed much quicker responses to dehydration stress. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0911	mlncR24	N/A	qRT-PCR	leaves	up-regulated	N/A	mlncR24 is expressed mainly in roots. Based on the expression patterns in response to dehydration stress, mlncRNAs can also be roughly classified into 3 groups (Figure 9). Group III consists of 6 mlncRNAs, including mlncR6, mlncR8, mlncR23, mlncR24, mlncR28 and mlncR30. Expression of mlncRNAs in this group was induced at 1 hour of stress and then immediately downregulated to far below the level in untreated tissues. It is similar to the pattern of type C mlncRNAs in response to cold stress. mlncR24 showed much quicker responses to dehydration stress. mlncR24 was induced at 1 hour of stress and then immediately down regulated to far below the level in untreated tissues. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0912	mlncR25	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0913	mlncR26	N/A	qRT-PCR	leaves and roots	up-regulated	N/A	Higher in leaves and roots than stems and flowers. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0914	mlncR27	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0915	mlncR28	N/A	qRT-PCR	leaves and stems	up-regulated	N/A	mlncR28 exhibit high expression in leaves and stems compared with that in flowers and roots. Based on the expression patterns in response to dehydration stress, mlncRNAs can also be roughly classified into 3 groups (Figure 9). Group III consists of 6 mlncRNAs, including mlncR6, mlncR8, mlncR23, mlncR24, mlncR28 and mlncR30. Expression of mlncRNAs in this group was induced at 1 hour of stress and then immediately downregulated to far below the level in untreated tissues. It is similar to the pattern of type C mlncRNAs in response to cold stress. mlncR28 showed much quicker responses to dehydration stress. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0916	mlncR29	N/A	qRT-PCR	leaves	up-regulated	N/A	mlncR29 is abundant in leaves, mlncR29 showed response to cold stress. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0917	mlncR3	N/A	qRT-PCR	leaves and roots	up-regulated	N/A	Higher in leaves and roots than stems and flowers. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0918	mlncR3	N/A	qRT-PCR	methyl jasmonate	up-regulated	N/A	This lncRNA is response to MeJA treatment in S. miltiorrhiza.(to see Fig 7 for details).	25601000	PLNlncRbase
EL0919	mlncR30	N/A	qRT-PCR	leaves	up-regulated	N/A	mlncR30 is abundant in leaves. Based on the expression patterns in response to dehydration stress, mlncRNAs can also be roughly classified into 3 groups (Figure 9). Group III consists of 6 mlncRNAs, including mlncR6, mlncR8, mlncR23, mlncR24, mlncR28 and mlncR30. Expression of mlncRNAs in this group was induced at 1 hour of stress and then immediately downregulated to far below the level in untreated tissues. It is similar to the pattern of type C mlncRNAs in response to cold stress. mlncR30 showed much quicker responses to dehydration stress. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment. The highest level was reached, for most type C mlncRNAs, At 1 h after stress, or in a few cases, at 5 (mlncR30). After reaching to a maximum, the mlncRNA levels quickly declined to near, or in most cases, far below the levels in untreated tissues. mlncR30 was induced at 1 hour of stress and then immediately down regulated to far below the level in untreated tissues.	22233149	PLNlncRbase
EL0920	mlncR31	N/A	qRT-PCR	roots	down-regulated	N/A	mlncR31, seems to play a role in post-transcriptional regulation of the corresponding protein-coding genes. It is evidenced by the negative correlation of expression between mlncR31 and the SPS gene after 5 hours of stress.	22233149	PLNlncRbase
EL0921	mlncR4	N/A	qRT-PCR	leaves	up-regulated	N/A	mlncR4 is abundant in leaves, mlncR4 showed response to cold stress. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0922	mlncR4	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment. mlncR1 and mlncR4 at the time-point of 36-h treatment; mlncR5, mlncR10, mlncR11 and mlncR13 at the time-points of 24- and 36-h treatments; mlncR6 at the time-points of 12-, 36- and 48-h treatments; and mlncR2 at all four points of time. It suggests that the majority of mlncRNAs were down-regulated after MeJA treatment.	25601000	PLNlncRbase
EL0923	mlncR5	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0924	mlncR5	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment. mlncR1 and mlncR4 at the time-point of 36-h treatment; mlncR5, mlncR10, mlncR11 and mlncR13 at the time-points of 24- and 36-h treatments; mlncR6 at the time-points of 12-, 36- and 48-h treatments; and mlncR2 at all four points of time. It suggests that the majority of mlncRNAs were down-regulated after MeJA treatment.	25601000	PLNlncRbase
EL0925	mlncR6	N/A	qRT-PCR	cold	up-regulated	N/A	Based on the expression patterns in response to dehydration stress, mlncRNAs can also be roughly classified into 3 groups (Figure 9). Group III consists of 6 mlncRNAs, including mlncR6, mlncR8, mlncR23, mlncR24, mlncR28 and mlncR30. Expression of mlncRNAs in this group was induced at 1 hour of stress and then immediately downregulated to far below the level in untreated tissues. It is similar to the pattern of type C mlncRNAs in response to cold stress. mlncR6 showed much quicker responses to dehydration stress. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0926	mlncR6	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment. mlncR1 and mlncR4 at the time-point of 36-h treatment; mlncR5, mlncR10, mlncR11 and mlncR13 at the time-points of 24- and 36-h treatments; mlncR6 at the time-points of 12-, 36- and 48-h treatments; and mlncR2 at all four points of time. It suggests that the majority of mlncRNAs were down-regulated after MeJA treatment.	25601000	PLNlncRbase
EL0927	mlncR7	N/A	qRT-PCR	leaves, roots and seeds	up-regulated	N/A	mlncR7, an mlncRNA detected in leaves, stems and flowers of one-year old mature plants, and mlncR11, which was also undetected in the analyzed tissues of mature plants (Figure 7, 8 and 9). D.purpurea mlncR7 exhibited opposite expression patterns with mlncR8, which expressed in plantlets but not in the analyzed tissues of one-year-old plants. It suggests that the expression of both mlncR7 and mlncR8 is developmentally regulated, while their biological functions are distinct.	22233149	PLNlncRbase
EL0928	mlncR7	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment.	25601000	PLNlncRbase
EL0929	mlncR8	N/A	qRT-PCR	leaves	up-regulated	N/A	D.purpurea mlncR7 exhibited opposite expression patterns with mlncR8, which expressed in plantlets but not in the analyzed tissues of one-year-old plants. It suggests that the expression of both mlncR7 and mlncR8 is developmentally regulated, while their biological functions are distinct. Based on the expression patterns in response to dehydration stress, mlncRNAs can also be roughly classified into 3 groups (Figure 9). Group III consists of 6 mlncRNAs, including mlncR6, mlncR8, mlncR23, mlncR24, mlncR28 and mlncR30. Expression of mlncRNAs in this group was induced at 1 hour of stress and then immediately downregulated to far below the level in untreated tissues. It is similar to the pattern of type C mlncRNAs in response to cold stress. mlncR8 showed much quicker responses to dehydration stress. Based on the expression patterns in response to cold stress, mlncRNAs can be roughly categorized into three major types. Type C mlncRNAs,including mlncR3, mlncR4, mlncR5, mlncR6, mlncR8, mlncR10, mlncR12, mlncR13, mlncR14, mlncR16, mlncR18, mlncR19, mlncR20, mlncR22, mlncR23, mlncR24, mlncR25, mlncR26, mlncR27, mlncR28, mlncR29, mlncR30, accounting for more than 80% or 22 of the total 27 mlncRNAs, showed a rapid increase after treatment.	22233149	PLNlncRbase
EL0930	mlncR8	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment.	25601000	PLNlncRbase
EL0931	mlncR9	N/A	qRT-PCR	methyl jasmonate	down-regulated	N/A	MeJA(methyl jasmonate) is a significant regulator in plant response to biotic and abiotic stresses. These 15 mlncRNAs are considered as MeJA-responsive mlncRNAs, of which 12 were significantly down-regulated at different time-points of treatment, such as mlncR7,mlncR8, mlncR9, mlncR14, mlncR16 and mlncR17 at the time-point of 24-h treatment.	25601000	PLNlncRbase
EL0935	MsENOD40-1	N/A	Southern blot	Nodule formation	down-regulated	N/A	ENOD40, an early nodulin gene, is expressed following inoculation with Rhizobium meliloti or by adding R.meliloti-produced nodulation (Nod) factors or the plant hormone cytokinin to uninoculated roots. We isolated two MsENOD40 clones, designated MsENOD40–1 and MsENOD40–2, with distinct promoters from an alfalfa (Medicago sativa cv Chief) genomic library. The promoters were fused to the reporter gene uidA (gus), and the constructs were introduced into alfalfa. We observed that the MsENOD40–1 construct was expressed almost exclusively under symbiotic conditions. Under nonsymbiotic conditions MsENOD40–1 was usually not expressed in the uninoculated root of the transgenic alfalfa plants, but was activated when lateral roots or nodule primordia are initiated. The expression of MsENOD40–1 as well as MsENOD40–2 was induced by BAP or Nod factor treatment, and the extent of induction is similar for both genes (2- to 3-fold), although the basal level of MsENOD40–2 expression is generally higher (Fig. 6). In addition, both genes were also expressed in a similar pattern in roots following treatment with cytokinin or Nod factor for 4d (see Fig. 3, G–Q).	9449836	PLNlncRbase
EL0936	MsENOD40-2	N/A	Southern blot	Nodule formation	down-regulated	N/A	ENOD40, an early nodulin gene, is expressed following inoculation with Rhizobium meliloti or by adding R.meliloti-produced nodulation (Nod) factors or the plant hormone cytokinin to uninoculated roots. We isolated two MsENOD40 clones, designated MsENOD40–1 and MsENOD40–2, with distinct promoters from an alfalfa (Medicago sativa cv Chief) genomic library. The promoters were fused to the reporter gene uidA (gus), and the constructs were introduced into alfalfa. We observed that the MsENOD40–1 construct was expressed almost exclusively under symbiotic conditions. The MsENOD40–2 construct was transcribed under both symbiotic and nonsymbiotic conditions and in nonnodular and nodular tissues. In contrast, the expression of MsENOD40–2 is likely to be constitutive, because the promoter construct was expressed in the vascular tissues of the root and the stem even in the absence of R. meliloti (see Fig. 3). In addition, the expression of the MsENOD40–2 promoter construct was also detected at the root tip and throughout lateral root development (Fig. 3). Moreover, MsENOD40–2 was expressed in the root tip, including the root cap in some transgenic plants. The expression of MsENOD40–1 as well as MsENOD40–2 was induced by BAP or Nod factor treatment, and the extent of induction is similar for both genes (2- to 3-fold), although the basal level of MsENOD40–2 expression is generally higher (Fig. 6). In addition, both genes were also expressed in a similar pattern in roots following treatment with cytokinin or Nod factor for 4d (see Fig. 3, G–Q).	9449836	PLNlncRbase
EL0939	Msx1os	N/A	In situ analysis	differentiated dental and bone cells, odontoblastic cell line (MO6-G3)	N/A	N/A	The ratio between msx1 sense and antisense rnas is a very important factor in the control of skeletal terminal differentiation.	11390985
EL0939	Msx1os	N/A	N/A	N/A	N/A	expression	The msx1 as rna involvement during tooth development and evidences a new degree of complexity in craniofacial developmental biology: the implication of endogenous as rnas.	16157866
EL0939	Msx1os	N/A	RT-PCR, Northern-blotting, In situ hybridization	dental and bone cells	N/A	interaction	The balance between antisense and sense msx1 mrnas appeared to control msx1 protein levels.	12489151
EL0941	MT1JP	N/A	applied to 76 pairs of matched normal and cancer tissue samples	tumor tissues	up-regulated	N/A	critical factor in restraining cell transformation by modulating p53 translation	26909858
EL0942	Mt4	N/A	Northern blot/qRT-PCR	roots	up-regulated	N/A	This lncRNAs work as a decoy of miRNAs,and exert their functions by binding miRNAs in a target mimicry mechanism to sequestrate the miRNAs’ regulation roles on their target genes, such as lncRNAs IPS1 and at4.	23726911	PLNlncRbase
EL0943	Mt4	N/A	Northern blot/Southern blot	roots	down-regulated	N/A	Mt4 gene expression is regulated in response to colonization by mycorrhizal fungi: transcripts were detected in non-colonized roots and levels decreased in M.sativa(alfalfa) roots after colonization by G.versiforme. Transcript levels also decreased during the incomplete interaction between G.versiforme and a M.sativa mycorrhizal minus (myc-) line, indicating that the down-regulation of this gene occurs early during the interaction between the fungus and its host plant. Phosphate levels in the nutrient media also affected the expression of the Mt4 gene: transcripts were present in the roots of plants grown under phosphate-deficient conditions, but were undetectable in the roots of plants grown under phosphate sufficient conditions. Northern blot analyses indicate that Mt4 transcripts are present primarily in roots and barely detectable in stems or leaves.	9207836	PLNlncRbase
EL0944	Mt4	N/A	RT-PCR	roots	up-regulated	N/A	Mt4 is a cDNA representing a phosphate-starvation-inducible gene from Medicago truncatula that is down-regulated in roots in response to inorganic phosphate (Pi) fertilization and colonization by arbuscular mycorrhizal fungi. The expression of the Mt4 gene in M.truncatula roots is down-regulated systemically by both Pi fertilization and colonization by arbuscular mycorrhizal fungi. Analysis of the expression of the Mt4-like Arabidopsis gene, At4, in wild-type Arabidopsis and pho1, a mutant unable to load Pi into the xylem, suggests that Pi must first be translocated to the shoot for down-regulation to occur. The data from the pho1 and split-root studies are consistent with the presence of a translocatable shoot factor responsible for mediating the systemic downregulation of Mt4-like genes in roots. (Burleigh et al., 1999) Mt4, a phosphate starvation inducible cDNA from Medicago truncatula which is down-regulated in roots in response to phosphate fertilization as well as colonization by arbuscular mycorrhizal (AM) fungi. Expression was highly sensitive to exogenous applications of phosphate fertilizer; transcripts were abundant in roots fertilized with nutrient solution lacking phosphate. Mt4 is the first cDNA reported to show independent regulation by both phosphate and mycorrhizal fungi. Mt4 gene expression exhibited an inverse, exponential correlation with soluble phosphorus levels in the leaves. The Mt4 gene from M.truncatulais the first plant gene identified whose expression is down-regulated by both phosphate starvation and mycorrhizal colonization and as such may provide the means to elucidate the signal transduction pathways involved in these two processes. The phosphate fertilization experiment indicated that Mt4 gene expression in roots was maximal under conditions of P-starvation and dramatically reduced by relatively low levels of phosphate fertilization. The response of Mt4 expression to P-starvation was similar to that of MtPT2, a P-starvation inducible phosphate transporter from M.truncatula. (Burleigh et al., 1998) A cDNA clone (Mt4) was isolated as a result of a differential screen to identify genes showing altered expression during the interaction between Medicago truncatula and the vesicular-arbuscular mycorrhizal (VAM) fungus Glomus versiforme. Mt4 represents a M.truncatula mRNA that contains numerous short open reading frames, the two longest of which are predicted to encode polypeptides of 51 amino acids each. One of these open reading frames shares a short region of identity with a phosphate starvation-inducible gene from tomato. Mt4 gene expression is regulated in response to colonization by mycorrhizal fungi: transcripts were detected in non-colonized roots and levels decreased in both M.truncatula and M.sativa(alfalfa) roots after colonization by G.versiforme. Northern blot analyses indicate that Mt4 transcripts are present primarily in roots and barely detectable in stems or leaves, Thus, Mt4 represents a M.truncatula gene whose expression is regulated in response to both colonization by mycorrhizal fungi and to the phosphate status of the plant. (Burleigh et al., 1997)	9880366, 9207836	PLNlncRbase
EL0945	MtENOD40-1	N/A	RT-PCR	Nodule formation	down-regulated	N/A	In M.truncatula, knock-down of MtENOD40-1 expression led to a 50% reduction in the number of nodules. To reduce MtENOD40-1 and MtENOD40-2 gene expression, Agrobacterium rhizogenes-mediated RNAi was applied in M.truncatula hairy roots. To this end, one vector (pRRsil401) was designed that is expected to lead to a reduction in expression of MtENOD40-1, and a second vector (pRRsil402) that is expected to lead to a reduction in MtENOD40-2 expression. To knock-down transcription of both genes simultaneously, a third vector (pRRsil4012) was used. MtENOD40-1 as well as MtENOD40-2 is involved in nodule initiation. On roots,in which the expression of both MtENOD40-1 and MtENOD40-2 is reduced, the average number of nodules per root is 1.5 (75% reduction). Thus knocking down of the expression of both genes has an additive effect, suggesting that MtENOD40 acts in a dose-dependent manner.	17452749	PLNlncRbase
EL0946	MtENOD40-2	N/A	RT-PCR	Nodule formation	down-regulated	N/A	In sections of roots collected 2d post-inoculation, GUS activity was present in dividing cortical cells, indicating that MtENOD40-2 is expressed in cells of the nodule primordium (Fig. 2C). Whole-mount staining for GUS activity of nodules showed that GUS activity is detected near the apex of the nodule and in vascular bundles (Fig. 2D). To localize the site of expression of MtENOD40-2 precisely in the nodule, in situ hybridization using [35S]UTP-labelled antisense MtENOD40-2 RNA was conducted (Fig. 2A, B). This showed that MtENOD40-2 is expressed in cells of the infection zone (Fig. 2B, IZ). Thus, the MtENOD40-2 expression pattern is similar to the MtENOD40-1 expression pattern (Crespi et al., 1994). Furthermore, the GUS expression studies are consistent with the in situ hybridization data, indicating that the 1.8 kb DNA fragment used contains the elements required for the regulation of MtENOD40-2 expression. Based on the combination of expression data and the sequence homology between both genes, it is likely that MtENOD40-2 is functional in nodule initiation and development.	17452749	PLNlncRbase
EL0949	Munc	N/A	knockdown	murine muscle	N/A	N/A	a promyogenic lncRNA that acts directly or indirectly on multiple promoters to increase myogenic gene expression	25403490
EL0953	Myh8	N/A	Northern blot, RT-PCR	neonatal rat heart	N/A	expression	In the neonatal heart naturally occurring antisense mrna may play a role in the regulation of mhc expression and, therefore, in the control of the energetical and contractile behaviour of the heart.	9632112
EL0971	Nctc1	N/A	ChIP, qRT-PCR	Myoblasts	N/A	N/A	Nctc1 is co-regulated with Igf2 and H19 and physically interacts with the shared muscle enhancer. In fact, all three co-regulated genes have the potential to interact not only with the shared enhancer but also with each other via their enhancer interactions	23221643
EL0971	Nctc1	N/A	N/A	N/A	N/A	expression	enhancer function requires transcription in cis of a long non-coding RNA, Nctc1.	23842673
EL0972	NDM29	N/A	RNA-seq, qRT-PCR	three different brain regions (cortex, white matter, and cerebellum) of human postmortem tissue	N/A	N/A	Thus, these 5 lncRNAs may be applicable as references for accurate normalisation of lncRNA profiling in multiple brain regions during long PMI, enabling the generation of highly reproducible datasets in lncRNA studies of the human brain.	25528156
EL0973	NEAT1	N/A	EM observation	mammalian cells	N/A	Interaction	Paraspeckle formation is initiated by transcription of the NEAT1 chromosomal locus and proceeds in conjunction with NEAT1 lncRNA biogenesis and a subsequent assembly step involving >40 paraspeckle proteins (PSPs).	25831520
EL0973	NEAT1	N/A	knockdown	HeLa epithelial adenocarcinoma,WI-38 normal female diploid fibroblast lung,Human EBV-transformed human lymphoblasts,primary mouse embryo fibroblasts	N/A	mutation	Depletion of NEAT1 RNA via RNAi eradicates paraspeckles, suggesting that it controls sequestration of the paraspeckle proteins PSP1 and p54, factors linked to A-I editing. Unlike overexpression of PSP1, NEAT1 overexpression increases paraspeckle number, and paraspeckles emanate exclusively from the NEAT1 transcription site	19217333
EL0973	NEAT1	N/A	N/A	Human cell	N/A	N/A	paraspeckle formation	20211624
EL0973	NEAT1	N/A	N/A	N/A	N/A	expression	Biogenesis, metabolism, and functions of lncRNAs are otherwise interconnected with known pathogenic mechanisms	23791884	LncRNADisease
EL0974	Neat1	N/A	expression patterns of two long noncoding RNAs; an animal model lacking NEAT1	adult mouse tissues	N/A	N/A	architectural integrity of nuclear bodies	21444682
EL0974	Neat1	N/A	expression patterns of two long noncoding RNAs;an animal model lacking NEAT1	adult mouse tissues	N/A	N/A	architectural integrity of nuclear bodies	21444682
EL0974	Neat1	N/A	N/A	mouse Neuro-2a cell line	N/A	N/A	the least stable lncRNAs is the well-characterized paraspeckle RNA Neat1, Neat1's instability contributes to the dynamic nature of this subnuclear domain.	22406755
EL0974	Neat1	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Neat1 has also been reported to interact with a number of chromatin binding protein/complexes in mouse embryonic stem cells including PRC1, PRC2, JARID1B, ESET and SUV39H1, with the general pattern being interaction with repressors of gene expression	21874018
EL0974	Neat1	N/A	RT-PCR, siRNA, RIP	3T3-L1 cells induced to differentiate by a media cocktail of insulin, dexamethasone, and isobutylmethyxanthine (IBMX)	down-regulated	expression	Levels of NEAT1 transcript, measured by RT-PCR, fluctuated in a temporal manner over the course of differentiation that suggested its role in alternative splicing of PPARγ mRNA, the major transcription factor driving adipogenesis.	25437750
EL0976	Nfkb2	N/A	microarray, qRT-PCR	bone marrow-derived macrophages (BMDMs)	N/A	expression	Many identified LPS-regulated lncRNAs, such as lncRNA-Nfkb2 and lncRNA-Rel, locate near to immune response protein-coding genes.	25652569
EL0985	NORAD	N/A	N/A	previously karyotypically stable cell lines	N/A	interaction	Inactivation of NORAD triggers dramatic aneuploidy in previously karyotypically stable cell lines.	26724866
EL0990	npc15	N/A	microarray/qRT-PCR	leaves	N/A	N/A	Differential expression of TAS3, npc43, and npc311 in roots and of npc15 and npc156 in leaves was confirmed, as we previously reported using semiquantitative RT-PCR. As the expression of several npcRNAs was affected by environmental stress, we explored the response to salt stress and phosphate starvation in lines overexpressing npc43, npc60, npc311, and npc536.	18997003	PLNlncRbase
EL0991	npc156	N/A	Microarray/qRT-PCR	leaves	up-regulated	N/A	Differential expression of TAS3, npc43, and npc311 in roots and of npc15 and npc156 in leaves was confirmed, as we previously reported using semiquantitative RT-PCR. As the expression of several npcRNAs was affected by environmental stress, we explored the response to salt stress and phosphate starvation in lines overexpressing npc43, npc60, npc311, and npc536.	18997003	PLNlncRbase
EL0992	npc311	N/A	Microarray/qRT-PCR	roots	down-regulated	N/A	Differential expression of TAS3, npc43, and npc311 in roots and of npc15 and npc156 in leaves was confirmed, as we previously reported using semiquantitative RT-PCR. As the expression of several npcRNAs was affected by environmental stress, we explored the response to salt stress and phosphate starvation in lines overexpressing npc43, npc60, npc311, and npc536.	18997003	PLNlncRbase
EL0993	npc33	N/A	RT-PCR	phosphate starvation	down-regulated	N/A	For the phosphate starvation assays, the up-regulation of npc43 and npc536 and the down-regulation of npc33 were confirmed (Fig. 5A).	18997003	PLNlncRbase
EL0994	npc34	N/A	RT-PCR	roots	up-regulated	N/A	Expression levels of npcRNAs 34 and 60 increased severalfold in phosphate-starved and in 6-benzylaminopurine (BA)-treated roots.	16500993	PLNlncRbase
EL0995	npc351	N/A	RT-PCR	stems	up-regulated	N/A	The majority of siRNAs deriving from this npcRNAs are 24 nt long and map to both DNA strands of the npcRNA region, suggesting that these npcRNAs correspond to 24-nt-small RNA precursors. Expression analysis in different organs revealed that npc351 is enriched in stems. Whereas the npc375 and npc523 levels appeared unchanged in the rdr2 rdr6 double mutant, the npc34 and npc351 were up-regulated in both seedlings and flowers of rdr2 rdr6 (Fig. 1, right panel), suggesting that RDR2 or RDR6 produces a dsRNA from these npcRNAs, consistent with small RNA production from both DNA strands of these loci.	18997003	PLNlncRbase
EL0996	npc375	N/A	RT-PCR	flowers	up-regulated	N/A	The majority of siRNAs deriving from these five npcRNAs are 24 nt long and map to both DNA strands of the npcRNA region, suggesting that these npcRNAs correspond to 24-nt-small RNA precursors. Expression analysis in different organs (Fig. 1) revealed that npc351 is enriched in stems and npc34 in aerial parts, whereas npc375 and npc523 show maximal levels in flowers.	18997003	PLNlncRbase
EL0997	npc43	N/A	Northern blot/RT-PCR	phosphate starvation	up-regulated	N/A	For the phosphate starvation assays, the up-regulation of npc43 and npc536 and the down-regulation of npc33 were confirmed (Fig. 5A).	18997003	PLNlncRbase
EL0998	npc48	N/A	qRT-PCR	leaf serration and flowering time	up-regulated	N/A	Overexpressing the npc48 showed drastic developmental anomalies, including an increase in the rosette diameter, leaf serration, and a delay in the flowering time compared with wild-type plants (Fig. 6A). Overexpression of npc48 led to leaf serration, a phenotype that has been observed in several Arabidopsis mutants such as se or ago1. Quantitative RT-PCR analysis of npc48 accumulation revealed that all transgenic lines exhibiting this phenotype overaccumulated npc48 (Supplemental Fig. 3).	18997003	PLNlncRbase
EL0999	npc523	N/A	RT-PCR	flowers	up-regulated	N/A	The majority of siRNAs deriving from these five npcRNAs are 24 nt long and map to both DNA strands of the npcRNA region, suggesting that these npcRNAs correspond to 24-nt-small RNA precursors. Expression analysis in different organs (Fig. 1) revealed that npc351 is enriched in stems and npc34 in aerial parts, whereas npc375 and npc523 show maximal levels in flowers. Specific oligonucleotides for real-time PCR studies could not be obtained for npc520. Whereas the npc375 and npc523 levels appeared unchanged in the rdr2 rdr6 double mutant.	18997003	PLNlncRbase
EL1000	npc531	N/A	qRT-PCR	dcl1-9 mutant	up-regulated	N/A	In addition to npcRNAs corresponding to conserved miRNAs, the npc531, which was not previously linked to RNA silencing mechanisms or known to encode a miRNA, also was upregulated in a dcl1-9 mutant, a difference confirmed using quantitative RT-PCR (Fig. 4A, left panel). No known miRNAs map to this gene, suggesting that, alternatively, it could be the target of a miRNA. We identified a putative miR319 target site in npc531 (Fig. 4A, right panel), but 5 RACE-PCR analyses did not reveal any specific cleavage of this transcript in this site (data not shown).	18997003	PLNlncRbase
EL1001	npc536	N/A	RT-PCR	phosphate starvation, salt	up-regulated	N/A	npc536 was up-regulated in phosphate starvation. overaccumulate npc536 displayed heightened root growth under salt stress conditions. Transformed plants over-expressing npc536 showed heightened root growth under salt stress conditions, with increased primary root growth and secondary root length; No phenotype could be observed in mutants that carry T-DNA insertions within npc536; In response to certain abiotic stresses such as drought or cold treatment, the root expression of these two genes (AT1G67930 and npc536) tends to be anti-correlated (Pearson correlation coefficient of -0.636 and -0.983, respectively). However, accumulation of the AT1G67930 transcript was not significantly modified in plants over-expressing npc536 or in npc536 mutants. (Ben et al., 2009) npc536 has a large dynamic variation of expression across a wide range of tissue and hormonal, biotic, or abiotic treatment. npc536 exists in the antisense strand of a Golgi-transport complex related protein. 35S::npc536 transformants displayed heigh tened root growth under salt stress conditions. (Matsui et al., 2013)	18997003, 24252906	PLNlncRbase
EL1002	npc60	N/A	Northern blot/RT-PCR	salt	up-regulated	N/A	Salt stress resulted in a dramatic 100-fold increase in npc60 accumulation. For npc60, npc82, and npc536, the change in expression observed after 3h of NaCl treatment was maintained after 24h (Fig. 5B), whereas for npc72 the induction was transient. Expression levels of npcRNAs 34 and 60 increased severalfold in phosphate-starved and in 6-benzylaminopurine (BA)-treated roots(Plant Physiol.2006 Apr;140(4):1192-204.).	18997003	PLNlncRbase
EL1003	npc78	N/A	RT-PCR	dcl1 mutant	up-regulated	N/A	The npcRNA78 gene contains the miR162 sequence in an alternative intron and corresponds to the MIR162a locus. Although DICER-LIKE 1 (DCL1) mRNA is known to be regulated by miR162-guided cleavage, its level does not change in a mir162a mutant. Alternative splicing of npcRNA78 leads to several transcript isoforms, which all accumulate in a dcl1 mutant. This suggests that npcRNA78 is a genuine substrate of DCL1 and that splicing of this microRNA primary transcript and miR162 processing are competitive nuclear events.	16500993	PLNlncRbase
EL1004	npc82	N/A	Northern blot/RT-PCR	NaCl treatment	up-regulated	N/A	For npc60, npc82, and npc536,the change in expression observed after 3 h of NaCl treatment was maintained after 24 h (Fig. 5B), whereas for npc72 the induction was transient (Fig. 5B).	18997003	PLNlncRbase
EL1005	npc83	N/A	RT-PCR	N/A	N/A	N/A	Some were already characterized small RNA precursors, such as the tasiRNA precursor TAS3 (npc41) or the MIR162A precursor (npc78) (Hirsch et al. 2006). The npc83 and npc521 corresponded to the miRNA precursors MIR869A and MIR160C, respectively. Among seven known miRNA precursors spotted on the RIBOCHIP, six (MIR160C, MIR162A, MIR164B, MIR166A, MIR166B, and MIR168A) were up-regulated in dcl1 inflorescences, consistent with DCL1-processed conserved miRNAs. In contrast, the nonconserved MIR869A precursor (npc83) did not overaccumulate in dcl1. This miRNA precursor has an unusually stable secondary structure.	18997003	PLNlncRbase
EL1009	NR024118	N/A	lncRNAs array, qPCR	Ang II-treated cardiac fibroblasts	down-regulated	expression	Ang II dynamically regulated the expression of lncRNA-NR024118 and Cdkn1c in cardiac fibroblasts, indicating the potential role of NR024118 in cardiac fibroblasts.	24817929
EL1009	NR024118	N/A	N/A	dult rat cardiac fibroblasts	down-regulated	expression	Our current studies showed that the decrease of lncRNA-NR024118 and Cdkn1c induced by Ang II is mediated by AT1 receptor-dependent not AT2 receptor-dependent, which is helpful to understand the molecular mechanism of Ang II receptors in adult rat cardiac fibroblasts.	25979571
EL1010	NRAV	N/A	overexpression	human cells or transgenic mice	down-regulated	expression	A lncRNA that we call negative regulator of antiviral response (NRAV) was dramatically downregulated during infection with several viruses, we ectopically expressed NRAV in human cells or transgenic mice and found that it significantly promotes influenza A virus (IAV) replication and virulence.	25525793
EL1015	nta-eTMX27	N/A	N/A	N/A	N/A	interaction	We identified a microRNA (nta-miRX27) and also a lncRNA (nta-eTMX27) as an endogenous target mimicry (eTM) in tobacco targeting the nicotine biosynthesis key gene QPT2 encoding quinolinate phosphoribosyltransferase (QPT) and thereby regulating the nicotine content.	27172239
EL1016	NtENOD40-1	N/A	RT-PCR	nodule initiation	up-regulated	N/A	Whereas Rhizobial Nod-factor signaling sets the process of nodulation in action, the process is further regulated by the phytohormones ethylene, cytokinin and auxin. ENOD40-1 expression is induced by Nod-factors or cytokinin in legumes suggesting that these could be candidate interactors of ENOD40.	1701140	PLNlncRbase
EL1017	NUTF2P3	N/A	N/A	N/A	up-regulated	interaction	After downregulating lncRNA-NUTF2P3-001, the proliferation and invasion of pancreatic cancer cell are significantly inhibited both in vitro and vivo, accompanying with decreased KRAS expression. Data from pancreatic cancer patients show a positive correlation between lncRNA-NUTF2P3-001 and KRAS, which is associated with advanced tumor stage and worse prognosis. lncRNA-NUTF2P3-001 and miR-3923 can be applied as novel predictors and therapeutic targets for pancreatic cancer.	26755660
EL1018	ObENOD40	N/A	RT-PCR	Nodule formation	up-regulated	N/A	ENOD40 has been proposed as playing a pivotal role in the organogenesis of legume root nodules. ObENOD40, in which an XbaI fragment (approximately 640 bp) contained a sequence for encoding an oligopeptide that is highly conserved in all legume ENOD40s.	10363365	PLNlncRbase
EL1020	OIP5-AS1	N/A	N/A	human cervical carcinoma HeLa cells	N/A	interaction	OIP5-AS1 reduces cell proliferation. OIP5-AS1 serves as a sponge or a competing endogenous (ce)RNA for HuR, restricting its availability to HuR target mRNAs and thereby repressing HuR-elicited proliferative phenotypes.	26819413
EL1024	OsIPS1	N/A	qRT-PCR	roots	down-regulated	N/A	OsIPS1 is a noncoding RNA. IPS1 sequesters miR399 (microRNA 399), which negatively regulates the gene PHO2 at the post-transcriptional level.	19566645	PLNlncRbase
EL1025	osk	N/A	N/A	Drosophila	N/A	mutation	The Drosophila oskar (osk) mRNA is unusual in having both coding and noncoding functions. The 3' UTR also mediates the noncoding function of osk, which is essential for progression through oogenesis. Mutations which most strongly disrupt the noncoding function are positioned in a short region (the C region) near the 3' end of the mRNA, in close proximity to elements required for activation of translation.	26433064
EL1026	OsPI1	N/A	qRT-PCR	phosphate starvation	up-regulated	N/A	OsPI1 cloned from rice roots. The OsPI1 gene was rapidly induced by phosphate starvation in both shoots and roots. When phosphate was supplied to phosphate-deficient plants, the OsPI1 transcripts rapidly disappeared. suggested that OsPI1 acts as riboregulator, that is, it binds with other molecules under phosphate starvation and regulates their function.	10.1046/j.1469-8137.2003.00748.x	PLNlncRbase
EL1046	PANDAR	N/A	N/A	N/A	N/A	expression	Biogenesis, metabolism, and functions of lncRNAs are otherwise interconnected with known pathogenic mechanisms	23791884	LncRNADisease
EL1048	Paupar	N/A	knockdown	N2A mouse neuroblastoma cells	N/A	N/A	Knockdown of Paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neural differentiation. Paupar acts in a transcript-dependent manner both locally, to regulate Pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with PAX6 protein. Paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is Modulated by Paupar transcript levels.	24488179
EL1058	PCGEM1	N/A	N/A	osteoarthritic human synoviocytes	up-regulated	interaction	Exogenous overexpression of PCGEM1 inhibited apoptosis, induced autophagy, and stimulated the proliferation of human synoviocytes. The increased expression of PCGEM1 in human synoviocytes also suppressed the expression of miR-770. Transfection of the miR-770 precursor resulted in reduced proliferation, and induced apoptosis of human synoviocytes. This effect of miR-770 expression was reversed by co-introduction of PCGEM1. PCGEM1 act as sponge lncRNA for miR-770 that regulates proliferation/apoptosis and autophagy, and suggest PCGEM1 as possible target for OA therapy.	26340084
EL1064	pGmENOD40	N/A	RT-PCR	root nodules	up-regulated	N/A	pGmENOD40 RNA is present at a high level in nodules and at a low level in uninoculated roots, stems and flowers. And induced in the nodule primordium and the region of the root pericycle opposite the primordium, and in mature nodules these genes are expressed in the pericycle of the vascular bundle. (Matvienko et al., 1994) In pea roots, ENOD40 is expressed in the region opposite the protoxylem poles, which is also the region where nodules form. This suggests that ethylene provides positional information for nodule primordia to form opposite protoxylem poles. (Vleghels et al., 2003)	7948896, 14508686	PLNlncRbase
EL1066	PHO84 antisense transcripts	N/A	Western Blotting,Northern Blotting,Epistasis and chromatin immunoprecipitation	Yeast strains	N/A	interaction	knockdown of antisense production prevents PHO84 gene repression, even in the absence of Rrp6.	18022365
EL1068	Pinc	N/A	microarray, qRT-PCR	inguinal mammary glands	N/A	mutation	PINC may contribute to the developmentally mediated changes previously observed in the terminal ductal lobular unit-like structures of the parous gland	16574773
EL1070	PINK1-AS	N/A	knockdown, qT-PCR	preadipocytes and adipocytes	down-regulated	interaction	PU.1 AS lncRNA promotes adipogenesis through preventing PU.1 mRNA translation via binding to PU.1 mRNA to form mRNA/AS lncRNA duplex in preadipocytes.	23749759
EL1072	Platr14	N/A	weighted gene coexpression network analysis	mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs)	down-regulated	expression	Among these, we show that acute depletion of Platr14 using antisense oligonucleotides impacts the differentiation- and development-associated gene expression program of ESCs.	26048247
EL1075	pncRNA-D	N/A	RNA pull down assay	N/A	N/A	interaction	N/A	26816614
EL1080	pouBW1	N/A	qPCR	different tissues of Gushi chickens and Anka broilers at different development stages	N/A	mutation	A single nucleotide polymorphism (SNP) at the 5'-end of the gene was identified. The SNP was significantly (P < 0.05) associated with leg muscle weight, chest breadth, sternal length and body weight in chickens at 1 day, 4 weeks and 6 weeks of age.	26643990
EL1084	Prep	N/A	knockdown; overexpression	primary ovarian granulosa cell and a hepatic cell line	N/A	interaction	this lncRNA could play a role in the POP gene activation in the granulosa cell.	24369296
EL1085	PRINS	N/A	N/A	renal tubular cells of wild type mice	up-regulated	interaction	Among HIF-1α dependent LncRNAs, PRINS (Psoriasis susceptibility-related RNA Gene Induced by Stress) was significantly up regulated in hypoxic conditions and had specific interaction with RANTES as confirmed through reporter assay.	26725683
EL1086	Prion-associated RNAs	N/A	N/A	N/A	N/A	interaction	These interactions between shsrnas and hrprp suggest possible roles of rnas in the modulation of prp structure and perhaps disease development.	12946346
EL1091	PsiLNCRNA00268512	N/A	N/A	perennial plants	N/A	interaction	PsiLNCRNA00268512 regulates miR396e levels by acting as a target mimic.	26712827
EL1093	psvA antisense RNA	N/A	excess transcription, inhibition of RNA synthesis	vegetative cells	N/A	expression	The inhibition of rna synthesis during disaggregation prevents destabilization of the mrna.	1555240
EL1099	Ptgs2os2	N/A	qPCR	dendritic cells, macrophages, splenocytes from Listeria-infected mice	N/A	N/A	mediates both the activation and repression of distinct classes of immune genes.Transcriptional repression of target genes is dependent on interactions of lincRNA-Cox2 with heterogeneous nuclear ribonucleoprotein A/B and A2/B1.	23907535
EL1099	Ptgs2os2	N/A	RNA-seq, qRT-PCR	innate immune cells	N/A	expression	A highly inflammatory inducible lncRNA that is responsible for activation and repression of distinct immune genes.	26803630
EL1101	PU.1 AS	N/A	RT-PCR, endogenous ribonuclease protection assay	porcine subcutaneous adipose, heart, liver, spleen, lympha, skeletal muscle and kidney tissues	N/A	expression	PU.1 AS lncRNA (vs. its mRNA translation) promotes adipogenesis through the formation of a sense-antisense RNA duplex with PU.1 mRNA.	25691151
EL1109	RBM5-AS1	N/A	N/A	N/A	N/A	expression	We identified a 326 bp bone marrow cdna fragment (termed je2) that suppresses, upon transfection, cd95-mediated apoptosis in jurkat t cells.	10949932
EL1109	RBM5-AS1	N/A	RNA-seq, qRT-PCR	three different brain regions (cortex, white matter, and cerebellum) of human postmortem tissue	N/A	N/A	Thus, these 5 lncRNAs may be applicable as references for accurate normalisation of lncRNA profiling in multiple brain regions during long PMI, enabling the generation of highly reproducible datasets in lncRNA studies of the human brain.	25528156
EL1111	RD29A	N/A	Northern blot/RT-PCR/Microarray	drought	up-regulated	N/A	Fig. 3A shows an fSAT of the drought-inducible gene, RD29A and the novel drought-inducible antisense TUs. The presence of novel drought-inducible TUs on the antisense strand was confirmed by real-time RT-PCR and Northern analyses using strand-specific RNA probes (Figs. 3B, 3C); The RD29A and CYP707A1 lancRNAs that were simultaneously accumulated with sense mRNAs, were accumulated by drought- and ABA treatments(Plant Cell Physiol.2008, 49, 1135–1149.).	18625610	PLNlncRbase
EL1115	RHOXF1P1	N/A	LncRHOXF1 knockdown using siRNAs	trophectoderm and primitive endoderm cells of human blastocyst-stage embryos	up-regulated	N/A	regulates the host response to viral infections in human placental progenitor cells	27066803
EL1116	Rian	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Rian was also found to interact with a number of other chromatin binding protein(s)/complexes in mouse embryonic stem cells including PRC1, JARID1B, JARID1C and CBX3, with the general pattern being interaction with repressors of gene expression.	21874018
EL1117	Rmrp	N/A	N/A	Rmrp gene mutation in mice	N/A	mutation	A targeted Rmrp gene mutation in mice, corresponding to a gene mutation in cartilage-hair hypoplasia patients, altered lncRNA chromatin occupancy, and reduced the DDX5-RORγt interaction and RORγt target gene transcription	26675721
EL1119	RMST	N/A	N/A	anterior neural tube	up-regulated	expression	Rmst expression appears to be restricted to the presumptive dopaminergic neurons of the ventral tegmental area	20062813
EL1119	RMST	N/A	tsRMST knockdown cells	human pluripotent stem cells	up-regulated	N/A	disruption of tsRMST expression in hESCs results in the up-regulation of WNT5A, EMT, and lineage-specific genes/markers	27090862
EL1120	RN7SK	N/A	Immunoprecipitation,Immunofluorescence microscopy,FISH analysis,	HeLa cell	N/A	interaction	N/A	17381310
EL1120	RN7SK	N/A	N/A	N/A	N/A	interaction	The 7sk/p-tefb interaction may serve as a principal control point for the induction of cellular and hiv-1 viral gene expression during stress-related responses.	11713532
EL1120	RN7SK	N/A	N/A	N/A	N/A	interaction	The transcription-dependent interaction of p-tefb with 7sk may therefore contribute to an important feedback loop modulating the activity of rna pol ii.	11713533
EL1120	RN7SK	N/A	RNA-seq, qRT-PCR	three different brain regions (cortex, white matter, and cerebellum) of human postmortem tissue	N/A	N/A	Thus, these 5 lncRNAs may be applicable as references for accurate normalisation of lncRNA profiling in multiple brain regions during long PMI, enabling the generation of highly reproducible datasets in lncRNA studies of the human brain.	25528156
EL1121	RN7SL1	N/A	a solid phase radioimmune assay	N/A	N/A	expression	Cellular function of 7sl-rna is as a part of srp.	6196367
EL1121	RN7SL1	N/A	N/A	N/A	N/A	expression	The rna is closely identified with the small cytoplasmic 7sl rna and is required for both structural and functional properties of signal recognition protein--which we therefore rename signal recognition particle.	6181418
EL1129	RNY1	N/A	Specific degradation	late-G(1)-phase human cells	down-regulated	mutation	Specific degradation of hY RNAs leads to the inhibition of semiconservative DNA replication in late-G(1)-phase template nuclei. This inhibition is negated by resupplementation of hY RNAs. All four hY RNAs (hY1, hY3, hY4, and hY5) can functionally substitute for each other in this system. Mutagenesis of hY1 RNA showed that the binding site for Ro60 protein, which is required for Ro RNP assembly, is not essential for DNA replication. Degradation of hY1 RNA in asynchronously proliferating HeLa cells by RNA interference reduced the percentages of cells incorporating bromodeoxyuridine in vivo.	16943439
EL1130	roX1	N/A	capture hybridization analysis of RNA targets (CHART)	N/A	N/A	N/A	roX2, a well-studied ncRNA involved in dosage compensation in Drosophila.	22143764
EL1130	roX1	N/A	N/A	N/A	N/A	mutation	Genetic rescue by roX orthologs and engineered synthetic lncRNAs showed that altering the number of focal, repetitive RNA structures determines roX ortholog function. Genomic occupancy maps of roX RNAs in four species revealed conserved targeting of X chromosome neighborhoods but rapid turnover of individual binding sites. Many new roX-binding sites evolved from DNA encoding a pre-existing RNA splicing signal, effectively linking dosage compensation to transcribed genes. Thus, dynamic change in lncRNAs and their genomic targets underlies conserved and essential lncRNA-genome interactions.	26773003
EL1131	roX2	N/A	N/A	N/A	N/A	mutation	Genetic rescue by roX orthologs and engineered synthetic lncRNAs showed that altering the number of focal, repetitive RNA structures determines roX ortholog function. Genomic occupancy maps of roX RNAs in four species revealed conserved targeting of X chromosome neighborhoods but rapid turnover of individual binding sites. Many new roX-binding sites evolved from DNA encoding a pre-existing RNA splicing signal, effectively linking dosage compensation to transcribed genes. Thus, dynamic change in lncRNAs and their genomic targets underlies conserved and essential lncRNA-genome interactions.	26773003
EL1138	AL353732.1	N/A	global lncRNA expression analysis	urine of patients with acute T cell-mediated renal allograft rejection	up-regulated	expression	RP11-354P17.15-001 was associated with higher decline in glomerular filtration rate 1 year after transplantation.	26506418
EL1141	RP11-395P13.3-001	N/A	global lncRNA expression analysis	urine of patients with acute T cell-mediated renal allograft rejection	up-regulated	expression	N/A	26506418
EL1146	RP11-457M11.2	N/A	N/A	N/A	N/A	N/A	N/A	26325208
EL1153	RP11-766N7.3	N/A	LncRNA microarray	Dermal papilla (DP) cells	up-regulated	expression	RP11-766N7.3, H19 and HOTAIR are specific lncRNAs that were aberrantly expressed in DP cells and played an important role in regulating Wnt signaling	25285630
EL1172	Rubie	N/A	positional cloning	wildtype SWR/J mice	N/A	N/A	Rubie is the gene mutated in Ecl mice, that it is involved in regulating inner ear expression of Bmp4, and that aberrant Bmp4 expression contributes to the Ecl phenotype.	22253730
EL1175	RZE1	N/A	single molecule fluorescent in situ hybridization (smFISH)	Cryptococcus neoformans	N/A	interaction	A long non-coding RNA (lncRNA) RZE1 functions upstream of ZNF2 in regulating yeast-to-hypha transition. This lncRNA controls Cryptococcus yeast-to-hypha transition through regulating the key morphogenesis regulator Znf2.	26588844
EL1176	SALRNA1	N/A	RNA-Seq, reverse transcription (RT) and real-time,quantitative (q)PCR	human diploid WI-38 fibroblasts, 'old' fibroblasts (PDL 52)	N/A	N/A	delay senescence, reducing SAL-RNA1 levels enhanced the appearance of phenotypic traits of senescence, including an enlarged morphology, positive β-galactosidase activity, and heightened p53 levels.	23758631
EL1182	SENCR	N/A	RNA-seq, RT-PCR and rapid amplification of cDNA, Western blotting, Loss-of-function studies	human coronary artery smooth muscle cells	N/A	N/A	SENCR is a new vascular cell-enriched, cytoplasmic lncRNA that seems to stabilize the smooth muscle cell contractile phenotype.	24578380
EL1184	SFTA3	N/A	N/A	lung and foregut endoderm	N/A	interaction	LL18/NANCI acts upstream of Nkx2.1 and downstream from Wnt signaling to regulate lung endoderm gene expression.	24939938
EL1186	Sho	N/A	RT-PCR	roots and young leaves	up-regulated	N/A	Sho is a natural antisense transcript. Sho may function in roots and young leaves, involve the production of small RNAs. In addition to cytokinin transport and inactivation, antisense transcription can be activated in a tissue-specific manner to adjust local cytokinin synthesis via degradation of Sho dsRNA. We therefore propose that, in addition to cytokinin transport and inactivation, regulation of local cytokinin synthesis via antisense transcription represents yet another device for the complex control of local cytokinin levels in plants.	17944812	PLNlncRbase
EL1187	Si lincRNA113	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1188	Si lincRNA121	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1189	Si lincRNA150	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1190	Si lincRNA18	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1191	Si lincRNA180	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1192	Si lincRNA212	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1193	Si lincRNA248	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1194	Si lincRNA288	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1195	Si lincRNA32	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1196	Si lincRNA373	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1197	Si lincRNA396	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1198	Si lincRNA403	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1199	Si lincRNA416	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1200	Si lincRNA438	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1201	Si lincRNA446	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1202	Si lincRNA489	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1203	Si lincRNA69	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1204	Si NAT52	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1205	Si NAT80	N/A	qRT-PCR	drought	N/A	N/A	Differential expression analysis showed that 19 (3.25 %) lncRNAs (17 lincRNAs and 2 NATs) in foxtail millet responded to PEG-induced drought stress (Table S12)	23860794	PLNlncRbase
EL1206	SIRT1-AS	N/A	sequencing and bioinformatic analysis	C2C12 cells	up-regulated	N/A	The expression of both Sirt1 mRNA and Sirt1 AS lncRNA decreased during C2C12 myogenic differentiation, whereas the levels of miR-34a, which targets Sirt1, increased gradually. overexpression of Sirt1 AS lncRNA mutant did not affect the level of Sirt1 protein in C2C12 cells. Moreover, downregulation of Sirt1 mRNA caused by miR-34a was counteracted by Sirt1 AS lncRNA in C2C12 cells.	24480449
EL1208	Six3os1	N/A	RNA-seq, RNA CaptureSeq, and ChIP-seq	adult mouse subventricular zone neural stem cell lineage	N/A	expression	shRNA-mediated knockdown of two such lncRNAs, Six3os and Dlx1as, indicate roles for lncRNAs in the glial-neuronal lineage specification of multipotent adult stem cells.	23583100
EL1208	Six3os1	N/A	SAGE, in situ hybridization	developing retina	N/A	expression	Multiple transcripts that were evolutionarily conserved that did not appear to encode open reading frames of more than 100 amino acids in length ("noncoding rnas") were found to be dynamically and specifically expressed in developing and mature retinal cell types.	15226823
EL1217	sme2	N/A	N/A	N/A	N/A	interaction	Meirna targets mei2 to the nucleus, where it can promote the first meiotic division.	10021358
EL1217	sme2	N/A	N/A	N/A	N/A	interaction	This rna is likely to facilitate the assembly of mei2p into a dot structure and trap the protein as such in the nucleus.	11423126
EL1217	sme2	N/A	N/A	N/A	N/A	interaction	Mei2p dot is a specialized structure, either to foster the assembly of mei2p and meirna or to perform some unidentified function indispensable for meiosis i.	12808043
EL1217	sme2	N/A	N/A	N/A	N/A	expression	Cells without meirna perform premeiotic dna synthesis but cannot undergo meiosis i.	7520368
EL1217	sme2	N/A	N/A	Fission yeast	N/A	interaction	Meirna contributes to the promotion of meiosis i exclusively as a cofactor that assists nuclear transport of mei2p.	9778252
EL1221	SNHG1	N/A	N/A	N/A	N/A	expression	The spliced uhg rna, although it is associated with polysomes, has little potential for protein coding, is short-lived, and is poorly conserved between human and mouse.	8559254
EL1221	SNHG1	N/A	N/A	HeLa cells	N/A	expression	Comparison of the human and mouse u17hg genes has revealed that snorna-encoding intron sequences but not exon sequences are conserved between the two species and that neither human nor mouse spliced u17hg poly(a)+ rnas have the potential to code for proteins.	9671460
EL1229	Snhg3	N/A	knockdown, Screening for pluripotency affects, Lineage expression affects, TF binding and regulation, Chromatin binding and overlap in expression	mouse embryonic stem (ES) cells	N/A	interaction	Involved in maintaining pluripotency in ESCs.	21874018
EL1232	SNHG6	N/A	N/A	N/A	N/A	expression	U87hg rna shows a relatively high degree of conservation suggesting a selective pressure and a possible functional activity of u87hg apart from producing u87 snorna.	16226852
EL1236	SOX2-OT	N/A	real-time polymerase chain reaction (RT-PCR)	NT-2 pluripotent cell line	down-regulated	N/A	the down-regulation of SOX2OT and SOX2 genes by an miRNA	26862518
EL1236	SOX2-OT	N/A	real-time RT-PCR	five human cancer cell lines	N/A	mutation	SOX2OT-7 is almost the most abundant form of SOX2OT transcript variants in the examined cancer cell lines particularly in NT2 teratocarcinoma cell line where its expression falls upon neuronal-like differentiation similar to SOX2 and OCT4A.	26703382
EL1236	SOX2-OT	N/A	real-time RT-PCR	five human cancer cell lines	N/A	mutation	N/A	26703382
EL1236	SOX2-OT	N/A	TaqMan gene expression assays, QPCR	human TK6 (p53 positive) and WTK1 (p53 negative) cells	up-regulated	expression	The lncRNA MALAT1 and SOX2OT were induced in both TK6 and WTK1 cells	23698766
EL1240	SPRY4-IT1	N/A	N/A	N/A	down-regulated	interaction	The lncRNA SPRY4-IT1 regulates the intestinal epithelial barrier function by altering expression of tight junction (TJ) proteins. SPRY4-IT1 silencing led to dysfunction of the epithelial barrier in cultured cells by decreasing the stability of mRNAs encoding TJ proteins claudin-1, claudin-3, occludin, and JAM-1 and repressing their translation. In contrast, increasing the levels of SPRY4-IT1 in the intestinal mucosa protected the gut barrier in mice exposed to septic stress by increasing the abundance of TJ proteins.	26678886
EL1241	SRA1	N/A	N/A	N/A	N/A	interaction	SRA is important for maintaining the stem cell state and for reprogramming of human fibroblasts to achieve the pluripotent state.	26496121
EL1241	SRA1	N/A	N/A	N/A	N/A	epigenetics	Mpus1p-dependent pseudouridylation of sra represents an additional type of posttranscriptional modification of a nr-coactivator complex that is important for nr signaling.	15327771
EL1241	SRA1	N/A	overexpression	a transgenic-mouse model, transgenic mammary glands	N/A	expression	Although coactivation of steroid-dependent transcription by sra is accompanied by a proliferative response, overexpression is not in itself sufficient to induce turmorigenesis.	14517287
EL1241	SRA1	N/A	TaqMan gene expression assays, QPCR	human TK6 (p53 positive) and WTK1 (p53 negative) cells	up-regulated	expression	SRA1 was induced in TK6 cells only.	23698766
EL1241	SRA1	N/A	transfected SRA, Biochemical fractionation	N/A	N/A	expression	Sra may act to confer functional specificity upon multiprotein complexes recruited by liganded receptors during transcriptional activation.	10199399
EL1242	SrENOD40-1	N/A	RT-PCR	Nodule formation	down-regulated	N/A	By reverse transcriptase PCR, enhanced SrENOD40-1 expression was observed in the adventitious root primordia between 4 and 8 h after inoculation with Azorhizobium caulinodans. SrENOD40-1 expression with highest levels in middle and inner cortical cells. SrENOD40-1 was expressed in these primordia and in parenchymatous cells surrounding the developing connecting vascular bundles. SrENOD40-1 transcripts were still most prominent around the nodule vascular bundles. In the root, expression was detected around the vascular bundle of lateral root primordia and of the younger parts of the main root. SrENOD40-1 expression was seen, both in longitudinal and in transverse sections.	9620265	PLNlncRbase
EL1243	SRG1	N/A	N/A	N/A	N/A	interaction	Expression of the srg1 rna is required for repression of ser3.	15175754
EL1243	SRG1	N/A	N/A	N/A	N/A	interaction	Intergenic transcription allows activators to act indirectly as repressors.	16291644
EL1244	SRP RNA	N/A	N/A	N/A	N/A	interaction	Reconstitutions with heterologous components revealed a significant potential of human srp proteins to bind to archaeal srp rnas. m.jannaschii srp rna bound to human srp54m quantitatively in the absence of srp19.	10684931
EL1251	TalIPS1	N/A	qRT–PCR	phosphate balance	up-regulated	N/A	The expression patterns of other members of the TPSI1/Mt4 family in monocots were also investigated. The induced expressions of OsIPS1, HvIPS1, ZmIPS2 and TalIPS2 were stronger than those of OsIPS2, HvIPS2 ZmIPS1 and TalIPS1 in roots after 4 or 10 d of Pi starvation, whereas higher induced expressions of OsIPS2, HvIPS1, ZmIPS1 and TalIPS1 were detected in shoots.	10.1111/j.1365-3040.2005.01272.x	PLNlncRbase
EL1252	TalncRNA106	N/A	RT-PCR	stripe rust pathogen	up-regulated	N/A	TalncRNA106 were located to wheat chromosome 5B. appeared higher level of expression in resistance genotypes. lncRNA106 could be detected in single-resistance genotype. For TalncRNA18 and TalncRNA106, there appeared higher level of expression in resistance genotypes than that in susceptible genotype at all time points, especially at 2 and 7 days post-infection,That suggests that the fluctuation maybe one primary characterization of long non-protein-coding RNA other than the induction expression. May play a crucial role in assisting the plant defence against pathogen attack in wheat.	24065539	PLNlncRbase
EL1253	TalncRNA108	N/A	RT-PCR	stripe rust pathogen	down-regulated	N/A	TalncRNA108 is a homolog to RRNA intron-encoded homing endonuclease(XP003614385.1) and an uncharacterized protein (XP003541241.1) from Medicago truncatula and Glycine max,respectively,the TalncRNA18 consists of 1,393 nt,was located to wheat chromosome 7A and the short arm of chromosome 4B. And played some roles in the proceeding of defense on stripe rust(caused by Puccinia striiformis f.sp.tritici (Pst)) in wheat though RNAi.	24065539	PLNlncRbase
EL1254	TalncRNA18	N/A	RT-PCR	stripe rust pathogen	up-regulated	N/A	TalncRNA18 is a partial cDNA of E3 ubiquitin-protein ligase UPL1-like gene. TalncRNA18 contains of six snRNP motifs at the position of 125, 361, 498, 920, 1,107 and 1,331 nt,was located to chromosome 5B. Following inoculation with Pst CYR 32, lncRNA18 transcripts were up-regulated rapidly at 1 dpi in the double-resistance genotype (YrSM139-1B+YrSM139-2D) plant-pathogen incompatible interaction and followed by a stable expression level. Based on statistical analyses, TalncRNA18 expression is significantly higher than that in susceptible line at 0 dpi. Although the expression decreased after 2 dpi, the accumulations of TalncRNA18 are higher than that in single-resistance genotype plant-pathogen incompatible interactions and compatible interactions except 7dpi. And played some roles in the proceeding of defense on stripe rust(caused by Puccinia striiformis f.sp.tritici (Pst)) in wheat though RNAi.	24065539	PLNlncRbase
EL1255	TalncRNA73	N/A	RT-PCR	stripe rust pathogen	up-regulated	N/A	TalncRNA73 is an antisense transcript of hypothetical protein,were located to wheat chromosome 7A and the short arm of chromosome 4B. TalncRNA73, a non-proteincoding gene is a natural antisense transcript from a hypothetical protein of S.bicolorand induced by inoculation with stripe rust (caused by Puccinia striiformis f.sp.tritici (Pst)) in wheat. The expression level of TalncRNA73 in double resistance genotype increased rapidly at 1 dpi and reached a peak at 3 dpi, and then decreased to the bottom at 4 dpi, followed by a steeply rise to another peak at 7 dpi and decline again at 10 dpi. The current work suggested that a possible role for TalncRNA73 is to modulate protein-coding gene that trigger a defense response in resistant plants.	24065539	PLNlncRbase
EL1256	TapmlnRNA19	N/A	Microarray/qRT-PCR	powdery mildew infection	up-regulated	N/A	TapmlnRNA19 was up-regulated after powdery mildew inoculation, and responsive to powdery mildew infection. TapmlnRNA19 was the precursors of miR2004. TapmlnRNA19 accumulated preferentially in young spike.	21473757	PLNlncRbase
EL1257	TapmlnRNA27	N/A	Microarray/qRT-PCR	seeds	N/A	N/A	A total of 48 putative long npcRNAs were only responsive to powdery mildew infection (designated TapmlnRNA), see details in additional file 1.	21473757	PLNlncRbase
EL1258	TapmlnRNA30	N/A	Microarray/qRT-PCR	seeds	up-regulated	N/A	TapmlnRNA30 was up-regulated after powdery mildew inoculation. TapmlnRNA30 was only detected in seed.	21473757	PLNlncRbase
EL1259	TapmlnRNA5	N/A	Microarray/qRT-PCR	seeds	N/A	N/A	A total of 48 putative long npcRNAs were only responsive to powdery mildew infection (designated TapmlnRNA), see details in additional file 1.	21473757	PLNlncRbase
EL1260	TapmlnRNA9	N/A	Microarray/qRT-PCR	young spikes	N/A	N/A	A total of 48 putative long npcRNAs were only responsive to powdery mildew infection (designated TapmlnRNA), see details in additional file 1.	21473757	PLNlncRbase
EL1261	TAR-191	N/A	RNA-seq/qRT-PCR	disease development	up-regulated	N/A	TAR-191, a spliced lincRNA located in the intergenic region (c.1.3kb) between At2g25295 and At2g25300, was confirmed by qRT-PCR to be highly induced by Fusarium oxysporum infection.	24117540	PLNlncRbase
EL1262	TAR-224	N/A	RNA-seq/qRT-PCR	disease development	down-regulated	N/A	TAR-224 was found c.550-bp downstream of At2g44745. Both TAR-224 and At2g44745 were induced upon Fusarium oxysporum infection but a much higher induction was observed for TAR-224. The expression level of TAR-224 was significantly knocked down in its RNAi plants.but an induction of TAR-224 was not abolished in F6DPI even though the level of induction was c.10-fold lower than that observed in Col-0 Nevertheless, the reduction was enough to enhance disease development.	24117540	PLNlncRbase
EL1264	TaS1	N/A	RT-PCR	leaves	up-regulated	N/A	TaS1 was specifically expressed in leaves and hardly detectable in roots. TaS1 could promote host susceptibility which contributed to the pathogen infection. TaS1 were expressed only in susceptible hosts and up-regulated during the phase of the primary fungus infection and haustorial development.the suppression of TaS1 and enhanced wheat resistance susceptibility to powdery mildew.	10.1007/s10535-014-0404-y	PLNlncRbase
EL1265	TaS2	N/A	RT-PCR	roots	up-regulated	N/A	TaS2 was detected in almost all of the three organs, but preferentially expressed in roots. TaS2 could promote host susceptibility which contributed to the pathogen infection. TaS2 were expressed only in susceptible hosts and up-regulated during the phase of the primary fungus infection and haustorial development.the suppression of TaS2 enhanced wheat resistance susceptibility to powdery mildew.	10.1007/s10535-014-0404-y	PLNlncRbase
EL1272	TCONS_00000649	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00000649 was obviously up-regulated in stressed leaves, exhibited leaf-specific expression as determined by qRT-PCR.	24892290	PLNlncRbase
EL1274	TCONS_00007700	N/A	qRT-PCR/RNA-seq	drought	down-regulated/up-regulated	N/A	TCONS_00007700 was obviously up-regulated in stressed leaves. TCONS_00007700, which was up-regulated in stressed leaves, was down-regulated in stressed roots as determined by qRT-PCR.	24892290	PLNlncRbase
EL1275	TCONS_00010027	N/A	RT-PCR/RNA-seq	roots	N/A	N/A	TCONS_00010027 is identified a pre-lncRNA,This pre-lncRNA (TCONS_00010027 ) has se-quence similarity with small RNAs and thus may be chopped into pieces and function as a small RNA.	24576388	PLNlncRbase
EL1277	TCONS_00012662	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00012662 is precursor sequences of MIR167j, TCONS_00012662 was intergenic lncRNAs, showed up-regulation in drought-stress leaves in comparison with RNA-seq.	24892290	PLNlncRbase
EL1278	TCONS_00012690	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00012690 was obviously up-regulated in stressed leaves as determined by qRT-PCR.	24892290	PLNlncRbase
EL1279	TCONS_00012703	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00012703 is homologous to multiple siRNA reads. In addition, the RT-qPCR result of TCONS_00012703 RNA demonstrates that the expression level of the lncRNAs is relatively low in both non-stressed leaves and roots but accumulates to high levels after drought stress in both plant tissues.	24892290	PLNlncRbase
EL1280	TCONS_00012768	N/A	qRT-PCR/RNA-seq	drought	down-regulated	N/A	TCONS_00012768 was down-regulated in drought-stressed roots as determined by qRT-PCR.	24892290	PLNlncRbase
EL1284	TCONS_00022311	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	In our study, TCONS_00022311 was predicted to target a GA2ox, suggesting that lncRNAs may take part in regulating wood for mation through gibberellin biosynthesis.	25230698	PLNlncRbase
EL1285	TCONS_00023843	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	We also checked the sequences for lncRNAs that correspond to miRNA precursors, and found that only three of the 1377 lncRNAs (0.2 %), i.e., TCONS_00061773,TCONS_00023843 and TCONS_00048079, harbor complete precursors, for four miRNAs (Ptc-miR1448, Ptc-miR482a.2, Ptu-172 and Ptu-37) (Table 4; Fig. 7).	25230698	PLNlncRbase
EL1286	TCONS_00024309	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00024309 is precursor sequences of MIR399e, TCONS_00024309 was intergenic lncRNAs, exhibited up-regulation in drought-stressed leaves as determined by qRT-PCR but showed down-regulation in comparison with RNA-seq.	24892290	PLNlncRbase
EL1287	TCONS_00024310	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00024310 is precursor sequences of MIR399e, TCONS_00024310 was intergenic lncRNAs, exhibited up-regulation in drought-stressed leaves as determined by qRT-PCR but showed down-regulation in comparison with RNA-seq.	24892290	PLNlncRbase
EL1290	TCONS_00026694	N/A	RNA-seq/qRT-PCR	wood formation	down-regulated	N/A	The expression of type A and B lncRNAs such as TCONS_00026694 and TCONS_00028236 was NW>TW>OW and NW>OW>TW, and these lncRNAs were similarly suppressed by tension and compression stresses (Supplementary material S6).	25230698	PLNlncRbase
EL1291	TCONS_00028236	N/A	RNA-seq/qRT-PCR	wood formation	down-regulated	N/A	The expression of type A and B lncRNAs such as TCONS_00026694 and TCONS_00028236 was NW>TW>OW and NW>OW>TW, and these lncRNAs were similarly suppressed by tension and compression stresses (Supplementary material S6).	25230698	PLNlncRbase
EL1292	TCONS_00032782	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	In our study, TCONS_00032782, which was predicted to target Pt-CSLD4, revealed that lncRNA might function in wood formation through regulation of CSLD in Populus.	25230698	PLNlncRbase
EL1293	TCONS_00037470	N/A	qRT-PCR/RNA-seq	drought	down-regulated/up-regulated	N/A	TCONS_00037470 was down-regulated in drought-stressed roots as determined by qRT-PCR. And this lncRNA was upregulated in drought-stress leaves(see Table S2 for details).	24892290	PLNlncRbase
EL1295	TCONS_00042984	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00042984 is precursor sequences of MIR169h, TCONS_00042984 was intergenic lncRNAs, showed up-regulation in drought-stress leaves in comparison with RNA-seq.	24892290	PLNlncRbase
EL1296	TCONS_00044116	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00044116 is precursor sequences of MIR399b, TCONS_00044116 was intergenic lncRNAs, exhibited up-regulation in drought-stressed leaves as determined by qRT-PCR but showed down-regulation in comparison with RNA-seq.	24892290	PLNlncRbase
EL1297	TCONS_00044376	N/A	RNA-seq/qRT-PCR	wood formation	down-regulated	N/A	The lncRNAs showing lowest expression in NW belonged to type C (TW>OW>NW) and D (OW>TW>NW), and included TCONS_00044376 and TCONS_00055243 (Supplementary material S6).	25230698	PLNlncRbase
EL1298	TCONS_00048079	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	We also checked the sequences for lncRNAs that correspond to miRNA precursors, and found that only three of the 1377 lncRNAs (0.2 %), i.e., TCONS_00061773,TCONS_00023843 and TCONS_00048079, harbor complete precursors, for four miRNAs (Ptc-miR1448, Ptc-miR482a.2, Ptu-172 and Ptu-37) (Table 4; Fig. 7).	25230698	PLNlncRbase
EL1300	TCONS_00053930	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	Another target gene( POPTR_0001s07400.1), predicted to be targeted by TCONS_00053930, encodes a protein similar to 4CL, the central enzyme of the plant-specific phenylpropanoid pathway, which has an important role in lignin biosynthesis (Table 3).	25230698	PLNlncRbase
EL1301	TCONS_00054544	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00054544 is precursor sequences of MIR827, TCONS_00054544 was an overlapping lncRNAs, exhibited up-regulation in drought-stressed leaves as determined by qRT-PCR but showed down-regulation in comparison with RNA-seq.	24892290	PLNlncRbase
EL1302	TCONS_00055243	N/A	RNA-seq/qRT-PCR	wood formation	down-regulated	N/A	The lncRNAs showing lowest expression in NW belonged to type C (TW>OW>NW) and D (OW>TW>NW), and included TCONS_00044376 and TCONS_00055243 (Supplementary material S6).	25230698	PLNlncRbase
EL1303	TCONS_00056386	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	Genes encoding glucosyltransferases were predicted as targets of TCONS_00056386 (Table 3; Fig. 3b). Besides the genes related to cellulose, lignin and glucosyltransferase, POPTR_0010s15950.1 (Pt-GA2.3) encodes GA2ox and was predicted as a target of TCONS_00022311 (Fig. 3c). TCONS_00056386) was detected as having its highest expression in OW, then TW and lowest in NW (Supplementary material S5) by RNA-seq and a similar expression pattern was also detected by qRT-PCR.	25230698	PLNlncRbase
EL1304	TCONS_00056395	N/A	qRT-PCR/RNA-seq	drought	down-regulated	N/A	A root-specific lncRNA of TCONS_00056395, down regulation in stressed leaves and exhibit maximum expression in leaves stressed for 5h as determined by qRT-PCR.	24892290	PLNlncRbase
EL1305	TCONS_00060049	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	Although CCOMTs play important roles in lignin content, little is known about the regulators of CCOMT. TCONS_00060049 was predicted to target CCOMT, suggesting that it may have a potential role in lignin formation by regulation of CCOMT (Table 3).	25230698	PLNlncRbase
EL1306	TCONS_00061773	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	TCONS_00061773 harbors precursors for two known miRNAs, Ptc-miR1448 and Ptc-miR482a.2 (Fig. 7). Previous studies supported the idea that Ptc-miR1448 may be involved in the resistance of plants to biotic and abiotic stresses (Lu et al. 2008) and Ptc-miR482a.2 has been reported as a tree-specific miRNA in tension wood (Lu et al. 2005, 2008). The expression measured by qRT-PCR revealed that Ptc-miR1448 is much more abundant than Ptc-miR482a.2, although both miRNAs occur in one cluster in the genome (Lu et al. 2005, 2008). These findings supported the idea that TCONS_00061773 may be associated with abiotic stress tolerance in Populus.	25230698	PLNlncRbase
EL1307	TCONS_00082174	N/A	qRT-PCR/RNA-seq	drought	up-regulated	N/A	TCONS_00082174, which was only expressed in leaves, was not detected in roots, which suggests leaf-specific expression as determined by qRT-PCR.	24892290	PLNlncRbase
EL1308	TCONS_00089485	N/A	RT-PCR/RNA-seq	embryo sac and ovule tissues	N/A	N/A	TCONS_00089485 is expressed from the Vgt1 regulatory region. This lncRNA is detected in embryo sac and ovule tissues where ZmRap2 is not detected. while ZmRap2 is expressed in other tissues where this HC-lncRNA is not detected, Suggesting the potential for antagonistic expression of this HC-lncRNA and the nearby coding sequence.	24576388	PLNlncRbase
EL1322	TER	N/A	N/A	Arabidopsis thaliana	N/A	interaction	TER works in concert with the telomerase reverse transcriptase (TERT) to maintain telomeres.	26442096
EL1323	TER1	N/A	RT-PCR	DNA damage	down-regulated	N/A	As the essential RNA subunit of telomerase, TER1 is required for telomere maintenance, while TER2 is assembled in distinct RNP complex (es)to modulate telomerase activity in response to DNA damage. (Wang et al., 2014) TER1 and TER2 copurify with telomerase activity and serve as templates for telomerase in vitro, depletion of TER1, but not TER2, leads to decreased telomerase activity and progressive telomere shortening in vivo. Moreover, mutation of the templating domain in TER1 results in the incorporation of mutant telomere repeats on chromosome ends. Thus, TER1 provides the major template for telomerase in vivo. Both TER1 and TER2 function as templates for TERT in vitro, but only TER1 plays a significant role in telomere maintenance in vivo. Moreover, we show that TER1, but not TER2, specifically binds POT1a in vitro and the two components assemble into an enzymatically active RNP in vivo. These findings underscore the evolution of telomerase and telomere proteins in Arabidopsis and argue that the process is driven by gene duplication. (Cifuentes-Rojas et al., 2011)	24398630, 21164032	PLNlncRbase
EL1324	TER2	N/A	RT-PCR	telomere shortening	down-regulated	N/A	We show that TER2 is spliced and its 3' end is truncated in vivo to generate a third TER isoform, TER2S. Plants null for TER2 display increased telomerase enzyme activity, while TER2 overexpression inhibits telomere synthesis from TER1 and leads to telomere shortening. These findings argue that TER2 negatively regulates telomerase by sequestering TERT in a nonproductive RNP complex. Introduction of DNA double-strand breaks by zeocin leads to an immediate and specific spike in TER2 and a concomitant decrease in telomerase enzyme activity. This response is not triggered by replication stress or telomere dysfunction and is abrogated in ter2 mutants. We conclude that Arabidopsis telomerase is modulated by TER2, a novel DNA damage induced noncoding RNA that works in concert with the canonical TER to promote genome integrity. (Cifuentes-Rojas et al., 2012) TER2 (GenBank accession no. HQ401285), was also uncovered. TER2 maps to chromosome 5, in the opposite direction and partially overlapping with the 5′ UTR of another unknown protein coding gene, AT5G24670. TER2 also contains 1.5 copies of the Arabidopsis telomere repeat. RT-PCR confirmed that both TER1 and TER2 RNAs were enriched in purified telomerase fractions, in contrast to a U6 snRNA control. (Cifuentes-Rojas et al., 2011) As the essential RNA subunit of telomerase, TER1 is required for telomere maintenance, while TER2 is assembled in distinct RNP complex (es)to modulate telomerase activity in response to DNA damage. (Wang et al., 2014)	23109676, 21164032, 24398630	PLNlncRbase
EL1326	TGFB2-OT1	N/A	microarray, RNA interference, RNA-chiP assay, bioinformatics, luciferase reporter assay	N/A	N/A	interaction	The protein level of MAP1LC3B-II was greatly increased in HUVECs with FLJ11812 overexpression.FLJ11812 could bind with MIR4459 targeting ATG13 (autophagy-related 13), and ATG13 protein level was decreased along with 3BDO-decreased FLJ11812 level.	25437332
EL1326	TGFB2-OT1	N/A	miRNA chip assay, overexpression, 3BDO	vascular endothelial cells (VECs)	N/A	interaction	TGFB2-OT1 regulated the levels of 3 microRNAs, MIR3960, MIR4488 and MIR4459. TGFB2-OT1 acted as a competing endogenous RNA, bound to MIR3960, MIR4488 and MIR4459, then regulated the expression of the miRNA targets CERS1 (ceramide synthase 1), NAT8L (N-acetyltransferase 8-like [GCN5-related, putative]), and LARP1 (La ribonucleoprotein domain family, member 1). TGFB2-OT1 increased the LARP1 level, which promoted SQSTM1 (sequestosome 1) expression, NFKB RELA and CASP1 activation, and then production of IL6, IL8 and IL1B in VECs.	26565952
EL1327	TH2LCRR	N/A	N/A	human T-cell cultures	N/A	expression	One lncRNA cluster selectively expressed by the effector TH2 lineage consists of four alternatively spliced transcripts that regulate the expression of TH2 cytokines, IL-4, IL-5 and IL-13.Genes encoding this lncRNA cluster in humans overlap the RAD50 gene and thus are contiguous with the previously described TH2 locus control region (LCR) in the mouse. Given its genomic synteny with the TH2-LCR, we refer to this lncRNA cluster as TH2-LCR lncRNA.	25903499
EL1337	TIP ncRNA	N/A	Profiling	murine in vitro neural differentiation system	N/A	N/A	TIP transcription may ensure coordinated regulation of gene networks via dynamic switching and recruitment of PcG proteins both in cis and in trans during lineage commitment.	22336714
EL1344	Tmevp3	N/A	Quantitative RT-PCR, chromatin immunoprecipitation	N/A	up-regulated	interaction	This lncRNA regulates epigenetic marking of IFN-γ-encoding chromatin, expression of IFN-γ, and susceptibility to a viral and a bacterial pathogen.	23415224
EL1345	Tmevpg1	N/A	N/A	N/A	N/A	N/A	The mouse gene and its human orthologue, which are expressed in the immune system at a low level, produce a noncoding mrna.	11735227
EL1348	Tog	N/A	qRT-PCR, ChIP on chip	cecal buds	N/A	interaction	N/A	24075990
EL1352	TPS1	N/A	Northern blot/qRT-PCR	roots	up-regulated	N/A	INDUCED BY PHOSPHATE STARVATION1 is a member of the TPS1/Mt4 gene family that acts as a miR399 target mimic in fine tuning of PHO2 (encoding an E2 ubiquintin conjugase-related enzyme)expression and phosphate uptake in Arabidopsis, tomato and Medicago truncatula but does not encode a protein.	24576388	PLNlncRbase
EL1353	TPS11	N/A	Northern blot/Southern blot	roots	up-regulated	N/A	This lncRNAs work as a decoy of miRNAs,and exert their functions by binding miRNAs in a target mimicry mechanism to sequestrate the miRNAs’ regulation roles on their target genes, such as lncRNAs IPS1 and at4.	23726911	PLNlncRbase
EL1354	TPSI1	N/A	Northern blot/Southern blot	roots	up-regulated	N/A	The TPSI1 transcripts are rapidly induced in roots and leaves during Pi starvation. Induction of the TPSI1 gene appears to be a response specific to Pi starvation since it is not affected by starvation of other nutrients (nitrogen, potassium and iron). The amount of TPSI1 transcript decreased rapidly when Pi-starved tomato plants were resupplied with Pi. These results suggest that TPSI1 gene expression may be a part of the early Pi starvation response mechanism in plants.	9106510	PLNlncRbase
EL1359	Trenod40	N/A	Northern blot/Southern blot	nodule development	up-regulated	N/A	Enod40 is one of the genes associated with legume nodule development and has a putative role in general plant organogenesis. In situ hybridization studies revealed that Trenod40 genes were highly expressed in non-symbiotic tissues, particularly in stolon nodes during nodal root and lateral shoot development. High levels of Trenod40 transcripts were also present in the vascular bundles of mature plant organs, mainly at sites of intensive lateral transport, suggesting a role in vascular tissue function. The expression pattern of Trenod40 genes was analyzed further using Trenod40 promoter-gus fusions in transgenic white clover and tobacco (Nicotiana tabacum), indicating that white clover and tobacco share the regulatory mechanisms for Trenod40-1/2 promoters and some aspects of Trenod40-3 regulation. Trenod40 expression occurs in the xylem parenchyma of vascular bundles in white clover nodes that conjoin both young and fully developed leaves provide support for a role in vascular tissue function.	12114565	PLNlncRbase
EL1360	Trenod40-1	N/A	Northern blot/Southern blot	nodule development	up-regulated	N/A	Enod40 is one of the genes associated with legume nodule development and has a putative role in general plant organogenesis. We have isolated a small enod40 gene family from white clover (Trifolium repens), with three genes designated Trenod40-1, Trenod40-2, and Trenod40-3, all containing the conserved enod40 regions I and II. Trenod40-1 and Trenod40-2 share over 90% homology in the transcribed regions and high levels of similarity in their upstream regulatory sequences. Trenod40-1 and Trenod40-2 are similar to the enod40 genes of legumes forming indeterminate nodules (group II) and are predominantly expressed in nodules.	12114565	PLNlncRbase
EL1361	Trenod40-2	N/A	Northern blot/Southern blot	nodule development	up-regulated	N/A	Enod40 is one of the genes associated with legume nodule development and has a putative role in general plant organogenesis. We have isolated a small enod40 gene family from white clover (Trifolium repens), with three genes designated Trenod40-1, Trenod40-2, and Trenod40-3, all containing the conserved enod40 regions I and II. Trenod40-1 and Trenod40-2 share over 90% homology in the transcribed regions and high levels of similarity in their upstream regulatory sequences. Trenod40-1 and Trenod40-2 are similar to the enod40 genes of legumes forming indeterminate nodules (group II) and are predominantly expressed in nodules.	12114565	PLNlncRbase
EL1362	Trenod40-3	N/A	Northern blot/Southern blot	nodule development	up-regulated	N/A	The developing lateral shoot of node N7 also has up-regulation of Trenod40-1/2 expression, which is confined to the vascular tissue at the base of the lateral shoot (Fig. 5E). Trenod40-3 was also expressed in developing lateral shoots, with high levels of expression localized mainly in the vascular tissue but also in other tissues of both the axillary bud of node N6 (Fig. 5F) and more mature lateral shoot of node N8 (Fig. 5G). Trenod40-3 transcript is only present at relatively low levels in nodules, but is abundant in some non-symbiotic tissues. Expression of Trenod40-3 being more prominent and induced both at early and later stages of lateral shoot development.	12114565	PLNlncRbase
EL1365	Trp53cor1	N/A	N/A	N/A	N/A	expression	Biogenesis, metabolism, and functions of lncRNAs are otherwise interconnected with known pathogenic mechanisms	23791884	LncRNADisease
EL1369	Tsix	N/A	N/A	mouse embryonic epiblasts, epiblast stem cells, and embryonic stem cells	N/A	mutation	Tsix RNA is believed to orchestrate the initiation of X-inactivation, influencing the choice of which X remains active by preventing expression of the antisense Xist RNA, which is required to silence the inactive-X.	25981039
EL1372	Ttc39aos1	N/A	Inhibition, ectopic expression	mouse erythroid cells	down-regulated	N/A	Long noncoding RNA-mediated anti-apoptotic activity in murine erythroid terminal differentiation . anti-apoptosis and promote erythoid differentiation	22155924
EL1373	tts-1	N/A	N/A	normal strains of Caenorhabditis elegans and those carrying the life-extending daf-2 mutation	N/A	expression	The expression of tts-1 functions in different longevity pathways to reduce ribosome levels in a way that promotes life extension	25600869
EL1374	TU1273	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes.	24932683	PLNlncRbase
EL1375	TU1378	N/A	RNA-seq, qRT-PCR	mycelia stage	up-regulated	N/A	The expression profiles of 5 lincRNAs were negatively correlated with those of their apcGenes (Figure 5B,r<-0.8). The apcGenes of TU718, TU1378, TU3327, and TU5007 are a putative hydrolase (GL15069), a Barwin-related endoglucanase (GL18494), a putative hydrolase (GL27846), and an alphaamylase (GL24914), respectively, which all belong to CAZy family.	24932683	PLNlncRbase
EL1376	TU1403	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes.	24932683	PLNlncRbase
EL1377	TU1555	N/A	RNA-seq, qRT-PCR	mycelia stage	up-regulated	N/A	The log ratios for the expression levels of lincRNAs to apcGenes were shown in Figure 4. The expression of three lincRNAs (TU1378, TU1555, and TU4508) and an apcGene (GL27157) were detected only in the mycelia stage, whereas the expression of TU3327 was detected in mycelia and primordia stages.	24932683	PLNlncRbase
EL1378	TU1567	N/A	RNA-seq, qRT-PCR	mycelia, primordia, stage	up-regulated	N/A	For the other three lincRNAs located at the 5' end of their apcGenes, TU1567 was adjacent to a pheromone B alpha 3 receptor gene. TU1567 was expressed bidirectionally only in the mycelia, consistent with its possible involvement in the mating process.	24932683	PLNlncRbase
EL1379	TU1970	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of five lincRNAs/apcGenes pairs exhibited significantly negative correlations (Figure 5B). In this group, four of five lincRNAs located in the 5' region of their apcGenes (Figure 3A and 3B), in which three (TU1970, TU3327, and TU5007) were transcribed in the opposite direction. TU718 was transcribed in the same direction. The other lincRNA (TU1378) located in the 3' region of its apcGenes and was transcribed in the same direction (Figure 3A and 3B). (see in the section "Potential roles of lincRNAs whose expression are significantly correlated with those of apcGenes"for details)	24932683	PLNlncRbase
EL1380	TU3327	N/A	RNA-seq, qRT-PCR	mycelia and primordia stages	up-regulated	N/A	The expression profiles of 5 lincRNAs were negatively correlated with those of their apcGenes (Figure 5B,r<-0.8). The apcGenes of TU718, TU1378, TU3327, and TU5007 are a putative hydrolase (GL15069), a Barwin-related endoglucanase (GL18494), a putative hydrolase (GL27846), and an alphaamylase (GL24914), respectively, which all belong to CAZy family.	24932683	PLNlncRbase
EL1381	TU3423	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	For the other three lincRNAs located at the 5' end of their apcGenes, TU1567 was adjacent to a pheromone B alpha 3 receptor gene. TU1567 was expressed bidirectionally only in the mycelia, consistent with its possible involvement in the mating process (Figure 3C, Table S4). Two bidirectional lincRNAs (TU532 and TU3423) were adjacent to the CAZy family genes and showed developmentally preferential expression among the three stages (Figure 3C, Table S4). TU532 was expressed bidirectionally in the primordia and expressed in the reverse direction in the mycelia or fruiting bodies (Figure 3C, Table S4). For TU3423, bidirectional transcription was not detected in the fruiting bodies. These two lincRNAs may be involved in carbohydrate metabolism as indicated by their expression profiles.	24932683	PLNlncRbase
EL1382	TU4313	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	TU4313 was adjacent to the gene GL24088, encoding a hydrox ymethylglutaryl-CoA reductase (HMGR). HMGR is involved in isopentenyl diphosphate production in the MVA pathway, which is the crucial precursor of triterpenoids. Also showed distinct expression profiles. As HMGR is a rate-limiting enzyme in the MVA pathway, the presence of these three lincRNAs with distinct expression profiles may reflect a novel regulatory mechanism of the MVA pathway.	24932683	PLNlncRbase
EL1383	TU4314	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	TU4314 was adjacent to the gene GL24088, encoding a hydroxy methylglutaryl-CoA reductase (HMGR). HMGR is involved in isopentenyl diphosphate production in the MVA pathway, which is the crucial precursor of triterpenoids. Also showed distinct expression profiles. As HMGR is a rate-limiting enzyme in the MVA pathway, the presence of these three lincRNAs with distinct expression profiles may reflect a novel regulatory mechanism of the MVA pathway.	24932683	PLNlncRbase
EL1384	TU4508	N/A	RNA-seq, qRT-PCR	mycelia stage	up-regulated	N/A	The log ratios for the expression levels of lincRNAs to apcGenes were shown in Figure 4. The expression of three lincRNAs (TU1378, TU1555, and TU4508) and an apcGene (GL27157) were detected only in the mycelia stage, whereas the expression of TU3327 was detected in mycelia and primordia stages.	24932683	PLNlncRbase
EL1385	TU4652	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes. The apcGenes of TU4652 and TU781 are a laccase 3 (GL29234) and a glyoxal oxidase precursor (GL20538), respectively, which belong to the lignin degradation pathway.	24932683	PLNlncRbase
EL1386	TU4684	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes. The apcGenes of TU4652 and TU781 are a laccase 3 (GL29234) and a glyoxal oxidase precursor (GL20538), respectively, which belong to the lignin degradation pathway. In contrast, The apcGenes of TU51, TU4779, and TU4684 are an alpha-glucosidase (GL30020), a putative hydrolase (GL19744), a chitinase 1 (GL24376), respectively, all of which belong to CAZy family.	24932683	PLNlncRbase
EL1387	TU4779	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes. The apcGenes of TU4652 and TU781 are a laccase 3 (GL29234) and a glyoxal oxidase precursor (GL20538), respectively, which belong to the lignin degradation pathway. In contrast, The apcGenes of TU51, TU4779, and TU4684 are an alpha-glucosidase (GL30020), a putative hydrolase (GL19744), a chitinase 1 (GL24376), respectively, all of which belong to CAZy family.	24932683	PLNlncRbase
EL1388	TU5007	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	On the other hand, the expression profiles of 5 lincRNAs were negatively correlated with those of their apcGenes (Figure 5B,r<-0.8). The apcGenes of TU718, TU1378, TU3327, and TU5007 are a putative hydrolase (GL15069), a Barwin-related endoglucanase (GL18494), a putative hydrolase (GL27846), and an alphaamylase (GL24914), respectively, which all belong to CAZy family.	24932683	PLNlncRbase
EL1389	TU506	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes.	24932683	PLNlncRbase
EL1390	TU51	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes. The apcGenes of TU4652 and TU781 are a laccase 3 (GL29234) and a glyoxal oxidase precursor (GL20538), respectively, which belong to the lignin degradation pathway. In contrast, The apcGenes of TU51, TU4779, and TU4684 are an alpha-glucosidase (GL30020), a putative hydrolase (GL19744), a chitinase 1 (GL24376), respectively, all of which belong to CAZy family.	24932683	PLNlncRbase
EL1391	TU5846	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes.	24932683	PLNlncRbase
EL1392	TU6607	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes.	24932683	PLNlncRbase
EL1393	TU6608	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes.	24932683	PLNlncRbase
EL1394	TU718	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	On the other hand, the expression profiles of 5 lincRNAs were negatively correlated with those of their apcGenes (Figure 5B,r<-0.8). The apcGenes of TU718, TU1378, TU3327, and TU5007 are a putative hydrolase (GL15069), a Barwin-related endoglucanase (GL18494), a putative hydrolase (GL27846), and an alphaamylase (GL24914), respectively, which all belong to CAZy family.	24932683	PLNlncRbase
EL1395	TU781	N/A	RNA-seq, qRT-PCR	fruiting bodies, mycelia and primordia stages	up-regulated	N/A	The expression profiles of 11 lincRNAs were positively correlated with their corresponding apcGenes (r>0.8; Figure 5A). The apcGenes of TU5846, TU506, TU6607, TU6608, TU1273, and TU1403 are all CYP450 genes. The apcGenes of TU4652 and TU781 are a laccase 3 (GL29234) and a glyoxal oxidase precursor (GL20538), respectively, which belong to the lignin degradation pathway.	24932683	PLNlncRbase
EL1400	Tug1	N/A	Northern blots and in situ hybridization, knockdown, Immunofluorescent staining and microarray analyses	retina	N/A	expression	Tug1 is necessary for the proper formation of photoreceptors in the developing rodent retina.	15797018
EL1400	Tug1	N/A	qRT-PCR, knockdown, MTT, TUNEL and Annexin V-FITC assays and western blot, GSIS, ELISA and immunochemistry	mouse pancreatic β cell	up-regulated	expression	Knockdown of lncRNA TUG1 expression resulted in an increased apoptosis ratio and decreased insulin secretion in β cells both in vitro and in vivo	25871529
EL1400	Tug1	N/A	RNA-seq, overexpression	mouse hepatocytes and liver sinusoidal endothelial cells LSECs	down-regulated	expression	Overexpression of TUG1 attenuated cold-induced apoptosis in mouse hepatocytes and liver sinusoidal endothelial cells LSECs, in part by blocking mitochondrial apoptosis and endoplasmic reticulum (ER) stress pathways. TUG1 attenuated apoptosis, inflammation, and oxidative stress in vivo in livers subjected to cold storage. Overexpression of TUG1 also improved hepatocyte function and prolonged hepatic graft survival rates in mice. These results suggest that the lncRNA TUG1 exerts a protective effect against cold-induced liver damage by inhibiting apoptosis in mice, and suggests a potential role for TUG1 as a target for the prevention of cold-induced liver damage in liver transplantation.	26785829
EL1430	uc022axw.1	N/A	lncRNA microarray	human bone marrow mesenchymal stem cells (MSCs)	up-regulated	expression	The results showed that the two up-regulated lncRNAs are likely to play important roles in osteogenic differentiation process。	25634249
EL1431	UCA1	N/A	N/A	Human Liver Stem Cell	N/A	interaction	CUDR plays a positive potential role in liver cancer stem cell through the cascade of CUDR-HULC/CUDR-β-catenin signaling.	26347501
EL1436	Uhg1	N/A	N/A	N/A	N/A	expression	We have identified two unusually compact box c/d multi-snorna host genes in d. melanogaster, duhg1 and duhg2, similar in their organization to the corresponding vertebrate non-protein-coding host genes.	11302516
EL1437	Uhg2	N/A	N/A	N/A	N/A	expression	We have identified two unusually compact box c/d multi-snorna host genes in d. melanogaster, duhg1 and duhg2, similar in their organization to the corresponding vertebrate non-protein-coding host genes.	11302516
EL1440	VAI	N/A	a peptide phosphorylation assay, U.V. crosslinking experiments and filter binding assay	N/A	N/A	interaction	Eber-1, eber-2 and vai rna exhibit mutually competitive binding to the native or recombinant enzyme	7901835
EL1440	VAI	N/A	construct mutants	N/A	N/A	expression	Analysis of the mutant's growth defect indicates that the adenovirus vai rna is required for efficient translation of viral mrnas at late times after infection.	6297772
EL1440	VAI	N/A	isothermal titration calorimetry and gel electrophoresis	N/A	N/A	interaction	Autophosphorylation assays confirmed that both EBER(I) and VA(I) are inhibitors of PKR activation, and profiled the kinetics of the inhibition. Binding affinities of dsRNAs to PKR double-stranded RNA-binding domains (dsRBDs) were determined by isothermal titration calorimetry and gel electrophoresis.	16580685
EL1440	VAI	N/A	N/A	N/A	N/A	interaction	The virus-associated rnas, va rnai and va rnaii, function as suppressors of rnai by interfering with the activity of dicer. the va rnas bind dicer and function as competitive substrates squelching dicer.	16014917
EL1441	VAII	N/A	N/A	N/A	N/A	interaction	The virus-associated rnas, va rnai and va rnaii, function as suppressors of rnai by interfering with the activity of dicer. the va rnas bind dicer and function as competitive substrates squelching dicer.	16014917
EL1442	Vax2os	N/A	N/A	photoreceptor progenitors in the mouse retina	N/A	N/A	regulate cell cycle in the mammalian retina during development. the overexpression of Vax2os1 in the developing early postnatal mouse retina causes an impaired cell cycle progression of photoreceptor rogenitors toward their final committed fate and a consequent delay of their differentiation processes. At later developmental stages, this perturbation is accompanied by an increase of apoptotic events in the photoreceptor cell layer, in comparison with control retinas, without affecting the proper cell layering in the adult retina. Similar results are observed in mouse photoreceptor-derived 661W cells in which Vax2os1 overexpression results in an impairment of the cell cycle progression rate and cell differentiation.	22128341
EL1442	Vax2os	N/A	RT-PCR and RNA in situ hybridization	retina	N/A	interaction	We found a significant reduction of the expression levels of one of these nats, vax2os (vax2 opposite strand) in a mouse mutant carrying the inactivation of vax2, the corresponding sense gene.	15703187
EL1445	VL30 RNAs	N/A	genetic subtraction and microarray analysis, In situ hybridization	neural stem cell (NSC)	N/A	expression	Vl30 is enriched in multiple stem cell populations and may have roles in determining "stemness", or stem cell function.	14651920
EL1445	VL30 RNAs	N/A	N/A	N/A	N/A	interaction	Psf also contains two rna-binding domains (rbd) that form a complex with a noncoding vl30 retroelement rna, releasing psf from a gene and reversing repression.	16079199
EL1445	VL30 RNAs	N/A	siRNA	mouse steroidogenic adrenal cells	N/A	interaction	Mvl30 rna regulates steroidogenesis, and possibly other physiological processes of mice, by complex formation with psf.	14704271
EL1445	VL30 RNAs	N/A	Southern hybridization analyses	an immunodeficient mouse model	N/A	expression	The metastatic effect might be mediated directly by a noncoding mvl30-1 rna or by a peptide or small protein encoded by one of the short orfs in the mvl30-1 rna.	11959915
EL1449	VsENOD40	N/A	RT-PCR	roots	up-regulated	N/A	VsENOD40 expression during Rhizobium-induced nodule formation on Vicia sativa roots. VsENOD40 is expressed at a high level in the pericycle of the nodule vascular bundle . vetch ENOD40 is only expressed in the uninfected cells in this zone. while in pea ENOD40 is expressed in both the uninfected and infected cells of this zone.	7548828	PLNlncRbase
EL1452	WFDC21P	N/A	knockdown	mouse bone marrow cells	N/A	N/A	The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation.	24744378
EL1458	XACT	N/A	Gene expression study	human pluripotent cells	N/A	N/A	act a role in the control of human X-chromosome inactivation (XCI) initiation.	23334669
EL1459	XIST	N/A	N/A	N/A	N/A	interaction	We describe gene targeting of xist, and provide evidence for its absolute requirement in the process of x chromosome inactivation.	8538762
EL1459	XIST	N/A	Targeted Structure-Seq	N/A	N/A	expression	We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function.	26646615
EL1460	Xist	N/A	chemical and enzymatic probes and FRET experiments; combination of RNP affinity chromatography, immunoprecipitation; assays, mass spectrometry, and Western blot analysis	mouse ES cell	N/A	N/A	N/A	20052282
EL1460	Xist	N/A	compared between freshly-isolated and cultured dental mesenchymal cells	mouse dental mesenchymal cells	down-regulated in dental mesenchymal cells; up-regulated in odontogenic dental mesenchymal tissue	N/A	loss of odontogenic potential	26986487
EL1460	Xist	N/A	mutant	mutant male and female mice	N/A	expression	The xist rna is required for female dosage compensation but plays no role in spermatogenesis.	9009199
EL1460	Xist	N/A	mutant	mouse embryonic fibroblasts	N/A	mutation	Loss of xist rna destabilizes the inactive state in somatic cells, leading to an increased reactivation frequency of an x-linked gfp transgene and of the endogenous hypoxanthine phosphoribosyl transferase (hprt) gene in mouse embryonic fibroblasts.	11352938
EL1460	Xist	N/A	mutation	mouse embryonic stem cells	N/A	expression	Silencing requires a conserved repeat sequence located at the 5' end of xist.	11780141
EL1460	Xist	N/A	N/A	mice embryos, differentiating embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs)	N/A	expression	Ectopic Xist RNA induction and subsequent X-linked gene silencing is sex specific in embryos and in differentiating embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs). A higher frequency of X(ΔTsix)Y male cells displayed ectopic Xist RNA coating compared with X(ΔTsix)X female cells. This increase reflected the inability of X(ΔTsix)Y cells to efficiently silence X-linked genes compared with X(ΔTsix)X cells, despite equivalent Xist RNA induction and coating. Silencing of genes on both Xs resulted in significantly reduced proliferation and increased cell death in X(ΔTsix)X female cells relative to X(ΔTsix)Y male cells. The increased expression of one or more X-inactivation escapees activates Xist and, separately, helps trigger X-linked gene silencing.	26739568
EL1460	Xist	N/A	N/A	ES cells	N/A	expression	Xist had to be activated within 48 hr of differentiation to effect silencing, suggesting that reversible repression by xist is a required initiation step that might occur during normal x inactivation in female cells.	10882105
EL1460	Xist	N/A	peptide nucleic acid (PNA) interference mapping	N/A	N/A	N/A	A single 19-bp antisense cell-permeating pna targeted against a particular region of xist rna caused the disruption of the xi.	11481485
EL1460	Xist	N/A	RT-PCR,RNA and DNA Fluorescence in Situ Hybridization,Immunofluorescence and Antibodies	ES cell	N/A	interaction	It coats and silences 1 of the 2 X chromosomes in female cells and initiates a chromosomewide change in chromatin structure that includes the recruitment of Polycomb proteins	19164542
EL1461	XLOC_000078	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1463	XLOC_000495	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1465	XLOC_000629	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1466	XLOC_000775	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1467	XLOC_000829	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1468	XLOC_000869	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1469	XLOC_000909	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1470	XLOC_000999	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1471	XLOC_001095	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1472	XLOC_001234	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1473	XLOC_001235	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1476	XLOC_004026	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1477	XLOC_004031	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1479	XLOC_004186	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1480	XLOC_004275	N/A	qRT-PCR	reproductive stage	N/A	N/A	XLOC_004275 are highly expressed in sperm (Figure 5A, D),and this type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1481	XLOC_004478	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1482	XLOC_004507	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1483	XLOC_004531	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1485	XLOC_004689	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1486	XLOC_004714	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1487	XLOC_004798	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1488	XLOC_004876	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1489	XLOC_004881	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1490	XLOC_004932	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1491	XLOC_004933	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1492	XLOC_004944	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1493	XLOC_005031	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1495	XLOC_007072	N/A	qRT-PCR	reproductive stage	N/A	N/A	lncRNA (XLOC_0063639 or XLOC_007072) that is highly expressed during the reproductive stage were introduced into rice protoplasts separately. Both XLOC_0063639 and XLOC_007072 dramatically increased the mRNA abundance of corresponding miRNA (OsmiR160 and OsmiR164) targets (LOC_Os02g36880 for miR164 [59]; LOC_Os06G47150 and LOC_Os10g33940 for miR160 [60]) in their transiently expressed protoplasts, suggesting that XLOC_0063639 and XLOC_007072 indeed inhibited the functions of OsmiR160 and miR164, respectively (Figure 6C,E-H).	25517485	PLNlncRbase
EL1498	XLOC_009232	N/A	qRT-PCR	reproductive stage	N/A	N/A	XLOC_009232 is specifically expressed in coleoptiles (Figure 5C),and this type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C;Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1504	XLOC_016182	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1505	XLOC_018316	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1506	XLOC_037529	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1507	XLOC_040350	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1508	XLOC_057324	N/A	qRT-PCR	panicle development and fertility	N/A	N/A	More importantly, one lncRNA, XLOC_057324, is demonstrated to play a role in panicle development and fertility. lncRNA (XLOC_057324) that is highly expressed in reproductive organs in relation to its physiological function in rice plants. This lncRNA is specifically expressed in young panicles and pistils (expression was restricted to ovules), suggesting that XLOC_057324 might play a role in regulating panicle and/or pistil development (Figure 7A,B).	25517485	PLNlncRbase
EL1509	XLOC_057981	N/A	qRT-PCR	reproductive stage	N/A	N/A	This type of lncRNA was expressed during the integrated sexual reproduction process (Figure 3C; Additional file 2), indicating that lncRNAs may function throughout the entire reproductive process in rice.	25517485	PLNlncRbase
EL1510	Xlsirts	N/A	molecular beacons	N/A	N/A	expression	Destruction of either of these transcripts results in disruption of the cytokeratin cytoskeleton in a transcript-specific manner and interferes with proper formation of the germinal granules and subsequent development of the germline.	16000384
EL1512	XRN1	N/A	RNA-seq, qRT-PCR	yeast	N/A	N/A	The majority of XUTs strongly accumulate in lithium-containing media, indicating that they might have a role in adaptive responses to changes in growth conditions. Notably, RNAPII chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) analysis of Xrn1-deficient strains revealed a significant decrease of RNAPII occupancy over273 genes with antisense XUTs. These genes show an unusual bias for H3K4me3 marks and require the Set1 histone H3 lysine 4 methyl-transferase for silencing. Furthermore, abolishing H3K4me3 triggers the silencing of other genes with antisense XUTs, supporting a model in which H3K4me3 antagonizes antisense ncRNA repessive activity. Our results demonstrate that antisense ncRNA-mediated regulation is a general regulatory pathway for gene expression in S. cerevisiae.	21697827
EL1513	Yam-1	N/A	ChIP-seq	Mouse C2C12 myoblasts (MBs)	down-regulated	N/A	Yam-1 is positively regulated by YY1, Yam-1 is downregulated upon differentiation and acts as an inhibitor of myogenesis.Yam-1 functions through in cis regulation of miR-715, which in turn targets Wnt7b.	23942234
EL1519	Zfhx2os	N/A	gene-targeting approach	mouse brain	N/A	interaction	The expression of zfh-5 is additionally regulated by a mechanism depending on this antisense rna.	16257534
EL1521	Zm401	N/A	RT-PCR	flower development	up-regulated	N/A	zm401 likely functions in pollen growth and/or development. RT-PCR amplification demonstrated that the ZM13-driven zm401 gene was spatially expressed in tobacco pollens. It was found that all transgenic tobacco plants expressing zm401 showed various levels of sterility, ranging from abortive flower development to male sterility. Further analyses on anther development of transgenic plants indicated multiple abnormalities in the late stages of anther development. These abnormalities include lagged degradation of the tapetum and connective tissue, failed deposition of fibrous bands in endothecium cells, and aborted pollen grain development. These results strongly suggest that zm401 plays an essential role in anther development. However the exact functions of zm401 is still unclear, and further analysis of zm401 is required to determine the exact mechanism involved in anther development.	10.1007/s10681-005-5272-2	PLNlncRbase
EL1522	Zm401	N/A	qRT-PCR	pollens	up-regulated	N/A	Zm401 is involved in the regulation of pollen development. Over expression of Zm401 in maize caused smaller tassels, degenerate or shriveled anthers. Zm401 may be involved in the development of male reproductive organs. Zm401, as a non-coding RNA, plays an essential role in pollen development. Zm401 gene is involved in the late stage of pollen development of maize. Zm401-overexpressed transgenic maize was generated to investigate its function in pollen development. (Dai et al., 2007) Zm401,is expressed specifically in pollens. Forward and reverse genetic studies have shown a function for Zm401 in regulating the expression of critical genes necessary for pollen development including ZmMADS2, MZm3-3 and ZmC5. MZm3-3 was up-regulated in Zm401 mutants while ZmMADS2 and ZmC5 were both down-regulated. Over-expression of Zm401 severely affects pollen development due to abnormal tassels and degenerate anthers. (Au et al., 2011) Zm401 is expressed primarily in the anthers (tapetal cells as well as microspores) in a developmentally regulated manner. That is, it is expressed from floret forming stage, increasing in concentration up to mature pollen. Knockdown of zm401 significantly affected the expression of ZmMADS2, MZm3-3, and ZmC5, critical genes for pollen development. zm401 could be one of the key growth regulators in anther development, the expression of zm401 is associated with the floret development, especially with the development of tapetal cells and microspores. (Ma et al., 2008) ZM401 was specifically or preferentially expressed in mature pollen. ZM401 was transcribed from tetrad stage of microspore development and increased in concentration up to mature pollen, which suggested that ZM401 belongs to lategene in pollen development. (Dai et al., 2004)	21525783, 18465785, 400866	PLNlncRbase
EL1523	Zm401p10	N/A	Western blot/RT-PCR	anther development	up-regulated	N/A	Overexpression of Zm401p10 in maize retarded tapetal degeneration and caused microspore abnormalities. The Zm401 gene is one of the major components of the molecular network regulating maize anther development and male fertility, and that Zm401p10 is expressed from the longest ORF of the gene. Zm401p10 plays a major role in pollen development. Overexpression of Zm401p10 in maize resulted in several severe phenotypes, including retardation of tapetum degeneration, accompanied by pollen abortion or pollen grains with low viability. These data suggest that Zm401p10 acts within the tapetum to promote normal pollen development and postmeiotic tapetal degradation.the overexpression of Zm401p10 did not affect ear development or fertilisation. Zm401p10 might play a role in guiding normal early anther development by maintaining the transcription of cysteine proteinases. Zm401p10 overexpression might abolish tapetum flavonoid biosynthesis and lead to male sterility.	10.1071/FP08187	PLNlncRbase
EL1525	ZmIPS1	N/A	qRT–PCR	phosphate balance	up-regulated	N/A	The expression patterns of other members of the TPSI1/Mt4 family in monocots were also investigated. The induced expressions of OsIPS1, HvIPS1, ZmIPS2 and TalIPS2 were stronger than those of OsIPS2, HvIPS2 ZmIPS1 and TalIPS1 in roots after 4 or 10 d of Pi starvation, whereas higher induced expressions of OsIPS2, HvIPS1, ZmIPS1 and TalIPS1 were detected in shoots.	10.1111/j.1365-3040.2005.01272.x	PLNlncRbase
EL1528	ZNF667-AS1	N/A	microarray, qRT-PCR	isogenic normal finite pre-stasis, abnormal finite post-stasis, and immortal human mammary epithelial cells (HMECs) from 4 individuals	down-regulated	epigenetics	The functional importance of DNA hypermethylation in MORT gene silencing is supported by the ability of 5-aza-2'-deoxycytidine to reactivate MORT expression. Analysis of TCGA data revealed deregulation of MORT expression due to DNA hypermethylation in 15 out of the 17 most common human cancers.	26646903
EL1530	ZPR4	N/A	qRT-PCR/RT-PCR	cold, drought and highlight	up-regulated	N/A	We found that 303 lncRNAs (including 245 poly (A)+ and 58 poly(A)- lncRNAs) were differentially expressed under at least one of the stress conditions, lncRNA AT2G36307 is upregulated by cold/drought/highlight stresses.(details are listed in Appendix S2)	25256571	PLNlncRbase
EL1299	TCONS_00049512	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	In our study, ptc-miR1445 was predicted to target TCONS_00049512, which has been predicted to function in cleaving the transcripts of development-related or stress responsive genes in Populus (Lu et al. 2008). Besides ptc-miR1445, miRNAs that were specifically expressed in xylem and reportedly participate in formation of tension wood (Lu et al. 2005, 2008; Puzey et al. 2012) were predicted to regulate some of the lncRNAs identified in our study. For example, ptr-miR172, which was only suppressed in compression tissue (Lu et al. 2005), may target TCONS_00012272 and TCONS_00012273, which were detected in our study and showed a type C expression pattern (TW	25230698	PLNlncRbase
EL1276	TCONS_00012273	N/A	RNA-seq/qRT-PCR	wood formation	up-regulated	N/A	In our study, ptc-miR1445 was predicted to target TCONS_00049512, which has been predicted to function in cleaving the transcripts of development-related or stress responsive genes in Populus (Lu et al. 2008). Besides ptc-miR1445, miRNAs that were specifically expressed in xylem and reportedly participate in formation of tension wood (Lu et al. 2005, 2008; Puzey et al. 2012) were predicted to regulate some of the lncRNAs identified in our study. For example, ptr-miR172, which was only suppressed in compression tissue (Lu et al. 2005), may target TCONS_00012272 and TCONS_00012273, which were detected in our study and showed a type C expression pattern (TW	24892290	PLNlncRbase
EL1294	TCONS_00039944	N/A	RNA-seq/qRT-PCR	wood formation	down-regulated	N/A	Figure 9a shows that a negative relationship between miRNAs and their potential target lncRNAs were detected; for example, miR2 (Ptc-miR168b-5p) is expressed in OW(OW	25230698	PLNlncRbase
EL1531	Apela	N/A	RNA-Seq, Rescue and overexpression, knockdown, In situ hybridization	N/A	N/A	interaction	Toddler is annotated as a non-coding RNA in zebrafish (ENSDARG00000094729), mouse [Gm10664; also called Ende], and human (LOC100506013) and is present in two lncRNA catalogs; however, it contains a 58–amino acid ORF with a predicted signal sequence and high conservation in vertebrates, including human. Local and ubiquitous production of Toddler promote cell movement, suggesting that Toddler is neither an attractant nor a repellent but acts globally as a motogen.	24407481
EL1532	APELA	N/A	RNA-Seq, Rescue and overexpression, knockdown, In situ hybridization	N/A	N/A	interaction	Toddler is annotated as a non-coding RNA in zebrafish (ENSDARG00000094729), mouse [Gm10664; also called Ende], and human (LOC100506013) and is present in two lncRNA catalogs; however, it contains a 58–amino acid ORF with a predicted signal sequence and high conservation in vertebrates, including human. Local and ubiquitous production of Toddler promote cell movement, suggesting that Toddler is neither an attractant nor a repellent but acts globally as a motogen.	26387754, 25639753, 20153842, 24316148, 24407481
EL1533	apela	N/A	RNA-Seq, Rescue and overexpression, knockdown, In situ hybridization	early zebrafish embryogenesis	N/A	interaction	Toddler is annotated as a non-coding RNA in zebrafish (ENSDARG00000094729), mouse [Gm10664; also called Ende], and human (LOC100506013) and is present in two lncRNA catalogs; however, it contains a 58–amino acid ORF with a predicted signal sequence and high conservation in vertebrates, including human. Local and ubiquitous production of Toddler promote cell movement, suggesting that Toddler is neither an attractant nor a repellent but acts globally as a motogen.	24407481
EL0388	ENOD40-1	N/A	Western blotting, peptide mass fingerprinting	nodules	N/A	expression	In vitro translation of soybean ENOD40 mRNA in wheat germ extracts revealed that the conserved nucleotide sequence at the 5′ end (region I) encodes two peptides of 12 and 24 aa residues (peptides A and B). ENOD40 peptides are involved in the control of sucrose use in nitrogen-fixing nodules.	11842184
EL1534	Gm34302	N/A	Northern Blot, Western Blot, Co-immunoprecipitations (CoIPs)	Knockout mice, Transgenic mice	N/A	interaction	DWORF is a transmembrane peptide that interacts with SERCA proteins and enhances muscle contractility	26816378
EL1535	DWORF	N/A	Northern Blot, Western Blot, Co-immunoprecipitations (CoIPs)	Human Heart Failure Tissue	N/A	interaction	We discovered a putative muscle-specific long noncoding RNA that encodes a peptide of 34 amino acids and that we named dwarf open reading frame (DWORF).	26816378
EL1536	MRLN	N/A	Radioisotopic In Situ Hybridization, Co-immunoprecipitations and Western Blot Analysis, Real-time PCR	N/A	N/A	interaction	We discovered a conserved micropeptide, which we named myoregulin (MLN), encoded by a skeletal muscle-specific RNA annotated as a putative long noncoding RNA. MLN as an important regulator of skeletal muscle physiology.	25640239
EL1537	Mrln	N/A	Radioisotopic In Situ Hybridization, Co-immunoprecipitations and Western Blot Analysis, Real-time PCR	pseudopregnant female ICR mice	N/A	interaction	We discovered a conserved micropeptide, which we named myoregulin (MLN), encoded by a skeletal muscle-specific RNA annotated as a putative long noncoding RNA. MLN as an important regulator of skeletal muscle physiology.	25640239
EL1538	SclA	N/A	RT-PCR, in situ hybridization	Drosophila heart	N/A	interaction	We describe two peptides of less than 30 amino acids regulating calcium transport, and hence influencing regular muscle contraction, in the Drosophila heart.	23970561
EL1539	SclB	N/A	RT-PCR, in situ hybridization	Drosophila heart	N/A	interaction	We describe two peptides of less than 30 amino acids regulating calcium transport, and hence influencing regular muscle contraction, in the Drosophila heart.	23970561
EL1540	tal-1A	N/A	Immunohistochemistry, In situ hybridisation, sequencing	N/A	N/A	expression	tal function is mediated by several 33-nucleotide–long open reading frames (ORFs), which are translated into 11-amino-acid–long peptides.	17486114, 17439302
EL1541	tal-2A	N/A	Immunohistochemistry, In situ hybridisation, sequencing	N/A	N/A	expression	tal function is mediated by several 33-nucleotide–long open reading frames (ORFs), which are translated into 11-amino-acid–long peptides.	17486114, 17439302
EL1542	tal-3A	N/A	Immunohistochemistry, In situ hybridisation, sequencing	N/A	N/A	expression	tal function is mediated by several 33-nucleotide–long open reading frames (ORFs), which are translated into 11-amino-acid–long peptides.	17486114, 17439302
EL1543	tal-AA	N/A	Immunohistochemistry, In situ hybridisation, sequencing	N/A	N/A	expression	tal function is mediated by several 33-nucleotide–long open reading frames (ORFs), which are translated into 11-amino-acid–long peptides.	17486114, 17439302