1	7SK	ABO	RNA-RNA	Regulatory	Promoters pU6 and p7SK proved to express high levels of siRNA activity and can be used in the experiment of silencing alpha-1,3galactosyltransferase gene.	Human	RN7SK; 7SK	NR_001445.2	22522162
2	7SK	Ars2	RNA-Protein	Regulatory	Ars2 contributes to histone mRNA 3'end formation and expression and these functional properties of Ars2 are negatively regulated by interaction with 7SK RNA.	Human	RN7SK; 7SK	NR_001445.2	22244333
3	7SK	BCDIN3	RNA-Protein	Regulatory	BCDIN3 is the 7SK snRNA methylphosphate capping enzyme (MePCE) present in an snRNP complex containing both RNA processing and transcription factors, including the elongation factor P-TEFb.	Human	RN7SK; 7SK	NR_001445.2	17643375
4	7SK	CDK9	RNA-Protein	Regulatory	Stable expression of cdNIPP1 increased CDK9 phosphorylation on Thr(186) and the association of CDK9 with 7SK RNA. The stable expression of cdNIPP1 disrupted the interaction of Tat and PP1 and inhibited HIV-1 transcription. Expression of cdNIPP1 as a part of the HIV-1 genome inhibited HIV-1 replication.	Human	RN7SK; 7SK	NR_001445.2	21098020
5	7SK	HEXIM1	RNA-Protein	binding	The Hexim1 binding site is located in the 24-87 region of 7SK RNA and that the protein residues outside the basic domain of Hexim1 are involved in specific RNA interactions.	Human	RN7SK; 7SK	NR_001445.2	19244621
6	7SK	HEXIM1	RNA-Protein	binding	Binding of the 7SK snRNA turns the HEXIM1 protein into a P-TEFb (CDK9/cyclin T) inhibitor.	Human	RN7SK; 7SK	NR_001445.2	15201869
7	7SK	HEXIM1	RNA-Protein	binding	When associated with 7SK small nuclear RNA, HEXIM1 binds to P-TEFb and inhibits the kinase activity of P-TEFb.	Human	RN7SK; 7SK	NR_001445.2	17671421
8	7SK	HEXIM1	RNA-Protein	binding	7SK RNA binding to a HEXIM1 multimer promotes the simultaneous recruitment and hence inactivation of multiple P-TEFb units.	Human	RN7SK; 7SK	NR_001445.2	15994294
9	7SK	HEXIM1	RNA-Protein	binding	HEXIM1 suppresses transcription elongation via sequestration of positive transcription elongation factor b (P-TEFb) using 7SK RNA  as a scaffold.	Human	RN7SK; 7SK	NR_001445.2	18407829
10	7SK	HEXIM1	RNA-Protein	binding	The activity of P-TEFb is negatively regulated by an RNA-binding protein HEXIM1 in association with 7SK snRNA.	Human	RN7SK; 7SK	NR_001445.2	22609015
11	7SK	HEXIM1	RNA-Protein	binding	HEXIM1 targets a repeated GAUC motif in the riboregulator of transcription 7SK and promotes base pair rearrangements.	Human	RN7SK; 7SK	NR_001445.2	20675720
12	7SK	HEXIM1	RNA-Protein	binding	Although HEXIM1 binds tightly to 7SK RNA in vitro, release of P-TEFb from the 7SK snRNP is accompanied by the loss of HEXIM1.	Human	RN7SK; 7SK	NR_001445.2	20808803
13	7SK	HEXIM1	RNA-Protein	binding	Dissociation of 7SK and HEXIM1 from P-TEFb promotes P-TEFb kinase activity, and thus enhances Pol II elongation	Human	RN7SK; 7SK	NR_001445.2	19239885
14	7SK	HEXIM1	RNA-Protein	binding	Human T-lymphotropic virus type 1 Tax protein complexes with P-TEFb and competes for Brd4 and 7SK snRNP/HEXIM1 binding. Tax can play a role in regulating the amount of HMW complex present in the cell by decreasing the binding of 7SK snRNP/HEXIM1 to P-TEFb.	Human	RN7SK; 7SK	NR_001445.2	20926576
15	7SK	hLARP7	RNA-Protein	binding	7SK snRNP assembly by hLARP7/PIP7S	Human	RN7SK; 7SK	NR_001445.2	20138158
16	7SK	HMGA1	RNA-Protein	binding	We provide evidence for 7SK RNA complexes containing simultaneously HMGA1 and P-TEFb.	Human	RN7SK; 7SK	NR_001445.2	21957495
17	7SK	HMGA1	RNA-Protein	Binding	7SK snRNA directly interacts through its loop2 (7SK L2) with the first A/T-hook DNA binding motif of HMGA1.	Human	RN7SK; 7SK	NR_001445.2	21282977
18	7SK	HMGA1	RNA-Protein	binding	The 7SK-HMGA1 interaction not only adds an essential facet to the comprehension of transcriptional plasticity at the coupling of initiation and elongation, but also might provide a molecular link between HIV reprogramming of cellular gene expression-associated oncogenesis.	Human	RN7SK; 7SK	NR_001445.2	21087998
19	7SK	LARP7	RNA-Protein	binding	LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated.	Human	RN7SK; 7SK	NR_001445.2	18281698
20	7SK	LARP7	RNA-Protein	binding	LARP7 negatively regulates positive transcription elongation factor-b (p-TEFb) by binding to and stabilizing 7sk RNA.	Human	RN7SK; 7SK	NR_001445.2	22488152
21	7SK	LARP7	RNA-Protein	binding	The La-related protein LARP7 is a component of the 7SK ribonucleoprotein and affects transcription of cellular and viral polymerase II genes.	Human	RN7SK; 7SK	NR_001445.2	18483487
22	7SK	LARP7	RNA-Protein	binding	PIP7S binds and stabilizes nearly all the nuclear 7SK via 3'-UUU-OH, leading to the sequestration and inactivation of P-TEFb.	Human	RN7SK; 7SK	NR_001445.2	18249148
23	7SK	LARP7	RNA-Protein	Regulatory	The Lupus antigen (La)-related protein 7 (LARP7) is a constitutive component, the methylphosphate capping enzyme (MePCE) associates secondarily to phosphorylate the 5' end of 7SK snRNA.	Human	RN7SK; 7SK	NR_001445.2	21853533
24	7SK	OCT1	DNA-TF	Regulatory	PTF and Oct-1 enhance transcription from the 7SK promoter in an interdependent manner.	Human	RN7SK; 7SK	NR_001445.2	1535687
25	7SK	PIP7S	RNA-Protein	binding	7SK snRNP assembly by hLARP7/PIP7S	Human	RN7SK; 7SK	NR_001445.2	20138158
26	7SK	PP1a	RNA-Protein	Regulatory	PP2B and PP1alpha cooperatively disrupt 7SK snRNP to release P-TEFb for transcription in response to Ca2+ signaling.	Human	RN7SK; 7SK	NR_001445.2	18483222
27	7SK	PP2B	RNA-Protein	Regulatory	PP2B and PP1alpha cooperatively disrupt 7SK snRNP to release P-TEFb for transcription in response to Ca2+ signaling.	Human	RN7SK; 7SK	NR_001445.2	18483222
28	7SK	P-TEFb	RNA-Protein	binding	Together with the HEXIM proteins, 7SK RNA associates with and sequesters a fraction of cellular P-TEFb into a catalytically inactive complex.	Human	RN7SK; 7SK	NR_001445.2	22377309
29	7SK	P-TEFb	RNA-Protein	binding	We provide evidence for 7SK RNA complexes containing simultaneously HMGA1 and P-TEFb.	Human	RN7SK; 7SK	NR_001445.2	21957495
30	7SK	P-TEFb	RNA-Protein	binding	TCR signaling led to the rapid dissociation of the large inactive P-TEFb:7SK RNP (small nuclear RNA 7SK ribonucleoprotein) complex and the release of active low-molecular-weight P-TEFb complexes.	Human	RN7SK; 7SK	NR_001445.2	21763495
31	7SK	P-TEFb	RNA-Protein	binding	Tat has been shown to bind 7SK directly and recruit P-TEFb to TAR.	Human	RN7SK; 7SK	NR_001445.2	20816986
32	7SK	P-TEFb	RNA-Protein	Regulatory	The kinase activity of P-TEFb is reversibly inhibited by formation of a complex with the 334nt 7SK RNA, from which it is released under conditions of stress.	Human	RN7SK; 7SK	NR_001445.2	22303389
33	7SK	P-TEFb	RNA-Protein	Regulatory	Regulation of P-TEFb by the d7SK snRNP is essential for the growth and differentiation of tissues required during Drosophila development.	Human	RN7SK; 7SK	NR_001445.2	22379134
34	7SK	P-TEFb	RNA-Protein	Regulatory	Dissociation of 7SK and HEXIM1 from P-TEFb promotes P-TEFb kinase activity, and thus enhances Pol II elongation.	Human	RN7SK; 7SK	NR_001445.2	19239885
35	7SK	PTF	DNA-TF	Regulatory	PTF and Oct-1 enhance transcription from the 7SK promoter in an interdependent manner.	Human	RN7SK; 7SK	NR_001445.2	1535687
36	7SK	Tat	RNA-Protein	binding	HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP.	Human	RN7SK; 7SK	NR_001445.2	20471949
37	7SK	Tat	RNA-Protein	binding	Tat efficiently replaces HEXIM1 on the 7SK snRNA in vivo and therefore, it promotes the disassembly of the 7SK/HEXIM/P-TEFb negative transcriptional regulatory snRNP to augment the nuclear level of active P-TEFb.	Human	RN7SK; 7SK	NR_001445.2	20976203
38	7SL	APOBEC3F	RNA-Protein	binding	Interaction with 7SL RNA but not with HIV-1 genomic RNA or P bodies is required for APOBEC3F virion packaging.	Human	RN7SL1; 7SL; 7L1a; RN7SL; RNSRP1	NR_002715.1	18067920
39	7SL	BRF1	DNA-TF	Regulatory	hBRF1 functions at 7SL promoter.	Human	RN7SL1; 7SL; 7L1a; RN7SL; RNSRP1	NR_002715.1	10921893
40	7SL	MnSOD	RNA-RNA	binding/Regulatory	The 7SL cytoplasmic non-coding RNA, thought to be related to the common ancestor sequence of Alu repeats, hybridizes to the reverse-Alu-element-containing 3′UTR of the human nuclear-encoded mitochondrial MnSOD gene, repressing MnSOD expression by mechanisms distinct from control of translational initiation.	Human	RN7SL1; 7SL; 7L1a; RN7SL; RNSRP1	NR_002715.1	20951849
41	7SL	SRP19	RNA-Protein	binding	SRP19 synthesized in a cell-free system specifically bound to 7SL RNA.	Human	RN7SL1; 7SL; 7L1a; RN7SL; RNSRP1	NR_002715.1	2460823
42	7SL	SRP54	RNA-Protein	binding	SRP54 may be linked to the rest of SRP through this domain by a direct interaction with 7SL RNA.	Human	RN7SL1; 7SL; 7L1a; RN7SL; RNSRP1	NR_002715.1	1702385
43	A130040M12Rik	PSF	RNA-Protein	binding	VL30-1 RNA binds and releases PSF from Rab23.	Mouse	A130040M12Rik; VL30; CA782090; H3053C11	NR_002860.2	19805375
44	A130040M12Rik	PSF	RNA-Protein	binding	Binding of mouse VL30 (A130040M12Rik) retrotransposon RNA to PSF protein induces genes repressed by PSF: effects on steroidogenesis and oncogenesis.	Mouse	A130040M12Rik; VL30; CA782090; H3053C11	NR_002860.2	14704271
45	AF087999	FLJ21870	RNA-RNA	Co-expression	Half-sbsRNA1 siRNA increased the levels of SERPINE1 and FLJ21870 mRNAs to 2-to-4.5-fold above normal.	Human	RBM4; LARK; RBM4A; ZCRB3A; ZCCHC21	AF087999	21307942
46	AF087999	SERPINE1	RNA-RNA	Co-expression	Half-sbsRNA1 siRNA increased the levels of SERPINE1 and FLJ21870 mRNAs to 2-to-4.5-fold above normal.	Human	RBM4; LARK; RBM4A; ZCRB3A; ZCCHC21	AF087999	21307942
47	Airn	G9a	RNA-Protein	binding	Airn transcription unit recruits G9a to its target promoter to bring about gene silencing	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	21925379
48	Airn	G9a	RNA-Protein	binding	The antisense transcript AIRN that is associated with the chromatin-modifying complex G9a.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	19571010
49	Airn	G9a	RNA-Protein	binding	The Airn lncRNA was found to coat its target genes but instead recruits the G9a histone methyltransferase rather than the subunits of PRC2	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	21874119
50	Airn	G9a	RNA-Protein	binding	The Airn noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Airn accumulates at the Slc22a3 promoter in correlation with localized H3K9 methylation and transcriptional repression.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	18988810
51	Airn	G9a	RNA-Protein	binding	Recruits G9a histone methyltransferase to epigenetically silence some target genes.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	11845212
52	Airn	G9a	RNA-Protein	binding	The Airn RNA also binds to G9a and appears to target this enzyme to a silenced gene in the cluster.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	19239885
53	Airn	Ig2fr	RNA-RNA	Co-expression	Neuron-specific lack of Airn expression results in neuronspecific lack of silencing at the Ig2fr locus.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	18184812
54	Airn	Igf2r	DNA-DNA	Regulatory	Deletion of the Airn promoter on the paternal allele results in aberrant activation of paternal Igf2r, Slc22a2, and Slc22a3 genes in cis.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	19727951
55	Airn	Igf2r	DNA-DNA	Regulatory	A CpG island (CGI) lies at the 5' end of the Airn macro non-protein-coding (nc) RNA that represses the flanking Igf2r promoter in cis on paternally inherited chromosomes.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	22396659
56	Airn	Igf2r	RNA-DNA	Regulatory	Controls Igf2r imprinting cluster in mouse	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	16874305
57	Airn	Igf2r	RNA-RNA	Co-expression	Insertion of a polyadenylation cassette leading to truncation of the Air transcript resulted in the derepression of imprinted genes in the locus, which is suggestive of a direct role for long ncRNAs in imprinting of insulin-like growth factor 2 receptor (Igf2r).	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	21831473
58	Airn	Slc22a2	DNA-DNA	Regulatory	Deletion of the Airn promoter on the paternal allele results in aberrant activation of paternal Igf2r, Slc22a2, and Slc22a3 genes in cis.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	19727951
59	Airn	Slc22a3	DNA-DNA	Regulatory	Deletion of the Airn promoter on the paternal allele results in aberrant activation of paternal Igf2r, Slc22a2, and Slc22a3 genes in cis.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	19727951
60	Airn	Slc22a3	RNA-DNA	Regulatory	The Airn noncoding RNA epigenetically silences transcription by targeting G9a to chromatin.  Air accumulates at the Slc22a3 promoter in correlation with localized H3K9 methylation and transcriptional repression.	Mouse	Airn; Air; AI256653; AI597500; AW049873; D17Ertd663e; 2810051F02Rik; 2810434M15Rik; B930018I07Rik	NR_002853.2	18988810
61	AK017619	Dab2	RNA-RNA	Co-expression	The expression profiles of Dab2 and the intronic ncRNA were correlated (R2 = 0.77), suggesting some relationship in their function and/or regulation.	Mouse	Dab2; p96; Doc2; Doc-2; AA960054; AI957090; D15Wsu122e; 5730435J12Rik; D630005B22Rik	12856954	18562676
62	AK018581	Gata6	RNA-RNA	Co-expression	The expression of Gata6bt was negatively correlated with Gata6, being up-regulated during pluripotent EB stages and down-regulated during progressive lineage specification.	Mouse	9130001E16Rik	12858360	18562676
63	AK020764	mir-142-3p	RNA-RNA	Co-expression	Two miRNAs, mir-142-5p and mir-142-3p, recently shown to be among the most highly expressed miRNAs in naive, memory, and effector CD8  T cell populations (76), are hosted within the first intron of a long ncRNA (AK020764) that is also strongly expressed in CD8  T cells.	Mouse	A430104N18Rik; AW909330	12861450	19494298
64	AK020764	mir-142-5p	RNA-RNA	Co-expression	Two miRNAs, mir-142-5p and mir-142-3p, recently shown to be among the most highly expressed miRNAs in naive, memory, and effector CD8  T cell populations (76), are hosted within the first intron of a long ncRNA (AK020764) that is also strongly expressed in CD8  T cells.	Mouse	A430104N18Rik; AW909330	12861450	19494298
65	AK021368	Cox2	RNA-RNA	Co-expression	AK021368 and Cox2 exhibit overlapping expression profiles in the cerebral cortex, raising the possibility that a similar regulatory mechanism occurs in the brain.	Mouse	E130102H24Rik	12862239	18184812
66	AK028326	Oct1	DNA-TF	Regulatory	AK028326 is activated by the transcription factor OCT4.	Mouse	Miat; Rncr2; gomafu; 3632434I06; A230057G18Rik	26080813	20026622
67	AK044422	Ptbp1	RNA-RNA	Co-expression	Ptbp1 and AK044422 exhibit complementary expression profiles.	Mouse	A930011O12Rik; Rncr3	26090347	20137068
68	AK045070	Coup-TfII	RNA-RNA	Co-expression	We also have identified a candidate imprinted long antisense ncRNA, AK045070, that encompasses >45 kb and shows expression within the thalamus, pyramidal cells in the ventral hippocampus, and cortical amygdalar area. The adjacent candidate imprinted expressed gene, Coup-TfII, an important nuclear receptor involved in regulating various hormonal and brain functions, also exhibits a similar expression profile within these regions	Mouse	B130024G19Rik	26337048	18184812
69	AK053922	Gli3	RNA-RNA	Co-expression	The downregulation of a ncRNA (AK053922) is associated with the Gli3 locus in all progeny of N/OPs, whereas Gli3 was upregulated in N/OPs but downregulated in all progeny of N/Ops.	Mouse	Gli3; Xt; Bph; Pdn; add; GLI3FL; AI854843; AU023367; GLI3-190	26096052	20137068
70	AK133808	Rab11b	RNA-RNA	Co-expression	A variety of ncRNAs were broadly upregulated in OLPs, PMOs and MYOs including AK141895 and AK133808, associated with the Slc44a1 and Rab11b genomic loci, respectively.	Mouse	N/A	74228720	20137068
71	AK133808	Slc44a1	RNA-RNA	Co-expression	A variety of ncRNAs were broadly upregulated in OLPs, PMOs and MYOs including AK141895 and AK133808, associated with the Slc44a1 and Rab11b genomic loci, respectively.	Mouse	N/A	74228720	20137068
72	AK141205	Nanog	DNA-TF	Regulatory	AK141205 is repressed by the transcription factor Nanog.	Mouse	Rbfa; AI595940; 1110032A13Rik	74189920	20026622
73	AK141895	Rab11b	RNA-RNA	Co-expression	A variety of ncRNAs were broadly upregulated in OLPs, PMOs and MYOs including AK141895 and AK133808, associated with the Slc44a1 and Rab11b genomic loci, respectively.	Mouse	Slc44a1; CTL1; CHTL1; Cdw92; AW547365; 2210409B22Rik; 4833416H08Rik	74202641	20137068
74	AK141895	Slc44a1	RNA-RNA	Co-expression	A variety of ncRNAs were broadly upregulated in OLPs, PMOs and MYOs including AK141895 and AK133808, associated with the Slc44a1 and Rab11b genomic loci, respectively.	Mouse	Slc44a1; CTL1; CHTL1; Cdw92; AW547365; 2210409B22Rik; 4833416H08Rik	74202641	20137068
75	AK154427	Ecsit	RNA-RNA	Co-expression	A cisantisense ncRNA (GenBank accession no. AK154427) exhibits a negative expression correlation (R2= -0.92) with its sense protein-coding gene Ecsit.	Mouse	Gm16845	74181733	18562676
76	asOct4-pg5	Oct4	RNA-RNA	Regulatory	These results indicate that the lncRNA asOct4-pg5 may function to regulate multiple Oct4 related transcripts.	N/A	N/A	N/A	21151833
77	ATXN8OS	GAT4	RNA-RNA	Co-expression	SCA8 CUG(exp) transcripts trigger splicing changes and increased expression of the CUGBP1-MBNL1 regulated CNS target, GABA-A transporter 4 (GAT4/Gabt4).	Human	ATXN8OS; SCA8; KLHL1AS; NCRNA00003	NR_002717.2	19680539
78	B2 SINE RNA	actin	RNA-RNA	Co-expression	Upon stress conditions such as heat shock, B2 expression is dramatically enhanced leading to repression of transcription for genes such as actin and hexokinase II.	Mouse	N/A	N/A	19239885
79	B2 SINE RNA	ALAS1	DNA-DNA	Regulatory	A B2 SINE can contribute to the regulation of ALAS1 and SINEs in 5'-UTR regions contribute to inter-individual differences in gene expression.	Mouse	N/A	N/A	18929534
80	B2 SINE RNA	CELO	DNA-TF	Regulatory	CELO protein Gam1 was able to mediate transcriptional activation of these B2 SINE-containing RNAs.	Mouse	N/A	N/A	12729754
81	B2 SINE RNA	Comt1	DNA-DNA	Regulatory	Comt1 is differentially expressed among the strains, and this differential expression is cis-regulated. A B2 short interspersed nuclear element (SINE) was inserted in the 3'-untranslated region (3'-UTR) of Comt1 in 14 strains generating a common haplotype that correlates with gene expression. A haplotype, defined by a 3'-UTR B2 SINE element, regulates Comt1 expression and some mouse behaviors.	Mouse	N/A	N/A	20659173
82	B2 SINE RNA	Comt1	DNA-DNA	Regulatory	A B2 SINE insertion in the Comt1 gene (Comt1(B2i)) results in an overexpressing, behavior modifying allele present in classical inbred mouse strains.Comt1(B2i) (a B2 SINE insertion) results in a relatively modest difference in Comt1 expression and enzyme activity (comparable to the human Val-Met polymorphism) which has a demonstrable behavioral phenotype across a variety of outbred genetic backgrounds.	Mouse	N/A	N/A	20618449
83	B2 SINE RNA	hexokinase II	RNA-RNA	Co-expression	Upon stress conditions such as heat shock, B2 expression is dramatically enhanced leading to repression of transcription for genes such as actin and hexokinase II.	Mouse	N/A	N/A	19239885
84	B2 SINE RNA	RNA polymerase II	DNA-DNA	Regulatory	Transposable B2 SINE elements can provide mobile RNA polymerase II promoters.	Mouse	N/A	N/A	11326281
85	B2 SINE RNA	RNA polymerase II	RNA-Protein	binding	A 33-nt piece of B2 RNA binds RNA polymerase II, associates with preinitiation complexes, but cannot repress transcription.	Mouse	N/A	N/A	17307818
86	BACE1-AS	APP	RNA-Protein	Regulatory	BACE1-AS is directly implicated in the increased abundance of Aβ 1–42 in Alzheimer’s disease.	Human	BACE1-AS; BACE1AS; FJ573250; BACE1-AS1; NCRNA00177	NR_037803.1	18587408
87	BACE1-AS	BACE1	RNA-RNA	Co-expression	We report here that BACE1-antisense prevents miRNA-induced repression of BACE1 mRNA by masking the binding site for miR-485-5p. Indeed, miR-485-5p and BACE1-antisense compete for binding within the same region in the open reading frame of the BACE1 mRNA.	Human	BACE1-AS; BACE1AS; FJ573250; BACE1-AS1; NCRNA00177	NR_037803.1	20507594
88	BACE1-AS	BACE1	RNA-RNA	Regulatory	The BACE1-antisense transcript (BACE1-AS) regulates BACE1 mRNA and subsequently BACE1 protein expression in vitro and in vivo.expression of BACE1-AS increases BACE1 mRNA stability.	Human	BACE1-AS; BACE1AS; FJ573250; BACE1-AS1; NCRNA00177	NR_037803.1	18587408
89	BACE1-AS	miR-485-5p	RNA-RNA	Regulatory	We report here that BACE1-antisense prevents miRNA-induced repression of BACE1 mRNA by masking the binding site for miR-485-5p. Indeed, miR-485-5p and BACE1-antisense compete for binding within the same region in the open reading frame of the BACE1 mRNA.	Human	BACE1-AS; BACE1AS; FJ573250; BACE1-AS1; NCRNA00177	NR_037803.1	20507594
90	BCYRN1	eIF4A	RNA-Protein	Binding	Inhibits translation. Binds PABP, SRP9/14 heterodimer and eIF4A.	Human	BCYRN1; BC200; BC200a; LINC00004; NCRNA00004	NR_001568.1	18316401
91	BCYRN1	PABP	RNA-Protein	Binding	Inhibits translation. Binds PABP, SRP9/14 heterodimer and eIF4A.	Human	BCYRN1; BC200; BC200a; LINC00004; NCRNA00004	NR_001568.1	7684772
92	BCYRN1	SRP9/14 heterodimer	RNA-Protein	Binding	Inhibits translation. Binds PABP, SRP9/14 heterodimer and eIF4A.	Human	BCYRN1; BC200; BC200a; LINC00004; NCRNA00004	NR_001568.1	17175535
93	BCYRN1P2	FMR1	RNA-Protein	binding	The neural phenotype of BC1 (BCYRN1P2) is consistent with its known interaction with both FMRP, the product of the fragile X mental retardation gene (FMR1), and with mRNAs regulated by FMRP.	Human	BCYRN1P2; BC200g	NG_001085.2?from=101&to=289&report=genbank	19239885
94	BDNF-AS1	BDNF	RNA-RNA	binding	BDNF and antiBDNF transcripts form dsRNA duplexes in the brain in vivo, suggesting an important role for antiBDNF in regulating BDNF expression in human.	Human	BDNF-AS; BDNF; BDNFOS; BDNF-AS1; ANTI-BDNF; NCRNA00049	NR_002832.2	17629449
95	BDNF-AS1	BDNF	RNA-RNA	binding	Human BDNF mRNA and BDNFOS (Opposite Strand) lncRNA form in-vivo RNA–RNA duplexes in brain, suggesting the possibility of post-transcriptional cis-regulation, by BDNFOS, of BDNF.	Human	BDNF-AS; BDNF; BDNFOS; BDNF-AS1; ANTI-BDNF; NCRNA00049	NR_002832.2	20951849
96	bxd	Ubx	DNA-DNA	Regulatory	bxd contains enhancer elements for the nearby Ubx gene.	Drosophila melanogaster	bxd; CR31273; CR31277; Dmel\CR31273	NR_002035.1	19191220
97	bxd	Ubx	RNA-RNA	Co-expression	Ubx and several bxd ncRNAs are expressed in nonoverlapping patterns in both embryos and imaginal discs, suggesting that transcription of these ncRNAs is associated with repression, not activation, of Ubx.	Drosophila melanogaster	bxd; CR31273; CR31277; Dmel\CR31273	NR_002035.1	17174895
98	C1QTNF9B-AS1	SET	RNA-Protein	Regulatory	PCOTH, a novel gene overexpressed in prostate cancers, promotes prostate cancer cell growth through phosphorylation of oncoprotein TAF-Ibeta/SET.	Human	C1QTNF9B-AS1; PCOTH	BC073902	15930275
99	CAR Intergenic 10	ADAM12	RNA-DNA	Regulatory	Regulates gene expression of FANK1 and ADAM12 flanking genes through modulating the chromatin structure in cis.	Human	SMC1A; SMC1; SMCB; CDLS2; SB1.8; SMC1L1; DXS423E; SMC1alpha	NG_006988.1?from=5001&to=53549&report=genbank	20404130
100	CAR Intergenic 10	FANK1	RNA-DNA	Regulatory	Regulates gene expression of FANK1 and ADAM12 flanking genes through modulating the chromatin structure in cis.	Human	SMC1A; SMC1; SMCB; CDLS2; SB1.8; SMC1L1; DXS423E; SMC1alpha	NG_006988.1?from=5001&to=53549&report=genbank	20404130
101	CBR3-AS1	AR	RNA-Protein	Regulatory	The prostate cancer-up-regulated long noncoding RNA PlncRNA-1 modulates apoptosis and proliferation through reciprocal regulation of androgen receptor.	Human	CBR3-AS1; PlncRNA-1	NR_038892.1	22264502
102	CDKN2B-AS1	ARF	RNA-DNA	Regulatory	Binding to RNA contributes to CBX7 function and disruption of either interaction impacts the ability of CBX7 to repress the INK4b/ARF/INK4a locus and control senescence.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	20541999
103	CDKN2B-AS1	CBX7	RNA-Protein	binding	Chromobox 7 (CBX7) within the polycomb repressive complex 1 (PRC1) binds to ANRIL.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	20541999
104	CDKN2B-AS1	CBX7	RNA-Protein	binding	ANRIL was also found to coimmunoprecipitate with CBX7, which is component of the polycomb repressive complex 1 (PRC1).	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21874119
105	CDKN2B-AS1	CBX7	RNA-Protein	Binding	Chromobox 7 (CBX7) within the polycomb repressive complex 1 (PRC1) has been shown to bind to ANRIL	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	20956613
106	CDKN2B-AS1	CBX7	RNA-Protein	binding	Here we report that chromobox 7 (CBX7) within the polycomb repressive complex 1 binds to ANRIL, and both CBX7 and ANRIL are found at elevated levels in prostate cancer tissues.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	20541999
107	CDKN2B-AS1	E2F1	DNA-TF	Regulatory	ANRIL is implicated in the regulation of nucleus and potential transcriptional target of E2F1.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	20664976
108	CDKN2B-AS1	INK4a	RNA-DNA	Regulatory	Binding to RNA contributes to CBX7 function and disruption of either interaction impacts the ability of CBX7 to repress the INK4b/ARF/INK4a locus and control senescence.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	20541999
109	CDKN2B-AS1	INK4b	RNA-DNA	Regulatory	Binding to RNA contributes to CBX7 function and disruption of either interaction impacts the ability of CBX7 to repress the INK4b/ARF/INK4a locus and control senescence.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	20541999
110	CDKN2B-AS1	p15	RNA-DNA	Regulatory	RNA immunoprecipitation demonstrates that ANRIL binds to SUZ12 in vivo. Collectively, these results suggest a model in which ANRIL binds to and recruits PRC2 to repress the expression of p15(INK4B) locus.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21151178
111	CDKN2B-AS1	p15INK4B	RNA-RNA	Co-expression	full-length ANRIL was shown to repress p15INK4B expression. Induction of p15INK4B and p16INK4A by oncogenic Ras was found to repress ANRIL expression.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21874119
112	CDKN2B-AS1	p16INK4A	RNA-RNA	Co-expression	induction of p15INK4B and p16INK4A by oncogenic Ras was found to repress ANRIL expression.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21874119
113	CDKN2B-AS1	PcG	RNA-Protein	Binding	PcG repress the expression of INK4b-ARF-INK4a locus by directly binding to the long noncoding RNA (lncRNA) transcript antisense noncoding RNA in the INK4 locus (ANRIL).	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21828241
114	CDKN2B-AS1	PcG	RNA-Protein	binding	The important role of PcG in mediating repression of the INK4b-ARF-INK4a locus, by directly binding to the long noncoding RNA (lncRNA) transcript antisense noncoding RNA in the INK4 locus (ANRIL), was recently shown.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21828241
115	CDKN2B-AS1	PRC1	RNA-Protein	binding	Work over the past few years has demonstrated a direct interaction between ANRIL and components from both PRC1 and PRC2 complexes. Binding to ANRIL contributes to the functions of both PRC1 and PRC2 proteins, and disruption of either interaction impacts transcriptional repression of the target INK4b locus.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21925379
116	CDKN2B-AS1	PRC1	RNA-Protein	Binding	ANRIL (i.e.antisense ncRNA in INK4 locus) has also been linked to transcriptional repression via interaction with both PRC1 and PRC2.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21831473
117	CDKN2B-AS1	PRC1	RNA-Protein	binding	Although lncRNA-mediated regulation of INK4b-ARF-INK4a gene is not restricted to ANRIL, both polycomb repressive complex-1 (PRC1) and -2 (PRC2) interact with ANRIL to form heterochromatin surrounding the INK4b-ARF-INK4a locus, leading to its repression.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21828241
118	CDKN2B-AS1	PRC1	RNA-Protein	Binding	Both polycomb repressive complex-1 (PRC1) and -2 (PRC2) interact with ANRIL to form heterochromatin surrounding the INK4b-ARF-INK4a locus, leading to its repression.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21828241
119	CDKN2B-AS1	PRC1	RNA-Protein	binding	Recruits Polycomb Repressor Complex 1 (PRC1) to epigenetically silence INK4b/ARF/INK4a tumour suppressor locus.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	20541999
120	CDKN2B-AS1	PRC2	RNA-Protein	binding	Work over the past few years has demonstrated a direct interaction between ANRIL and components from both PRC1 and PRC2 complexes. Binding to ANRIL contributes to the functions of both PRC1 and PRC2 proteins, and disruption of either interaction impacts transcriptional repression of the target INK4b locus.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21925379
121	CDKN2B-AS1	PRC2	RNA-Protein	Binding	Both polycomb repressive complex-1 (PRC1) and -2 (PRC2) interact with ANRIL to form heterochromatin surrounding the INK4b-ARF-INK4a locus, leading to its repression.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21828241
122	CDKN2B-AS1	PRC2	RNA-Protein	binding	RNA immunoprecipitation demonstrates that ANRIL binds to SUZ12 in vivo. Collectively, these results suggest a model in which ANRIL binds to and recruits PRC2 to repress the expression of p15(INK4B) locus.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21151178
123	CDKN2B-AS1	PRC2	RNA-Protein	binding	Although lncRNA-mediated regulation of INK4b-ARF-INK4a gene is not restricted to ANRIL, both polycomb repressive complex-1 (PRC1) and -2 (PRC2) interact with ANRIL to form heterochromatin surrounding the INK4b-ARF-INK4a locus, leading to its repression.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21828241
124	CDKN2B-AS1	PRC2	RNA-Protein	Binding	ANRIL (i.e.antisense ncRNA in INK4 locus) has also been linked to transcriptional repression via interaction with both PRC1 and PRC2.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21831473
125	CDKN2B-AS1	Suz12	RNA-Protein	binding	ANRIL was found to co-immunoprecipitate with Suz12, which is component of PRC2.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21874119
126	CDKN2B-AS1	SUZ12	RNA-Protein	binding	RNA immunoprecipitation demonstrates that ANRIL binds to SUZ12 in vivo. Collectively, these results suggest a model in which ANRIL binds to and recruits PRC2 to repress the expression of p15(INK4B) locus.	Human	CDKN2B-AS1; ANRIL; p15AS; CDKN2BAS; CDKN2B-AS; NCRNA00089; RP11-145E5.4	NR_003529.3	21151178
127	DGCR5	REST	DNA-TF	Regulatory	The DiGeorge syndrome-associated noncoding RNA, DGCR5, is repressed by REST through a proximal upstream binding site.	Human	DGCR5; LINC00037; NCRNA00037	NR_002733.2	19050060
128	DHFR upstream transcripts	DHFR	RNA-DNA	Regulatory	Regulates DHFR expression by forming a of triple helix with the DHFR major promoter and interacting with TFIIB.	N/A	N/A	N/A	21256239
129	DHFR upstream transcripts	TFIIB	RNA-Protein	Binding	Regulates DHFR expression by forming a of triple helix with the DHFR major promoter and interacting with TFIIB.	N/A	N/A	N/A	21256239
130	Dleu2	Trim13	RNA-RNA	Co-expression	A study found that Dleu2, a previously described ncRNA overlapping but transcribed in the opposite direction of the Trim13 (RFP2/LEU5) gene whose expression is upregulated during early OL maturation and terminal differentiation.	Mouse	Dleu2; Alt1; Leu2; Gm9069; AI197277; AI788824; 1810047A16Rik; 4932411A06Rik; 7730401J12Rik	NR_028264.1	20137068
131	Dlx1as	Dlx	RNA-RNA	Co-expression	Evf2, Dlx1as, and Dlx4as exhibit similar expression profiles to the associated Dlx genes.	Mouse	Dlx1as	NR_002854.2	18562676
132	Dlx4as	Dlx	RNA-RNA	Co-expression	Evf2, Dlx1as, and Dlx4as exhibit similar expression profiles to the associated Dlx genes.	Mouse	A730090H04Rik; Dlx4as	NR_040279.1	18562676
133	DNM3OS	TWIST1	DNA-TF	Regulatory	Twist-1 regulates the miR-199a/214 cluster during development.	Human	DNM3OS; DNM3-AS1; MIR199A2HG	NR_038397.1	19029138
134	dutA	STAT	RNA-DNA	Regulatory	Thought to function upstream of Dictyostelium STAT transcription factor Dd-STATa.	Dictyostelium discoideum AX4	dutA	D16417	21256239
135	EMX2OS	EMX2	RNA-RNA	Regulatory	EMX2OS post-transcriptionally regulates the abundance of the coding transcript, thereby regulating activity of EMX2.	Human	EMX2OS; EMX2-AS1; NCRNA00045	NR_002791.2	21128942
136	Evf2	DLX	DNA-TF	Regulatory	the lincRNA Evf2 is transcribed from an ultraconserved distal enhancer that recruits positive (i.e., DLX) and negative (i.e., MECP2) transcription factors to the enhancer to modulate the expression of adjacent protein-coding genes	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20380817
137	Evf2	DLX2	DNA-TF	Regulatory	Evf2 regulates the binding of the DLX2 transcription factor to its originating enhancer element, which in turn regulates the transcriptional activity of the enhancer.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	18562676
138	Evf2	Dlx2	RNA-Protein	Binding	Evf2 interacts in trans with the homeobox transcription factor Dlx2 to regulate the expression of the Dlx6 gene that it encompasses.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	18184812
139	Evf2	Dlx2	RNA-Protein	Binding	Evf-2 was previously shown to regulate binding of the Dlx2 transcription factor to the ultraconserved enhancer to activate the expression of the encompassed Dlx6 gene during neurogenesis.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20137068
140	Evf2	DLX2	RNA-Protein	Binding	Evf-2 modulates transcription of Dlx6 by recruiting DLX2 and MECP2 to the ultraconserved ei enhancer element that is also transcribed as part of Evf-2 itself.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	21936910
141	Evf2	Dlx2	RNA-Protein	Binding	Single-stranded Evf2 forms a complex with the product of a third homeodomain gene Dlx2 whose sequence lies elsewhere in the mouse genome.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	19239885
142	Evf2	Dlx2	RNA-Protein	binding	The 3.8-kb Evf-2 ncRNA, which is transcribed from an ultraconserved region, forms a complex with the homeodomain-containing protein Dlx2.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	19571179
143	Evf2	Dlx2	RNA-Protein	binding	Evf2 interacts in trans with the homeobox transcription factor Dlx2 to regulate the expression of the Dlx6 gene that it encompasses. Consistent with this function, Evf exhibits a coincident expression profile with Dlx2.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	18184812
144	Evf2	Dlx-2	RNA-Protein	binding	Evf2 forms a complex with Dlx-2 and recruits Dlx-2 to induce the enhancer activities of ei and eii, resulting in induced expression of both Dlx-5 and -6.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20573714
145	Evf2	Dlx-2	RNA-Protein	Regulatory	The lncRNA Evf-2 is a putative direct positive regulator of the transcription factor Dlx-2.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20951849
146	Evf2	DLX5	RNA-DNA	Regulatory	DLX6-AS1 specifically cooperates with Dlx-2 to increase the transcriptional activity of the Dlx-5/6 enhancer in a target and homeodomain-specific manner.	Human	DLX6-AS1; Evf-2; DLX6AS; DLX6-AS; NCRNA00212	NR_015448.1	16705037
147	Evf2	Dlx-5	DNA-DNA	Regulatory	Evf2 is a long, polyadenylated ncRNA transcribed from an ultraconserved intergenic enhancer region associated with the Dlx-5/6 locus.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20573714
148	Evf2	Dlx-5	RNA-DNA	Regulatory	Evf2 forms a complex with Dlx-2 and recruits Dlx-2 to induce the enhancer activities of ei and eii, resulting in induced expression of both Dlx-5 and -6.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20573714
149	Evf2	Dlx-5	RNA-Protein	Regulatory	The lncRNA Evf-2 is a putative direct positive regulator of the transcription factor Dlx-2, and is consequently an indirect positive regulator of Dlx-5 and Dlx-6.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20951849
150	Evf2	Dlx-5/6 enhancer	RNA-DNA	Regulatory	Cooperates with Dlx-2 in vivo to increase the transcriptional activity of the Dlx-5/6 enhancer.	Mouse	Dlx2; Dlx-2; Tes-1; AW121999	NM_010054.2	21256239
151	Evf2	Dlx-5/6 enhancer	RNA-DNA	Regulatory	Cooperates with Dlx-2 in vivo to increase the transcriptional activity of the Dlx-5/6 enhancer.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	21256239
152	Evf2	Dlx6	RNA-DNA	Regulatory	Evf2 interacts in trans with the homeobox transcription factor Dlx2 to regulate the expression of the Dlx6 gene that it encompasses.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	18184812
153	Evf2	Dlx6	RNA-DNA	Regulatory	Evf-2 was previously shown to regulate binding of the Dlx2 transcription factor to the ultraconserved enhancer to activate the expression of the encompassed Dlx6 gene during neurogenesis.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20137068
154	Evf2	Dlx6	RNA-DNA	Regulatory	Evf-2 modulates transcription of Dlx6 by recruiting DLX2 and MECP2 to the ultraconserved ei enhancer element that is also transcribed as part of Evf-2 itself.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	21936910
155	Evf2	Dlx6	RNA-DNA	Regulatory	Evf2 interacts in trans with the homeobox transcription factor Dlx2 to regulate the expression of the Dlx6 gene that it encompasses. Consistent with this function, Evf exhibits a coincident expression profile with Dlx2.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	18184812
156	Evf2	DLX6	RNA-DNA	Regulatory	DLX6-AS1 specifically cooperates with Dlx-2 to increase the transcriptional activity of the Dlx-5/6 enhancer in a target and homeodomain-specific manner.	Human	DLX6-AS1; Evf-2; DLX6AS; DLX6-AS; NCRNA00212	NR_015448.1	16705037
157	Evf2	Dlx-6	DNA-DNA	Regulatory	Evf2 is a long, polyadenylated ncRNA transcribed from an ultraconserved intergenic enhancer region associated with the Dlx-5/6 locus.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20573714
158	Evf2	Dlx-6	RNA-DNA	Regulatory	Evf2 forms a complex with Dlx-2 and recruits Dlx-2 to induce the enhancer activities of ei and eii, resulting in induced expression of both Dlx-5 and -6.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20573714
159	Evf2	Dlx-6	RNA-Protein	Regulatory	The lncRNA Evf-2 is a putative direct positive regulator of the transcription factor Dlx-2, and is consequently an indirect positive regulator of Dlx-5 and Dlx-6.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20951849
160	Evf2	MECP2	DNA-TF	Regulatory	the lincRNA Evf2 is transcribed from an ultraconserved distal enhancer that recruits positive (i.e., DLX) and negative (i.e., MECP2) transcription factors to the enhancer to modulate the expression of adjacent protein-coding genes	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	20380817
161	Evf2	MECP2	RNA-Protein	Binding	Evf-2 modulates transcription of Dlx6 by recruiting DLX2 and MECP2 to the ultraconserved ei enhancer element that is also transcribed as part of Evf-2 itself.	Mouse	Dlx6as1; Evf1; Evf2; Evf-1; Evf-2; Shhrs; Evf1/2; mEvf-1; Dlx6os1; A230055N17Rik	NR_015388.1	21936910
162	Ftx	XIST	RNA-DNA	Regulatory	Ftx has both a global role in the adjustment of the transcription levels of several genes in the Xic and a positive effect on Xist expression that coincides with a role in preventing the methylation of the Xist promoter.	Mouse	B230206F22Rik; Ftx; BB219131; NCRNA00182	NR_028380.1	21329697
163	Ftx	XIST	RNA-RNA	Co-expression	Ftx is upregulated specifically in female cells at the time of Xist upregulation and X inactivation.	Mouse	B230206F22Rik; Ftx; BB219131; NCRNA00182	NR_028380.1	21496640
164	G22	PABP	RNA-Protein	binding	Binds PABP and the SRP9/14 heterodimer.	N/A	N/A	N/A	21256239
165	G22	SRP9/14 heterodimer	RNA-Protein	binding	Binds PABP and the SRP9/14 heterodimer.	N/A	N/A	N/A	21256239
166	GAL10	H3	RNA-Protein	Regulatory	Cryptic ncRNA transcription can direct H3 K36me3 formation over repressed genes and intergenic regions, which otherwise lack this histone modification.	Saccharomyces cerevisiae S288c	GAL10	NM_001178367.1	19061643
167	GAL10	RAT1	RNA-RNA	Co-expression	The importance of RAT1 was reinforced by the finding that GAL10 lncRNA was more functionally compromised by loss of RAT1 than XRN1.	Saccharomyces cerevisiae S288c	GAL10	NM_001178367.1	22325347
168	GAL10	Reb1	DNA-TF	Regulatory	Transcription of GAL10-ncRNA is driven by the DNA-binding protein Reb1.	Saccharomyces cerevisiae S288c	GAL10	NM_001178367.1	19061643
169	GAL10	Reb1	RNA-Protein	Regulatory	Reb1-driven ncRNA transcription causes reduced acetylation of specific histone residues over the GAL1 and GAL10 coding regions.	Saccharomyces cerevisiae S288c	GAL10	NM_001178367.1	19061643
170	GAL10	TRAMP complexes	RNA-Protein	Regulatory	The GAL10-ncRNA is targeted for degradation by the TRAMP complexes.	Saccharomyces cerevisiae S288c	GAL10	NM_001178367.1	19061643
171	GAS5	NR3C1	RNA-Protein	binding	Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Gas5 bound to the DNA-binding domain of the glucocorticoid receptor (GR) by acting as a decoy glucocorticoid response element (GRE), thus competing with DNA GREs for binding to the GR.	Human	GAS5; SNHG2; NCRNA00030	NR_002578.2	20124551
172	GAS5	NR3C1	RNA-Protein	Regulatory	The multifunctional GAS5 lncRNA is a negative regulator of the glucocorticoid receptor and other nuclear receptors.	Human	GAS5; SNHG2; NCRNA00030	NR_002578.2	20951849
173	H19	c-myc	DNA-TF	Regulatory	H19 has been linked to the oncogene, c-myc, which positively regulates its expression in diverse cell types including T98G human glioblastoma cells.	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	20380817
174	H19	CTCF1	RNA-RNA	Co-expression	Significant reductions at the H19 CTCF 1  and CTCF 2  binding sites were observed in the offspring of ethanol-treated sires, which was significantly correlated with reduced weight at postnatal days 35-42 (p?<?0.05).	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	22395465
175	H19	CTCF2	RNA-RNA	Co-expression	Significant reductions at the H19 CTCF 1 and CTCF 2  binding sites were observed in the offspring of ethanol-treated sires, which was significantly correlated with reduced weight at postnatal days 35-42 (p<=0.05).	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	22395465
176	H19	CTCF3	RNA-RNA	Co-expression	There is a CTCF-binding site (CTCF3) in the imprinting control region (ICR) upstream of H19.	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	22395465
177	H19	E2F1	RNA-Protein	Regulatory	H19 transcription is positively regulated by the cell cycle regulatory factor, E2F1, during the S-phase of growth-stimulated cells.	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	20380817
178	H19	GLI1	DNA-TF	Regulatory	H19 is a target of the GLI1 transcription factor, which mediates SHH signaling and is amplified more than 50-fold in human gliomas.	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	20380817
179	H19	Igf2	RNA-RNA	Co-expression	Complex functions, influences growth by down-regulating a number of imprinted genes including Igf2, also implicated as both a tumour suppressor and an oncogene.	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	21256239
180	H19	miR-675	RNA-RNA	Co-expression	Recently, it was found that the H19 RNA is host to an exonic microRNA, miR-675, which, as a result, is also imprinted and maternally expressed.	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	19239885
181	H19	p53	DNA-TF	Regulatory	H19 has been linked to the tumor suppressor, p53, which negatively regulates its expression.	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	20380817
182	H19	SHH	DNA-TF	Regulatory	H19 is a target of the GLI1 transcription factor, which mediates SHH signaling and is amplified more than 50-fold in human gliomas.	Human	H19; ASM; BWS; WT2; ASM1; PRO2605; D11S813E; LINC00008; NCRNA00008	NR_002196.1	20380817
183	HAR1A	RELN	DNA-TF	Regulatory	The lncRNA HAR1F is transcribed from one of these regions and specifically co-expressed in Cajal-Retzius cells of the human neocortex with the critical neural factor RELN (Pollard et al., 2006), which mediates seminal neural developmental processes and is implicated in the pathophysiology of a broad range of neurological and psychiatric disorders.	Human	HAR1A; HAR1F; LINC00064; NCRNA00064	NR_003244.1	20380817
184	HAR1A	REST	DNA-TF	Regulatory	RNA in-situ hybridization showed that HAR1F is expressed in developing neurons of the human embryonic neocortex, and its expression was recently shown to be regulated by the master neural transcriptional repressor, REST.	Human	HAR1A; HAR1F; LINC00064; NCRNA00064	NR_003244.1	20951849
185	HEIH	EZH2	RNA-Protein	binding	It was shown that lncRNAHEIH associates with EZH2 and that this association is required for the expression of EZH2-regulated target genes.	Human	EZH2; ENX1; EZH1; KMT6; WVS2; ENX-1; KMT6A	NM_001203247.1	21769904
186	HOTAIR	CoREST	RNA-Protein	Binding	Epigenetically silences gene expression at many loci by recruitment of LSD1/CoREST/REST and PRC2 repressive chromatin modifying complexes. Oncogene: promotes tumour metastasis.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21256239
187	HOTAIR	EZH2	RNA-Protein	Binding	HOTAIR, Kcnq1ot and Xist all mediate their effects by interacting with the Polycomb-repressive complex 2 (PRC2) component Ezh2 (enhancer of zeste homolog 2 (Drosophila)) and modulating histone methylation.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21936910
188	HOTAIR	Ezh2	RNA-Protein	binding	HOTAIR RNA plays a critical role in establishing H3K27me3 enriched chromosomal domains through interaction with PRC2 complex members such as Suz12 and Ezh2.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	19015002
189	HOTAIR	Ezh2	RNA-Protein	binding	Ezh2 interacts with HOTAIR and Xist.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21123648
190	HOTAIR	H3	RNA-Protein	Regulatory	HOTAIR expression may be involved in human cancer by promoting genomic relocalization of Polycomb complex and H3K27 trimethylation.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20393566
191	HOTAIR	H3	RNA-Protein	Regulatory	HOTAIR, a paradigm of this new class of RNAs, is localized within the human HOXC gene cluster and was shown,in human cells, to regulate HOXD genes in trans via the recruitment of Polycomb Repressive Complex 2 (PRC2), followed by the trimethylation of lysine 27 of histone H3.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21637793
192	HOTAIR	H3	RNA-Protein	Regulatory	HOTAIR expression may be involved in human cancer by promoting genomic relocalization of Polycomb complex and H3K27 trimethylation.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20393566
193	HOTAIR	Hox	RNA-DNA	Regulatory	HOTAIR is transcribed from within specific Hox gene clusters but regulates the expression of Hox genes located on different chromosomes.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21936910
194	HOTAIR	HOXD	RNA-DNA	Regulatory	HOTAIR, a paradigm of this new class of RNAs, is localized within the human HOXC gene cluster and was shown,in human cells, to regulate HOXD genes in trans via the recruitment of Polycomb Repressive Complex 2 (PRC2), followed by the trimethylation of lysine 27 of histone H3.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21637793
195	HOTAIR	HOXD	RNA-DNA	Regulatory	The lincRNA HOTAIR is transcribed from the HOXC locus and targets Polycomb Repressive Complex 2 (PRC2, comprised of H3K27 methylase EZH2, SUZ12, and EED) to silence HOXD and select genes on other chromosomes.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20616235
196	HOTAIR	HOXD	RNA-DNA	Regulatory	HOTAIR represses transcription in trans across 40 kilobases of the HOXD locus.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	17604720
197	HOTAIR	HOXD	RNA-DNA	Regulatory	HOTAIR is transcribed at the intersection of opposing chromatin domains in the HOXC locus, but targets Polycomb Repressive Complex 2 (PRC2) to  represses transcription in trans across 40 kilobases of the HOXD locus.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	17604720
198	HOTAIR	HOXD	RNA-DNA	Regulatory	HOTAIR represses the expression in trans of genes in the HOXD cluster. Depletion of HOTAIR by siRNA resulted in the activation of HOXD genes in trans.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	19015002
199	HOTAIR	HOXD	RNA-Protein	Regulatory	The lncRNA HOTAIR is a putative direct positive regulator of the Polycomb repressor complex, and is consequently an indirect negative regulator of homeobox-D transcription factors.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20951849
200	HOTAIR	HOXD	RNA-RNA	Co-expression	HOTAIR showed negative association with HOXD genes.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	19182780
201	HOTAIR	LSD1	RNA-Protein	binding	Immunoprecipitation (IP) of LSD1 retrieved endogenous HOTAIR with comparable enrichment to that of PRC2 IP. It was hypothesized that HOTAIR may also bind the LSD1-CoREST complex.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20616235
202	HOTAIR	LSD1	RNA-Protein	binding	A 3' domain of HOTAIR binds the LSD1/CoREST/REST complex.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20616235
203	HOTAIR	LSD1	RNA-Protein	Binding	Epigenetically silences gene expression at many loci by recruitment of LSD1/CoREST/REST and PRC2 repressive chromatin modifying complexes. Oncogene: promotes tumour metastasis.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21256239
204	HOTAIR	LSD1	RNA-Protein	binding	Analysis of HOTAIR revealed that a 5' end domain binds PRC2 and a 3' end domain binds an LSD1 (H3K4me2 demethylase) containing complex.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21496640
205	HOTAIR	PRC2	RNA-Protein	binding	HOTAIR expression may be involved in human cancer by promoting genomic relocalization of Polycomb complex and H3K27 trimethylation.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20393566
206	HOTAIR	PRC2	RNA-Protein	Binding	HOTAIR, a paradigm of this new class of RNAs, is localized within the human HOXC gene cluster and was shown,in human cells, to regulate HOXD genes in trans via the recruitment of Polycomb Repressive Complex 2 (PRC2), followed by the trimethylation of lysine 27 of histone H3.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21637793
207	HOTAIR	PRC2	RNA-Protein	binding	CDK1 and CDK2 phosphorylate EZH2 at threonine 350 (T350) and that T350 phosphorylation is important for the binding of EZH2 to PRC2 recruiters, such as noncoding RNAs (ncRNAs) HOTAIR and XIST.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21278485
208	HOTAIR	PRC2	RNA-Protein	Binding	The lincRNA HOTAIR is transcribed from the HOXC locus and targets Polycomb Repressive Complex 2 (PRC2, comprised of H3K27 methylase EZH2, SUZ12, and EED) to silence HOXD and select genes on other chromosomes.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20616235
209	HOTAIR	PRC2	RNA-Protein	binding	A 5'domain of HOTAIR binds polycomb repressive complex 2 (PRC2).	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20616235
210	HOTAIR	PRC2	RNA-Protein	binding	HOTAIR, a paradigm of this new class of RNAs, is localized within the human HOXC gene cluster and was shown,in human cells, to regulate HOXD genes in trans via the recruitment of Polycomb Repressive Complex 2 (PRC2), followed by the trimethylation of lysine 27 of histone H3.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21637793
211	HOTAIR	PRC2	RNA-Protein	binding	HOTAIR coprecipitated with PRC2 in both HeLa and hFFs, but not in hLFs.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	19571010
212	HOTAIR	PRC2	RNA-Protein	binding	HOTAIR is transcribed at the intersection of opposing chromatin domains in the HOXC locus, but targets Polycomb Repressive Complex 2 (PRC2) to silence 40 kilobases of HOXD.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	17604720
213	HOTAIR	PRC2	RNA-Protein	Binding	Epigenetically silences gene expression at many loci by recruitment of LSD1/CoREST/REST and PRC2 repressive chromatin modifying complexes. Oncogene: promotes tumour metastasis.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21256239
214	HOTAIR	PRC2	RNA-Protein	binding	Analysis of HOTAIR revealed that a 5' end domain binds PRC2 and a 3' end domain binds an LSD1 (H3K4me2 demethylase) containing complex.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21496640
215	HOTAIR	PRC2	RNA-Protein	Regulatory	The lncRNA HOTAIR is a putative direct positive regulator of the Polycomb repressor complex.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	20951849
216	HOTAIR	REST	RNA-Protein	Binding	Epigenetically silences gene expression at many loci by recruitment of LSD1/CoREST/REST and PRC2 repressive chromatin modifying complexes. Oncogene: promotes tumour metastasis.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	21256239
217	HOTAIR	Suz12	RNA-Protein	binding	HOTAIR RNA plays a critical role in establishing H3K27me3 enriched chromosomal domains through interaction with PRC2 complex members such as Suz12 and Ezh2.	Human	HOTAIR; HOXAS; HOXC-AS4; HOXC11-AS1; NCRNA00072	NR_047517.1	19015002
218	HOTAIRM1	HOXA1	RNA-RNA	Co-expression	HOTAIRM1 knockdown in NB4 cells prevented RA induction of HOXA1 and A4.	Human	HOTAIRM1; HOXA-AS1; HOXA1-AS1; NCRNA00179	NR_038366.1	21874119
219	HOTAIRM1	HOXA4	RNA-RNA	Co-expression	HOTAIRM1 knockdown in NB4 cells prevented RA induction of HOXA1 and A4.	Human	HOTAIRM1; HOXA-AS1; HOXA1-AS1; NCRNA00179	NR_038366.1	21874119
220	HOTTIP	HOXA	DNA-DNA	Regulatory	This study identified HOTTIP in association with the promoter regions of downstream 5'HOXA genes.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21831473
221	HOTTIP	HOXA	RNA-DNA	Regulatory	Recently, another trans-acting lincRNA, called HOTTIP, has been described activating the transcription of several HOXA genes in vivo by recruiting the proteins Mll1 and Wdr5 on the transcription start sites of the 5' HOXA genes.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
222	HOTTIP	HOXA	RNA-DNA	Regulatory	Recently, another trans-acting lincRNA, called HOTTIP, has been described activating the transcription of several HOXA genes in vivo by recruiting the proteins Mll1 and Wdr5 on the transcription start sites of the 5' HOXA genes.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
223	HOTTIP	HOXA	RNA-Protein	binding	HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA, driving histone H3 lysine 4 trimethylation and gene transcription.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
224	HOTTIP	HOXA	RNA-Protein	binding	HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA, driving histone H3 lysine 4 trimethylation and gene transcription.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
225	HOTTIP	HOXA	RNA-RNA	Co-expression	Knockdown of HOTTIP in foreskin fibroblasts resulted in lower 5’HOXA gene expression.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21874119
226	HOTTIP	Mll1	RNA-Protein	binding	Recently, another trans-acting lincRNA, called HOTTIP, has been described activating the transcription of several HOXA genes in vivo by recruiting the proteins Mll1 and Wdr5 on the transcription start sites of the 5' HOXA genes.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
227	HOTTIP	Mll1	RNA-Protein	binding	Recently, another trans-acting lincRNA, called HOTTIP, has been described activating the transcription of several HOXA genes in vivo by recruiting the proteins Mll1 and Wdr5 on the transcription start sites of the 5' HOXA genes.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
228	HOTTIP	WDR5	RNA-Protein	binding	HOTTIP and Mistral recruit chromatin-activating complexes (WDR5/MLL1) in cis to neighboring genes.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	22190456
229	HOTTIP	WDR5	RNA-Protein	binding	HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA, driving histone H3 lysine 4 trimethylation and gene transcription.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
230	HOTTIP	WDR5	RNA-Protein	binding	HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA, driving histone H3 lysine 4 trimethylation and gene transcription.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
231	HOTTIP	Wdr5	RNA-Protein	binding	Recently, another trans-acting lincRNA, called HOTTIP, has been described activating the transcription of several HOXA genes in vivo by recruiting the proteins Mll1 and Wdr5 on the transcription start sites of the 5' HOXA genes.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
232	HOTTIP	Wdr5	RNA-Protein	binding	Recently, another trans-acting lincRNA, called HOTTIP, has been described activating the transcription of several HOXA genes in vivo by recruiting the proteins Mll1 and Wdr5 on the transcription start sites of the 5' HOXA genes.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21423168
233	HOTTIP	WDR5	RNA-Protein	binding	HOTTIP was shown to mediate enhancerlike effects on the adjacent genes through a mechanism involving direct interaction with the adaptor protein WDR5.	Human	HOTTIP; HOXA-AS6; HOXA13-AS1; NCRNA00213	NR_037843.2	21831473
234	HSR1	HSF1	RNA-Protein	binding	Heat-shock RNA 1 (HSR1) binds heat-shock transcription factor 1 (HSF1), facilitating its ability to activate genes encoding heat-shock proteins.	Candida albicans SC5314	"""HSR1"		22190456
235	HSR1	HSF1	RNA-Protein	binding	Heat-shock factor 1 (HSF1) A third protein-binding lncRNA is HSR1 (heat shock RNA-1), a 604 nucleotide RNA that, together with eukaryotic translationelongation factor 1A, stimulates trimerization of heat-shock factor 1 (HSF1).	Candida albicans SC5314	"""HSR1"		19239885
236	HSR1	HSF-1	RNA-Protein	Regulatory	The ncRNAs NRSE and HSR have been shown to regulate the activity of REST and HSF-1, respectively.	Human	HSR	N/A	19191220
237	HULC	miR-372	RNA-DNA	Regulatory	highly upregulated in liver cancer (HULC) lncRNA sequesters endogenous miR-372 to modulate its own transcriptional upregulation in HCC.	Human	HULC; LINC00078; NCRNA00078	NR_004855.2	21802130
238	HULC	miR-372	RNA-RNA	Binding/Regulatory	Acts as a sponge/target mimic for miR-372 reducing its expression and activity.	Human	HULC; LINC00078; NCRNA00078	NR_004855.2	21256239
239	ICR1	FLO11	RNA-DNA	Regulatory	ICR1 could repress FLO11 transcription by occluding its promoter.	Saccharomyces cerevisiae S288c	ICR1	N/A	19805129
240	ICR1	Flo8	RNA-Protein	Regulatory	These data implicate Flo8 and Rpd3L as repressors of ICR1.	Saccharomyces cerevisiae S288c	ICR1	N/A	19805129
241	ICR1	Rpd3L	RNA-Protein	Regulatory	These data implicate Flo8 and Rpd3L as repressors of ICR1.	Saccharomyces cerevisiae S288c	ICR1	N/A	19805129
242	ICR1	Sfl1	DNA-TF	Regulatory	ICR1 is barely detectable in sfl1 mutants in which Rpd3L function is still intact, indicating that Sfl1 function normally promotes ICR1 transcription.	Saccharomyces cerevisiae S288c	ICR1	N/A	19805129
243	IPS1	miR-399	RNA-RNA	Regulatory	The IPS1 ncRNA is poorly evolutionarily conserved except for a short motif that is highly complementary to miR-399, a miRNA that is induced in response to phosphate starvation, although the basepairing is interrupted by a mismatched loop at the expected miRNA cleavage site. This interruption in basepairing causes the IPS1 ncRNA to be noncleavable and instead allows IPS1 to sequester miR-399, resulting in increased expression of miR-399 target genes.	Arabidopsis thaliana	IPS1; A. THALIANA INDUCED BY PHOSPHATE STARVATION1; ATIPS1; INDUCED BY PHOSPHATE STARVATION1; IPS1	NM_180219.1	19571179
244	Jpx	XIST	RNA-DNA	Regulatory	Jpx lncRNA acts as a positive regulator of Xist.	Mouse	Enox; Jpx; 2010000I03Rik; 2510040I06Rik	NR_015508.2	21329697
245	Jpx	XIST	RNA-DNA	Regulatory	Xist expression and X inactivation could be rescued by a Jpx transgene located on another chromosome, indicating that Jpx can exert its effects in trans.	Mouse	Enox; Jpx; 2010000I03Rik; 2510040I06Rik	NR_015508.2	21496640
246	Jpx	XIST	RNA-RNA	Regulatory	Regulates X chromosome inactivation in mammals via activation of the Xist lncRNA.	Mouse	Enox; Jpx; 2010000I03Rik; 2510040I06Rik	NR_015508.2	21256239
247	Jpx	XIST	RNA-RNA	Regulatory	Xist is controlled by two parallel RNA switches – Tsix for Xa and Jpx for Xi. Jpx activates Xist on Xi.	Mouse	Enox; Jpx; 2010000I03Rik; 2510040I06Rik	NR_015508.2	21029862
248	JPX	XIST	RNA-RNA	Regulatory	For the inactive X, here, Xic-encoded Jpx is an Xist activator. Jpx is trans-acting and functions as ncRNA.	Mouse	Enox; Jpx; 2010000I03Rik; 2510040I06Rik	NR_015508.2	21029862
249	Kcnq1ot1	Dnmt1	RNA-Protein	binding	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
250	Kcnq1ot1	Dnmt1	RNA-Protein	binding	Kcnq1ot1 mediates transcriptional gene silencing by interacting with Dnmt1. Kcnq1ot1 recruits Dnmt1 to somatic DMRs by interacting with Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	20573698
251	Kcnq1ot1	Dnmt1	RNA-Protein	Binding	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
252	Kcnq1ot1	EZH2	RNA-Protein	Binding	HOTAIR, Kcnq1ot and Xist all mediate their effects by interacting with the Polycomb-repressive complex 2 (PRC2) component Ezh2 (enhancer of zeste homolog 2 (Drosophila)) and modulating histone methylation.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21936910
253	Kcnq1ot1	G9a	RNA-Protein	binding	The Kcnq1ot1 transcript that binds both G9a and PRC2.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	19571010
254	Kcnq1ot1	G9a	RNA-Protein	binding	Kcnq1ot1 interacts with chromatin and with the H3K9- and H3K27-specific histone methyltransferases G9a and the PRC2 complex in a lineage-specific manner.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	18951091
255	Kcnq1ot1	G9a	RNA-Protein	binding	Kcnq1ot1 interacts with the histone methyltransferases G9a and PRC2, effectively forming a repression domain in cis to its transcription site through recruitment of polycomb complexes.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21925379
256	Kcnq1ot1	G9a	RNA-Protein	binding	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
257	Kcnq1ot1	G9a	RNA-Protein	binding	The Kcnq1ot1 RNA also binds to the histone methyltransferase G9a.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	19239885
258	Kcnq1ot1	G9a	RNA-Protein	Binding	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
259	Kcnq1ot1	Kcnq	DNA-DNA	Regulatory	Kcnq1ot is important for silencing of the Kcnq locus resulting from parental imprinting.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21936910
260	Kcnq1ot1	Kcnq1	RNA-DNA	Regulatory	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
261	Kcnq1ot1	Kcnq1	RNA-DNA	Regulatory	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
262	Kcnq1ot1	PRC1	RNA-Protein	binding	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
263	Kcnq1ot1	PRC1	RNA-Protein	Binding	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
264	Kcnq1ot1	PRC2	RNA-Protein	binding	PRC2 recruitment to the domain requires expression of the long ncRNA Kcnq1ot1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	19760321
265	Kcnq1ot1	PRC2	RNA-Protein	binding	Kcnq1ot1 interacts with chromatin and with the H3K9- and H3K27-specific histone methyltransferases G9a and the PRC2 complex in a lineage-specific manner.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	18951091
266	Kcnq1ot1	PRC2	RNA-Protein	binding	The Kcnq1ot1 transcript that binds both G9a and PRC2.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	19571010
267	Kcnq1ot1	PRC2	RNA-Protein	binding	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
268	Kcnq1ot1	PRC2	RNA-Protein	binding	Kcnq1ot1 interacts with the histone methyltransferases G9a and PRC2, effectively forming a repression domain in cis to its transcription site through recruitment of polycomb complexes.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21925379
269	Kcnq1ot1	PRC2	RNA-Protein	Binding	Epigenetically silences the Kcnq1 imprinting control region by recruiting repressive chromatin remodelling complexes such as G9a, PRC1 and PRC2, and the DNA methylase Dnmt1.	Mouse	Kcnq1ot1; Lit1; Kvlqt1-as	NR_001461.5	21256239
270	KDM5B-AS1	KLHL12	RNA-RNA	Co-expression	When ncRNA-a2 was depleted, the KLHL12, a gene known for its negative regulation of the Wnt-beta catenin pathway, on the opposite strand displayed a significant reduction.	Human	KDM5B-AS1; ncRNA-a2	NR_046325.1	20887892
271	KDM5B-AS1	KLHL12	RNA-RNA	Regulatory	KLHL12, ROCK2, TAL1, CMPK1, Snai2, and Snai1 are regulated by ncRNA-a2 through ncRNA-a7, respectively.	Human	KDM5B-AS1; ncRNA-a2	NR_046325.1	21502407
272	Khps1a	Sphk1	RNA-DNA	Regulatory	Regulates DNA methylation in the tissue-dependent differentially methylated region of Sphk1.	N/A	N/A	N/A	21256239
273	LINC00312	ERA	RNA-DNA	Regulatory	ERR-10 (LINC00312): a new repressor in transcriptional signaling activation of estrogen receptor-alpha.	Human	LINC00312; NAG7; ERR10; NAG-7; ERR-10; LOH3CR2A; NCRNA00312	NR_024065.2	15474036
274	LINC00568	ECM1	RNA-RNA	Co-expression	Depletion of ncRNA-a1 (activating long ncRNA 1, LINC00568), results in decreased ECM1 levels, suggesting a direct activating function of ncRNA-a1 on its neighboring gene.	Human	LINC00568; ncRNA-a1	NR_051960.1	21502407
275	LINC00570	CMPK1	RNA-RNA	Regulatory	KLHL12, ROCK2, TAL1, CMPK1, Snai2, and Snai1 are regulated by ncRNA-a2 through ncRNA-a7, respectively.	Human	LINC00570; ncRNA-a5	NR_047499.1	21502407
276	LINC00570	ROCK2	RNA-RNA	Co-expression	depletion of ncRNA-a5 resulted in a specific reduction in ROCK2 expression levels in HeLa cells, which is located upstream of ncRNA-a5.	Human	LINC00570; ncRNA-a5	NR_047499.1	20887892
277	lincDR1	IgG	RNA-Protein	binding	binding with IgG shown by RIP-Chip data.	N/A	N/A	N/A	19571010
278	lincDR1	PRC2	RNA-Protein	binding	binding with PRC2 shown by RIP-Chip data.	N/A	N/A	N/A	19571010
279	lincFoxF1	PRC2	RNA-Protein	binding	Numerous lincRNAs are physically associated with PRC2.	N/A	N/A	N/A	19571010
280	lincGARS	IgG	RNA-Protein	binding	binding with IgG shown by RIP-Chip data.	N/A	N/A	N/A	19571010
281	lincGARS	PRC2	RNA-Protein	binding	binding with PRC2 shown by RIP-Chip data.	N/A	N/A	N/A	19571010
282	lincMLKN1	IgG	RNA-Protein	binding	binding with IgG shown by RIP-Chip data.	N/A	N/A	N/A	19571010
283	lincMLKN1	PRC2	RNA-Protein	binding	binding with PRC2 shown by RIP-Chip data.	N/A	N/A	N/A	19571010
284	lincRNA-p21	hnRNP-K	RNA-DNA	Regulatory	The depletion of lincRNA-p21 causes a significant reduction in the association of hnRNP-K at the promoter regions of genes that are normally repressed in a lincRNA-p21 and p53-dependent fashion.	Mouse	Gm16197; OTTMUSG00000031656	NR_036469.1	20673990
285	lincRNA-p21	hnRNP-k	RNA-Protein	Binding	Induced by p53 and mediates p53 repression of many genes in association with hnRNP-k.	Mouse	Gm16197; OTTMUSG00000031656	NR_036469.1	21256239
286	lincRNA-p21	hnRNP-K	RNA-Protein	binding	hnRNP-K interacted with a 50 domain of lincRNA-p21 that was necessary but not sufficient to induce apoptosis, suggesting that other regions of the RNA are required to recruit other factors or target the complex to chromatin or both.	Mouse	Gm16197; OTTMUSG00000031656	NR_036469.1	21496640
287	lincRNA-p21	hnRNP-K	RNA-Protein	binding	p53 regulates lincRNA-p21 by directly inducing its expression, likely through direct binding to the lincRNA-p21 promoter, while reduction of large intergenic ncRNA (lincRNA)-p21 increases expression of numerous p53-repressed transcripts. lincRNA-p21 repressed p53-regulated genes through its binding to and modulation of heterogeneous nuclear ribonucleoprotein K (hnRNP-K) localization.	Mouse	Gm16197; OTTMUSG00000031656	NR_036469.1	21925379
288	lincRNA-p21	p53	DNA-TF	Regulatory	Induced by p53 and mediates p53 repression of many genes in association with hnRNP-k.	Mouse	Gm16197; OTTMUSG00000031656	NR_036469.1	21256239
289	lincRNA-p21	p53	DNA-TF	Regulatory	lincRNA-p21 is induced by p53 in different cell systems. lincRNA-p21 as a repressor in the p53 pathway.lincRNA-p21 is a direct p53 transcriptional target in response to DNA damage.	Mouse	Gm16197; OTTMUSG00000031656	NR_036469.1	20673990
290	lincRNA-p21	p53	DNA-TF	Regulatory	p53 regulates lincRNA-p21 by directly inducing its expression, likely through direct binding to the lincRNA-p21 promoter, while reduction of large intergenic ncRNA (lincRNA)-p21 increases expression of numerous p53-repressed transcripts. lincRNA-p21 repressed p53-regulated genes through its binding to and modulation of heterogeneous nuclear ribonucleoprotein K (hnRNP-K) localization.	Mouse	Gm16197; OTTMUSG00000031656	NR_036469.1	21925379
291	lincRNA-p21	p53	RNA-DNA	Regulatory	lincRNA-p21 acts as a transcriptional repressor turning off multiple genes during the p53 response.	Mouse	Gm16197; OTTMUSG00000031656	NR_036469.1	21496640
292	LINC-ROR	Nanog	DNA-TF	Regulatory	lincRNA-RoR, was shown to be directly targeted by the key pluripotency factors Oct4, Sox2, and Nanog through colocalization of the three factors close its promoter region.	Human	LINC-ROR; lincRNA-RoR	NR_048536.1	21925379
293	LINC-ROR	Oct4	DNA-TF	Regulatory	lincRNA-RoR, was shown to be directly targeted by the key pluripotency factors Oct4, Sox2, and Nanog through colocalization of the three factors close its promoter region.	Human	LINC-ROR; lincRNA-RoR	NR_048536.1	21925379
294	LINC-ROR	Sox2	DNA-TF	Regulatory	lincRNA-RoR, was shown to be directly targeted by the key pluripotency factors Oct4, Sox2, and Nanog through colocalization of the three factors close its promoter region.	Human	LINC-ROR; lincRNA-RoR	NR_048536.1	21925379
295	lincSFPQ	IgG	RNA-Protein	binding	binding with IgG shown by RIP-Chip data.	N/A	N/A	N/A	19571010
296	lincSFPQ	PRC2	RNA-Protein	binding	Numerous lincRNAs are physically associated with PRC2.	N/A	N/A	N/A	19571010
297	lincSFPQ	PRC2	RNA-Protein	binding	binding with PRC2 shown by RIP-Chip data.	N/A	N/A	N/A	19571010
298	LSINCT5	PSPC1	RNA-RNA	Co-expression	Two genes that were significantly downregulated were the lncRNA NEAT-1 and a protein coding gene PSPC1.	N/A	N/A	N/A	21532345
299	LUST	RBM5	RNA-RNA	Co-expression	These results suggest that LUST is a novel, functional, non-coding RNA that plays a role in determining the apoptotic fate of a cell by regulating the expression of RBM5 splice variants.	Human	LUST	NR_045388.1	19559772
300	MALAT1	CREB	DNA-TF	Regulatory	We identified a shorter transcriptional initiation site and found that CREB binds to the defined proximal promoter of the MALAT1 gene. The expression of the tumor marker MALAT1 ncRNA is sensitive to cell surface receptor activation by oxytocin in a neuroblastoma cell line.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	20149803
301	MALAT1	IBP160	RNA-Protein	Regulatory	RNAi-mediated repression of the nuclear speckle proteins, RNPS1, SRm160, or IBP160, which are well-known mRNA processing factors, resulted in the diffusion of MALAT-3 to the nucleoplasm.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	22355166
302	MALAT1	p54nrb	RNA-Protein	binding	In the current model， NEAT1_2 interacts with core paraspeckle proteins PSF and p54nrb, which recruit PSP1 and NEAT1_1 and other associating molecules to the periphery of paraspeckles.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	21444682
303	MALAT1	Pc2	DNA-Protein	Regulatory	methylation/demethylation of Polycomb 2 protein (Pc2) controls relocation of growth-control genes between Polycomb bodies (PcGs) and interchromatin granules (ICGs) in response to growth signals. This movement is the consequence of binding of methylated and unmethylated Pc2 to the ncRNAs TUG1 and MALAT1/NEAT2.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	22078878
304	MALAT1	Pc2	DNA-Protein	Regulatory	Methylation/demethylation of Polycomb 2 protein (Pc2) controls relocation of growth-control genes between Polycomb bodies (PcGs) and interchromatin granules (ICGs) in response to growth signals. This movement is the consequence of binding of methylated and unmethylated Pc2 to the ncRNAs TUG1 and MALAT1/NEAT2.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	22078878
305	MALAT1	PSF	RNA-Protein	binding	In the current model， NEAT1_2 interacts with core paraspeckle proteins PSF and p54nrb, which recruit PSP1 and NEAT1_1 and other associating molecules to the periphery of paraspeckles.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	21444682
306	MALAT1	RNPS1	RNA-Protein	Regulatory	RNAi-mediated repression of the nuclear speckle proteins, RNPS1, SRm160, or IBP160, which are well-known mRNA processing factors, resulted in the diffusion of MALAT-1 to the nucleoplasm.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	22355166
307	MALAT1	SR	RNA-Protein	binding	MALAT1 interacts with SR proteins and influences the distribution of these and other splicing factors in nuclear speckle domains.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	20797886
308	MALAT1	SR protein family	RNA-Protein	Regulatory	MALAT1 regulates the expression level, localization, and activity SR proteins.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	20864030
309	MALAT1	SRm160	RNA-Protein	Regulatory	RNAi-mediated repression of the nuclear speckle proteins, RNPS1, SRm160, or IBP160, which are well-known mRNA processing factors, resulted in the diffusion of MALAT-2 to the nucleoplasm.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	22355166
310	MALAT1	SRSF1	RNA-Protein	Regulatory	Upon MALAT1 depletion, expression of SRSF1 protein is increased.	Human	MALAT1; HCN; NEAT2; MALAT-1; PRO2853; LINC00047; NCRNA00047	NR_002819.2	20864030
311	MEG3	cAMP	DNA-TF	Regulatory	Deletion and mutation analysis suggest that a cAMP response element (CRE), located between -69 and -49 of the MEG3 proximal promoter region, is critical for promoter activity. Furthermore, gel shifting, ChIP analysis, and co-transfection experiments show that CREB directly binds to the CRE site and stimulates MEG3 promoter activity. Therefore, MEG3 is a downstream target gene of cAMP.	Human	MEG3; GTL2; FP504; prebp1; PRO0518; PRO2160; LINC00023; NCRNA00023	NR_002766.2	16793321
312	MEG3	GDF15	RNA-DNA	Regulatory	We further found that MEG3 stimulates expression of the growth differentiation factor 15 (GDF15) by enhancing p53 binding to the GDF15 gene promoter.	Human	MEG3; GTL2; FP504; prebp1; PRO0518; PRO2160; LINC00023; NCRNA00023	NR_002766.2	17569660
313	MEG3	p53	RNA-DNA	Regulatory	Putative tumour suppressor. Regulates p53 expression. Inhibits cell proliferation in the absence of p53.	N/A	N/A	N/A	21256239
314	MEG3	p53	RNA-Protein	binding	We further found that MEG3 stimulates expression of the growth differentiation factor 15 (GDF15) by enhancing p53 binding to the GDF15 gene promoter.	Human	MEG3; GTL2; FP504; prebp1; PRO0518; PRO2160; LINC00023; NCRNA00023	NR_002766.2	17569660
315	MEG3	p53	RNA-Protein	Regulatory	The lncRNA MEG3 is a positive regulator of p53.	Human	MEG3; GTL2; FP504; prebp1; PRO0518; PRO2160; LINC00023; NCRNA00023	NR_002766.2	20951849
316	MEG3	p53	RNA-RNA	Co-expression	MEG3 functions to suppress tumor cell growth, increase protein expression of the tumor suppressor p53, and selectively activate p53 target genes.	Human	MEG3; GTL2; FP504; prebp1; PRO0518; PRO2160; LINC00023; NCRNA00023	NR_002766.2	20211686
317	MEG3	Tp53	RNA-DNA	Regulatory	The lncRNA MEG3 activates the expression of Tp53 and enhances its binding affinity to the promoter of its target gene.	Human	MEG3; GTL2; FP504; prebp1; PRO0518; PRO2160; LINC00023; NCRNA00023	NR_002766.2	21247874
318	MIAT	IRES-GFP	DNA-DNA	Regulatory	fusion of RNCR2 to an IRES-GFP sequence results in mislocalization of this nuclear RNA to the cytoplasm.	Human	MIAT; RNCR2; GOMAFU; C22orf35; LINC00066; NCRNA00066	NR_003491.2	20459797
319	MIR155HG	MYB	DNA-TF	Regulatory	MYB transcriptionally regulates the miR-155 host gene in chronic lymphocytic leukemia.	Human	MIR155HG; BIC; MIRHG2; NCRNA00172	NR_001458.3	21296997
320	MIR17HG	E2F1	DNA-TF	Regulatory	Aurora kinase A induces miR-17-92 cluster through regulation of E2F1 transcription factor.	Human	MIR17HG; MIHG1; MIRH1; FGLDS2; MIRHG1; C13orf25; LINC00048; miR-17-92; NCRNA00048	NR_027350.1	20300951
321	Mistral	Hoxa6	RNA-DNA	Regulatory	Here, we demonstrate that the long, noncoding RNA (lncRNA) Mistral (Mira) activates transcription of the homeotic genes Hoxa6 and Hoxa7 in mouse embryonic stem cells (mESC) by recruiting MLL1 to chromatin.	Mouse	Mira	NR_045199.1	21925392
322	Mistral	Hoxa7	RNA-DNA	Regulatory	Here, we demonstrate that the long, noncoding RNA (lncRNA) Mistral (Mira) activates transcription of the homeotic genes Hoxa6 and Hoxa7 in mouse embryonic stem cells (mESC) by recruiting MLL1 to chromatin.	Mouse	Mira	NR_045199.1	21925392
323	Mistral	MLL1	RNA-Protein	binding	Here, we demonstrate that the long, noncoding RNA (lncRNA) Mistral (Mira) activates transcription of the homeotic genes Hoxa6 and Hoxa7 in mouse embryonic stem cells (mESC) by recruiting MLL1 to chromatin.	Mouse	Mira	NR_045199.1	21925392
324	Msx1 AS RNA	Bmp4	RNA-RNA	Co-expression	Transient transfection of Msx1 expression vector increased Bmp4 expression by 118% and 48% in 705IC5 and 705IH8 cell lines.	N/A	N/A	N/A	18728357
325	Msx1 AS RNA	Dlx5	RNA-RNA	Co-expression	Transient transfection of Msx1 expression vector clearly decreased Dlx5 expression by 40–61% in 705IC5 and 705IH8 cell lines.	N/A	N/A	N/A	18728357
326	Msx1 AS RNA	Msx1	RNA-RNA	Co-expression	In vitro, Msx1 AS RNA decreased endogenous Msx1 S expression and modified Msx1 protein cell distribution.Msx1 AS RNA could also modulate Msx1 function.	N/A	N/A	N/A	18728357
327	Ncrms	miR-135a	RNA-RNA	Co-expression	Ncrms serves as a host gene for miR-135a (Rodriguez et al., 2004), an oncogenic miRNA that is dysregulated in medulloblastoma.	Mouse	Rmst; M2; Dmt2; Ncrms; AI853140; C230053E11Rik; D930049J19Rik	NR_028262.1	20380817
328	Ncrms	Pax2	DNA-TF	Regulatory	The transcription factor, Pax2, plays a role in patterning of the mouse embryonic midbrain and hindbrain, and Ncrms, a lncRNA, is specifically regulated by Pax2 in this region.	Mouse	Rmst; M2; Dmt2; Ncrms; AI853140; C230053E11Rik; D930049J19Rik	NR_028262.1	20380817
329	ncRNA-a3	CYP4A11	RNA-RNA	Co-expression	When ncRNA-a3 was depleted, a significant reduction in CYP4A11 gene on the opposite strand of the DNA was detected.	N/A	N/A	N/A	20887892
330	ncRNA-a3	ROCK2	RNA-RNA	Regulatory	KLHL12, ROCK2, TAL1, CMPK1, Snai2, and Snai1 are regulated by ncRNA-a2 through ncRNA-a7, respectively.	N/A	N/A	N/A	21502407
331	ncRNA-a3	TAL1	RNA-RNA	Co-expression	Depletion of ncRNA-a3 resulted in a specific and potent reduction of TAL1 expression.	N/A	N/A	N/A	20887892
332	ncRNA-a6	Snai2	RNA-RNA	Co-expression	Snai2 shows a significant reduction in expression when the adjacent ncRNA-a6 is depleted.	N/A	N/A	N/A	20887892
333	ncRNA-a6	Snai2	RNA-RNA	Regulatory	KLHL12, ROCK2, TAL1, CMPK1, Snai2, and Snai1 are regulated by ncRNA-a2 through ncRNA-a7, respectively.	N/A	N/A	N/A	21502407
334	ncRNA-a7	Snai1	RNA-RNA	Regulatory	KLHL12, ROCK2, TAL1, CMPK1, Snai2, and Snai1 are regulated by ncRNA-a2 through ncRNA-a7, respectively. Knockdown of ncRNA-a7 in A549 cells represses the expression of Snai1 specifically and diminishes cell migration to levels similar to that seen when knocking down Snai1. NcRNA-a7 serves as a transcriptional enhancer of Snai1.	Human	LOC100887755	NR_051976.1	21502407
335	ncRNACCND1	CCND1	RNA-DNA	Regulatory	Interacts with CCND1 (cyclin D1) locus and the RNA-binding protein TLS to repress CCND1 expression.	N/A	N/A	N/A	18509338
336	ncRNACCND1	DROSHA	RNA-Protein	binding	We found that knock-down of the miRNA regulator DROSHA, but not DICER, increased the expression level of CCND1ncRNA about four-fold, suggesting that CCND1ncRNA may be processed in a DROSHA-dependent manner.	N/A	N/A	N/A	20573714
337	NCRUPAR	PAR-1	RNA-DNA	Regulatory	The ncR-uPAR upregulated PAR-1-core promoter-driven luciferase activity and mRNA expression in vitro in a Pol II-dependent manner. This noncoding RNA appears to act in trans, albeit locally at the adjacent PAR-1 promoter.	Human	NCRUPAR; ncR-uPAR; NCRNA00193	NR_028375.1	12084570
338	ND5	PTCD2	RNA-RNA	Regulatory	PTCD2 decreased the levels of ND5 lncRNA and the lncND6 RNA, which can form the 39 UTR of the ND5 mRNA.	Human	ND5; MTND5	N/A	22028365
339	ND6	PTCD2	RNA-RNA	Regulatory	PTCD2 decreased the levels of ND5 lncRNA and the lncND6 RNA, which can form the 39 UTR of the ND5 mRNA.	Human	ND6; MTND6	N/A	22028365
340	NEAT1	DBHS	RNA-Protein	binding	DBHS protein expression did not vary between the two cellular contexts, instead, paraspeckle induction and increased RNA nuclear retention correlated with the expression of the paraspeckle-specific structural ncRNA species NEAT1.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	19720872
341	Neat1	Neat2	RNA-RNA	Co-expression	Neat1 and Neat2 associate with nuclear paraspeckles and adjacent SC35 speckles, respectively;domains where transcription and co-transcriptional premRNA processing occur.	Mouse	Neat1; VINC; 2310043N10Rik	NR_003513.2	20137068
342	NEAT1	p54nrb	RNA-Protein	binding	In the current model， NEAT1_2 interacts with core paraspeckle proteins PSF and p54nrb, which recruit PSP1 and NEAT1_1 and other associating molecules to the periphery of paraspeckles.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	21444682
343	NEAT1	P54NRB/NONO	RNA-Protein	binding	NEAT1 associates with DBHS proteins in vivo, as immunoprecipitation of PSF/SFPQ, P54NRB/NONO, and PSPC1 all copurify NEAT1 RNA to varying levels.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	19720872
344	NEAT1	Proteins of the Drosophila behavior/human splicing	RNA-Protein	binding	Additionally, mammalian DBHS proteins associate with the architectural long noncoding RNA NEAT1 to form paraspeckles, subnuclear bodies that alter gene expression via the nuclear retention of RNA.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	22416126
345	NEAT1	PSF	RNA-Protein	binding	In the current model， NEAT1_2 interacts with core paraspeckle proteins PSF and p54nrb, which recruit PSP1 and NEAT1_1 and other associating molecules to the periphery of paraspeckles.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	21444682
346	NEAT1	PSF/SFPQ	RNA-Protein	binding	NEAT1 associates with DBHS proteins in vivo, as immunoprecipitation of PSF/SFPQ, P54NRB/NONO, and PSPC1 all copurify NEAT1 RNA to varying levels.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	19720872
347	NEAT1	PSP1	RNA-Protein	binding	NEAT1 directly interacts with the paraspeckle protein PSP1. NEAT1 knockdown abolishes paraspeckles and relaxes the constraints on export of Alu-containing RNAs into the cytoplasm.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	20951849
348	NEAT1	PSP-1	RNA-Protein	binding	The PSP-1 RNA binding domain is required for its colocalization with NEAT1 RNA in paraspeckles, and biochemical analyses support that NEAT1 RNA binds with paraspeckle proteins.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	19217333
349	NEAT1	PSPC1	RNA-Protein	binding	NEAT1 associates with DBHS proteins in vivo, as immunoprecipitation of PSF/SFPQ, P54NRB/NONO, and PSPC1 all copurify NEAT1 RNA to varying levels.	Human	NEAT1; TncRNA; LINC00084; NCRNA00084	NR_028272.1	19720872
350	Nespas	Nesp	RNA-RNA	Co-expression	Transcription of one of its ncRNAs, the Nesp antisense (Nespas) seems important for repression of Nesp on the paternal allele.	Mouse	Nespas;Gnas-as	NR_002846.2	19760321
351	Nkx2.2AS	Nkx2.2	RNA-DNA	Regulatory	Nkx2.2, a transcription factor that is critical for OL lineage specification, is also subject to regulation by a lncRNA, Nkx2.2AS, which is transcribed antisense to the Nkx2.2 gene.	Mouse	Nkx2-2as; Gm14112; OTTMUSG00000015691	NR_030769.2	20380817
352	NRON	LRRK2	RNA-Protein	binding	Mechanistic studies showed that LRRK2 was a potent negative regulator of the transcription factor NFAT and was a component of a complex that included the large noncoding RNA NRON.	Human	NRON; NCRNA00194	NR_045006.1	21983832
353	NRON	NFAT	RNA-Protein	Regulatory	The conserved lncRNA, named NRON,regulated the nucleocytoplasmic shuttling of the NFAT transcription factor by functioning in a nuclear pore ribonucleoprotein complex.	Human	NRON; NCRNA00194	NR_045006.1	20951849
354	NRON	NFAT	RNA-Protein	Regulatory	By binding to members of the nucleocytoplasmic trafficking machinery, NRON specifically inhibits the nuclear accumulation of NFAT.	Human	NRON; NCRNA00194	NR_045006.1	19571179
355	NRSE	REST	RNA-Protein	Regulatory	The ncRNAs NRSE and HSR have been shown to regulate the activity of REST and HSF-1, respectively.	N/A	N/A	N/A	19191220
356	PAN	E1B-AP5	RNA-Protein	binding	E1B-AP5 interacts with the PAN MRE-II motif outside of the 9-nt core in the MRE-II loop.	N/A	N/A	N/A	22043172
357	PAN	PABPC1	RNA-Protein	binding	PABPC1 binds to the 9-nt core of PAN MRE-II.	N/A	N/A	N/A	22043172
358	PCAT1	EZH2	RNA-RNA	Co-expression	Knockdown of EZH2 by shRNA or pharmacologic inhibition of EZH2 with the inhibitor 3-deazaneplanocin A (DZNep) caused a dramatic upregulation in PCAT-1 expression levels.	Human	PCAT1; PCAT-1	NR_045262.1	21804560
359	PCAT1	PRC2	RNA-Protein	binding	PCAT-1 is a prostate-specific regulator of cell proliferation and show that it is a target of the Polycomb Repressive Complex 2 (PRC2). Patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1-repressed target genes.	Human	PCAT1; PCAT-1	NR_045262.1	21804560
360	PCAT1	SUZ12	DNA-TF	Regulatory	Chromatin immunoprecipitation (ChIP) assays also demonstrated that SUZ12, a core PRC2 protein, directly binds the PCAT-1 promoter approximately 1kb upstream of the TSS.	Human	PCAT1; PCAT-1	NR_045262.1	21804560
361	PCNA-AS1	E2F	RNA-Protein	binding	The binding of S phase-specific E2F complexes at the +583 element may help to overcome the negative effect of the antisense transcript, which results in up-regulation of PCNA expression in proliferating cells.	Human	PCNA-AS1; PCNAAS; PCNA-AS	NR_028370.1	10488129
362	PDZK1IP1-AS1	CMPK1	RNA-RNA	Co-expression	reduced levels of ncRNA-a4 resulted in a consistent and significant decrease in the level of the gene CMPK1 which is over 150 kb downstream of ncRNA-a4.	Human	PDZK1IP1-AS1; ncRNA-a4	NR_047498.1	20887892
363	PHO84 antisense	histone deacetylases	RNA-Protein	Binding	Silences PHO84 in aged cells by recruiting histone deacetylases to the locus.	N/A	N/A	N/A	21256239
364	PHO84 antisense	PHO84	RNA-DNA	Regulatory	Silences PHO84 in aged cells by recruiting histone deacetylases to the locus.	N/A	N/A	N/A	21256239
365	PRINS	G1P3	RNA-RNA	Co-expression	Here, we report that PRINS regulates G1P3, a gene with anti-apoptotic effects in keratinocytes. siRNA-mediated inhibition of PRINS gene resulted in altered cell morphology and gene expression alterations, as demonstrated in a microarray experiment.	Human	PRINS; NCRNA00074	NC_000010.10?from=24536051&to=24544975&report=genbank	20377629
366	pRNA	PARP1	RNA-Protein	binding	We demonstrate that PARP1 associates with TIP5, a subunit of the NoRC complex, via the noncoding pRNA and binds to silent rRNA genes after their replication in mid-late S phase.	Dictyostelium discoideum AX4	pRNA	N/A	22405650
367	PTENP1	PTEN	RNA-RNA	Co-expression	We find that PTENP1 is biologically active as it can regulate cellular levels of PTEN and exert a growth-suppressive role.	Human	PTENP1; PTH2; PTEN2; PTEN-rs; psiPTEN	NR_023917.1	20577206
368	PVT1	c-Myc	DNA-TF	Regulatory	PVT-1 regulates c-Myc gene transcription over a long distance. PVT-1 is also a downstream target of Myc proteins.	Human	PVT1; LINC00079; NCRNA00079	NR_003367.2	17503467
369	PVT1	c-Myc	RNA-DNA	Regulatory	PVT-1 regulates c-Myc gene transcription over a long distance. PVT-1 is also a downstream target of Myc proteins.	Human	PVT1; LINC00079; NCRNA00079	NR_003367.2	17503467
370	PVT1	P53	DNA-TF	Regulatory	The non-protein coding locus PVT1 is a p53-inducible target gene.	Human	PVT1; LINC00079; NCRNA00079	NR_003367.2	22110125
371	PVT1	YY1	RNA-DNA	Regulatory	The risk allele (G) of rs378854 reduces binding of the transcription factor YY1 in vitro. The region surrounding rs378854 interacts with the MYC and PVT1 promoters.Expression of the PVT1 oncogene in normal prostate tissue increased with the presence of the risk allele of rs378854, while expression of MYC was not affected.	Human	PVT1; LINC00079; NCRNA00079	NR_003367.2	21814516
372	PWR1	FLO11	RNA-DNA	Regulatory	PWR1 could promote FLO11 transcription by interfering with ICR1 transcription.	Saccharomyces cerevisiae S288c	PWR1	N/A	19805129
373	PWR1	Flo8	DNA-TF	Regulatory	PWR1 transcription requires Flo8 and is promoted by Rpd3L activity, but is repressed by Sfl1 function.	Saccharomyces cerevisiae S288c	PWR1	N/A	19805129
374	PWR1	ICR1	RNA-DNA	Regulatory	The fact that low level ICR1 is detected even in sfl1 mutants suggests that ICR1 may be constitutive, supporting a model in which its levels are tuned by PWR1 transcription.	Saccharomyces cerevisiae S288c	PWR1	N/A	19805129
375	PWR1	Rpd3L	DNA-TF	Regulatory	PWR1 transcription requires Flo8 and is promoted by Rpd3L activity, but is repressed by Sfl1 function.	Saccharomyces cerevisiae S288c	PWR1	N/A	19805129
376	PWR1	Sfl1	DNA-TF	Regulatory	PWR1 transcription requires Flo8 and is promoted by Rpd3L activity, but is repressed by Sfl1 function.	Saccharomyces cerevisiae S288c	PWR1	N/A	19805129
377	RepA	Ezh2	RNA-Protein	Regulatory	Recently, it was shown that a segment of the Xist RNA (called RepA) is important for the targeting of Ezh2 (a component of PRC2) and hence H3K27me3 to the X chromosome.	N/A	N/A	N/A	19239885
378	RepA	PRC2	RNA-Protein	Binding	Recruits PRC2 to the inactive X chromosome in mammals. Necessary for initiation of Xist upregulation and X chromosome silencing.	N/A	N/A	N/A	21256239
379	RepA	PRC2	RNA-Protein	Binding	Tsix represses Xist induction by several means, including altering the chromatin state of Xist, deploying Dnmt3a’s DNA methyltransferase activity, recruiting the RNAi machinery, and interfering with the ability of Xist and RepA RNA to engage Polycomb proteins.	N/A	N/A	N/A	21029862
380	RepA	PRC2	RNA-Protein	binding	RepA is sufficient to recruit PRC2 to chromatin in vivo.	N/A	N/A	N/A	19571179
381	RepA	PRC2	RNA-Protein	binding	We discovered a 1.6-kilobase ncRNA (RepA) within Xist and identified the Polycomb complex, PRC2, as its direct target.	N/A	N/A	N/A	18974356
382	RepA	XIST	RNA-DNA	Regulatory	Recruits PRC2 to the inactive X chromosome in mammals. Necessary for initiation of Xist upregulation and X chromosome silencing.	N/A	N/A	N/A	21256239
383	rncs-1	Dicer	RNA-Protein	binding	rncs-1 RNA Inhibits Dicer Cleavage，presumably by competing with dsRNA substrate for binding to Dicer or RDE-4.	Caenorhabditis elegans	rncs-1	NR_000961.1	18723671
384	rncs-1	RDE-4	RNA-Protein	binding	rncs-1 can bind RDE-4 in vitro.	Caenorhabditis elegans	rncs-1	NR_000961.1	18723671
385	roX1	MSL complex	RNA-Protein	binding	In Drosophila, dosage compensation is controlled by the male-specific lethal (MSL) complex consisting of at least five proteins and two noncoding RNAs, roX1 and roX2.	Drosophila melanogaster	roX1; BcDNA:GH10432; CR32777; Dmel\CR32777; EG:EG0002.2; roX; rox1	NR_002098.1	15229655
386	roX1	MSL1	RNA-Protein	binding	MSL/MSL2 is recruited by roX.	Drosophila melanogaster	roX1; BcDNA:GH10432; CR32777; Dmel\CR32777; EG:EG0002.2; roX; rox1	NR_002098.1	20573714
387	roX1	MSL2	RNA-Protein	binding	MSL/MSL2 is recruited by roX.	Drosophila melanogaster	roX1; BcDNA:GH10432; CR32777; Dmel\CR32777; EG:EG0002.2; roX; rox1	NR_002098.1	20573714
388	roX2	MSL complex	RNA-Protein	binding	Comparison of the high-resolution map from roX2 CHART with published data for the MSL complex achieved by using ChIP revealed that roX2 binds at the same sites in chromatin as the MSL complex.	Drosophila melanogaster	roX2; CR32665; Dmel\CR32665; roX; rox2; RoX2	NR_002105.2	22143764
389	roX2	MSL complex	RNA-Protein	binding	In Drosophila, dosage compensation is controlled by the male-specific lethal (MSL) complex consisting of at least five proteins and two noncoding RNAs, roX1 and roX2.	Drosophila melanogaster	roX2; CR32665; Dmel\CR32665; roX; rox2; RoX2	NR_002105.2	15229655
390	RRP1B	CSDA	RNA-Protein	binding	Tandem affinity purification demonstrated that RRP1B physically interacts with many nucleosome binding factors, including histone H1X, poly(ADP-ribose) polymerase 1, TRIM28 (tripartite motif-containing 28), and CSDA (cold shock domain protein A).	Human	RRP1B; Nnp1; RRP1; NNP1L; KIAA0179	NM_015056.2	19710015
391	RRP1B	H1X	RNA-Protein	binding	Tandem affinity purification demonstrated that RRP1B physically interacts with many nucleosome binding factors, including histone H1X, poly(ADP-ribose) polymerase 1, TRIM28 (tripartite motif-containing 28), and CSDA (cold shock domain protein A).	Human	RRP1B; Nnp1; RRP1; NNP1L; KIAA0179	NM_015056.2	19710015
392	RRP1B	PARP1	RNA-Protein	binding	However, it is highly unlikely that the RRP1B-PARP1 interaction is an experimental artifact, since there is loss of binding with the ΔC-term sample.	Human	RRP1B; Nnp1; RRP1; NNP1L; KIAA0179	NM_015056.2	19710015
393	RRP1B	TRIM28	RNA-Protein	binding	Tandem affinity purification demonstrated that RRP1B physically interacts with many nucleosome binding factors, including histone H1X, poly(ADP-ribose) polymerase 1, TRIM28 (tripartite motif-containing 28), and CSDA (cold shock domain protein A).	Human	RRP1B; Nnp1; RRP1; NNP1L; KIAA0179	NM_015056.2	19710015
394	SAF	Fas	RNA-RNA	Regulatory	Saf might regulate the expression of Fas alternative splice forms through pre-mRNA processing.	Human	FAS-AS1; SAF; FASAS; FAS-AS	NR_028371.1	15829500
395	Six3OS	Eya1	RNA-Protein	binding	Ezh2 and Eya1/3/4 directly bind Six3OS.	Mouse	Six3os1; Rncr1; Six3os; D17Mgi26; E130112H22Rik	NR_038082.1	21936910
396	Six3OS	Eya3	RNA-Protein	binding	Ezh2 and Eya1/3/4 directly bind Six3OS.	Mouse	Six3os1; Rncr1; Six3os; D17Mgi26; E130112H22Rik	NR_038082.1	21936910
397	Six3OS	Eya4	RNA-Protein	binding	Ezh2 and Eya1/3/4 directly bind Six3OS.	Mouse	Six3os1; Rncr1; Six3os; D17Mgi26; E130112H22Rik	NR_038082.1	21936910
398	Six3OS	Ezh2	RNA-Protein	binding	Ezh2 and Eya1/3/4 directly bind Six3OS.	Mouse	Six3os1; Rncr1; Six3os; D17Mgi26; E130112H22Rik	NR_038082.1	21936910
399	Six3OS	Six3	RNA-RNA	Co-expression	Six3OS was coexpressed with Six3 in retinal progenitors.	Mouse	Six3os1; Rncr1; Six3os; D17Mgi26; E130112H22Rik	NR_038082.1	21936910
400	Sox2dot	H3	RNA-Protein	Regulatory	The expression of Sox2dot and isoforms of Sox2ot with alternative TSSs in the mouse brain is supported by the presence of H3K4me3 histone modifications associated with their promoter regions.	N/A	N/A	N/A	19767420
401	Sox2ot	Sox2	RNA-RNA	Co-expression	Sox2 is a key transcription factor that is required for neural induction and maintenance of neural stem and progenitor cells, and a recent study demonstrated that the Sox2OT lncRNA, which contains the Sox2 gene within one of its introns and is transcribed in the same direction (Fantes et al., 2003), is expressed in regions of constitutive adult neurogenesis.	Mouse	Sox2ot; B230215L15Rik	NR_015580.1	20380817
402	SRA1	CCL20	RNA-Protein	binding	Eight bona fide SRA downstream target genes were identified (SLC2A3, SLC2A12, CCL20, TGFB2, DIO2, TMEM65, TBL1X, and TMPRSS2).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20219889
403	SRA1	cohesin complex	RNA-Protein	binding	p68/SRA also interacts with members of the cohesin complex.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20966046
404	SRA1	CTCF	RNA-Protein	binding	Here we showed that the DEAD-box RNA helicase p68 (DDX5) and its associated noncoding RNA, steroid receptor RNA activator (SRA), form a complex with CTCF that is essential for insulator function.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20966046
405	SRA1	CTCF	RNA-Protein	binding	DEAD-box RNA helicase p68 (DDX5) and its associated lncRNA, SRA (steroid receptor RNA activator), form a complex with CTCF. CTCF binds to specific genomic binding sequences and plays an important role in transcriptional insulation and long-range physical interaction with other CTCF sites.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	21496640
406	SRA1	DDX5	RNA-Protein	binding	DEAD-box RNA helicase p68 (DDX5) and its associated lncRNA, SRA (steroid receptor RNA activator), form a complex with CTCF. CTCF binds to specific genomic binding sequences and plays an important role in transcriptional insulation and long-range physical interaction with other CTCF sites.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	21496640
407	SRA1	DIO2	RNA-Protein	binding	Eight bona fide SRA downstream target genes were identified (SLC2A3, SLC2A12, CCL20, TGFB2, DIO2, TMEM65, TBL1X, and TMPRSS2).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20219889
408	SRA1	IGF2	RNA-RNA	Co-expression	In vivo depletion of SRA or p68 reduced CTCF-mediated insulator activity at the IGF2/H19 ICR, increased levels of IGF2 expression, and increased interactions between the endodermal enhancer and IGF2 promoter.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20966046
409	SRA1	MyoD	RNA-Protein	binding	We have found that the RNA helicases p68/p72 are MyoD-associated proteins and that the noncoding RNA SRA also immunoprecipitates with MyoD.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	17011493
410	SRA1	MyoD	RNA-RNA	Co-expression	SRA ncRNA is known to increase the activity of a range of nuclear receptors as well as the master regulator of muscle differentiation MyoD.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20855289
411	SRA1	p68	RNA-Protein	binding	Here we showed that the DEAD-box RNA helicase p68 (DDX5) and its associated noncoding RNA, steroid receptor RNA activator (SRA), form a complex with CTCF that is essential for insulator function.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20966046
412	SRA1	p68	RNA-Protein	binding	One of the RNAs associated with p68/p72 is the noncoding Steroid Receptors RNA Activator (SRA).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	17495528
413	SRA1	p72	RNA-Protein	binding	One of the RNAs associated with p68/p72 is the noncoding Steroid Receptors RNA Activator (SRA).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	17495528
414	SRA1	PPARG	RNA-Protein	binding	We show that the non-coding RNA, Steroid receptor RNA Activator (SRA), associates with PPARgamma and coactivates PPARgamma-dependent reporter gene expression.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	21152033
415	SRA1	SHARP	RNA-DNA	Regulatory	SRA is sequestered by the transcriptionally silent TRa2 to a repressive protein complex containing RNA-binding proteins SHARP and SLIRP.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20573714
416	SRA1	SLC2A12	RNA-Protein	binding	Eight bona fide SRA downstream target genes were identified (SLC2A3, SLC2A12, CCL20, TGFB2, DIO2, TMEM65, TBL1X, and TMPRSS2).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20219889
417	SRA1	SLC2A3	RNA-Protein	binding	Eight bona fide SRA downstream target genes were identified (SLC2A3, SLC2A12, CCL20, TGFB2, DIO2, TMEM65, TBL1X, and TMPRSS2).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20219889
418	SRA1	SLIRP	RNA-DNA	Regulatory	SRA is sequestered by the transcriptionally silent TRa2 to a repressive protein complex containing RNA-binding proteins SHARP and SLIRP.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20573714
419	SRA1	SRC1	RNA-Protein	binding	SRC1 complex is recruited by SRA.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20573714
420	SRA1	TBL1X	RNA-Protein	binding	Eight bona fide SRA downstream target genes were identified (SLC2A3, SLC2A12, CCL20, TGFB2, DIO2, TMEM65, TBL1X, and TMPRSS2).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20219889
421	SRA1	TGFB2	RNA-Protein	binding	Eight bona fide SRA downstream target genes were identified (SLC2A3, SLC2A12, CCL20, TGFB2, DIO2, TMEM65, TBL1X, and TMPRSS2).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20219889
422	SRA1	TMEM65	RNA-Protein	binding	Eight bona fide SRA downstream target genes were identified (SLC2A3, SLC2A12, CCL20, TGFB2, DIO2, TMEM65, TBL1X, and TMPRSS2).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20219889
423	SRA1	TMPRSS2	RNA-Protein	binding	Eight bona fide SRA downstream target genes were identified (SLC2A3, SLC2A12, CCL20, TGFB2, DIO2, TMEM65, TBL1X, and TMPRSS2).	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20219889
424	SRA1	TRa2	RNA-Protein	binding	SRA is sequestered by the transcriptionally silent TRa2 to a repressive protein complex containing RNA-binding proteins SHARP and SLIRP.	Human	SRA1; SRA; SRAP; STRAA1; pp7684	NM_001035235.3	20573714
425	SRG1	Cha4	RNA-Protein	binding	This regulation requires Cha4, a serine-dependent activator that binds to the SRG1 promoter and is required for SRG1 induction in the presence of serine.	Saccharomyces cerevisiae S288c	SRG1	N/A	16291644
426	SRG1	SER3	RNA-DNA	Regulatory	The 3' end of SRG1 contains regulatory elements within the SER3 promoter, and premature termination of SRG1 transcription prevents repression of SER3.	Saccharomyces cerevisiae S288c	SRG1	N/A	19239885
427	SRG1	SER3	RNA-DNA	Regulatory	Some cases, such as the SRG1 transcript in yeast that blocks activation of the SER3 gene, involve transcriptional regulation of a protein coding gene by an ncRNA.	Saccharomyces cerevisiae S288c	SRG1	N/A	19191220
428	SRG1	SER3	RNA-DNA	Regulatory	SRG1 transcription deposits nucleosomes over the SER3 promoter to prevent transcription factors from binding and activating SER3.	Saccharomyces cerevisiae S288c	SRG1	N/A	21873510
429	SRG1	Spt2	N/A	N/A	We find that Spt2 and Spt6 are required for the repression of SER3 by SRG1 transcription.	Saccharomyces cerevisiae S288c	SRG1	N/A	21220514
430	SRG1	Spt6	N/A	N/A	Repression by SRG1 transcription is dependent on the Spt6 and Spt16 transcription elongation factors.	Saccharomyces cerevisiae S288c	SRG1	N/A	21156811
431	SRG1	Spt6	N/A	N/A	We find that Spt2 and Spt6 are required for the repression of SER3 by SRG1 transcription.	Saccharomyces cerevisiae S288c	SRG1	N/A	21220514
432	TERRA	telomerase	RNA-Protein	binding	TERRA has now been demonstrated to physically interact with the telomerase through a repeat sequence complementary to the template sequence of telomerase RNA.	Mouse	Dmrt2; Terra	NM_145831.3	21925379
433	TERRA	TERT	RNA-Protein	binding	TERRA also contacts the telomerase reverse transcriptase (TERT) protein subunit independently of the telomerase template RNA moiety.	Mouse	Dmrt2; Terra	NM_145831.3	21925379
434	tie-1AS	TIE1	RNA-RNA	Co-expression	The tie-1AS lncRNA selectively binds tie-1 mRNA in vivo and regulates tie-1 transcript levels, resulting in specific defects in endothelial cell contact junctions in vivo and in vitro.	N/A	N/A	N/A	19880500
435	TK105282	Bai3	RNA-RNA	Co-expression	TK105282 were both co-expressed with their host gene Bai3,a brain specific inhibitor of angiogenesis.	N/A	N/A	N/A	21247874
436	TK111271	Lck	RNA-RNA	Co-expression	the lncRNA TK111271 is co-expressed and co-located with Lck, a key signal gene in T-cell development.	N/A	N/A	N/A	21247874
437	TK99129	Bai3	RNA-RNA	Co-expression	TK99129 and TK105282 were both co-expressed with their host gene Bai3,a brain specific inhibitor of angiogenesis.	N/A	N/A	N/A	21247874
438	TP53TG1	TP53	DNA-TF	Regulatory	TP53 target gene 1	Human	TP53TG1; P53TG1; TP53AP1; P53TG1-D; LINC00096; NCRNA00096	NR_015381.1	9713990
439	TRE1	Ash1	RNA-Protein	binding	Ash1 is recruited by TRE1-3.	N/A	N/A	N/A	20573714
440	TRE2	Ash1	RNA-Protein	binding	Ash1 is recruited by TRE1-3.	N/A	N/A	N/A	20573714
441	TRE3	Ash1	RNA-Protein	binding	Ash1 is recruited by TRE1-3.	N/A	N/A	N/A	20573714
442	Tsix	Oct4	RNA-Protein	binding	Oct4 directly binds Tsix and Xite, two regulatory noncoding RNA genes of the X-inactivation centre, and also complexes with XCI trans-factors, Ctcf and Yy1.	Mouse	Tsix	NR_002844.2	19536159
443	Tsix	RepA	RNA-RNA	Regulatory	Epigenetically silences Xist expression by inhibiting RepA recruitment of polycomb complexes to maintain the active X chromosome in females.	Mouse	Tsix	NR_002844.2	21256239
444	Tsix	XIST	RNA-DNA	Regulatory	Tsix is associated with both enrichment of the H3K4me3 active mark and prevention of the deposition of the repressive mark H3K27me3 within the body of the Xist gene. Tsix, for instance, may be subject to Xist silencing at the onset of XCI.	Mouse	Tsix	NR_002844.2	21329697
445	Tsix	XIST	RNA-DNA	Regulatory	Epigenetically silences Xist expression by inhibiting RepA recruitment of polycomb complexes to maintain the active X chromosome in females.	Mouse	Tsix	NR_002844.2	21256239
446	Tsix	XIST	RNA-DNA	Regulatory	Tsix represses Xist induction by several means, including altering the chromatin state of Xist, deploying Dnmt3a’s DNA methyltransferase activity, recruiting the RNAi machinery, and interfering with the ability of Xist and RepA RNA to engage Polycomb proteins.	Mouse	Tsix	NR_002844.2	21029862
447	Tsix	XIST	RNA-DNA	Regulatory	Tsix directly regulates its transcription.	Mouse	Tsix	NR_002844.2	16507360
448	Tsix	XIST	RNA-RNA	Regulatory	The noncoding Tsix RNA is an antisense repressor of Xist and regulates X inactivation in mice.	Mouse	Tsix	NR_002844.2	21852535
449	Tsix	XIST	RNA-RNA	Regulatory	Xist is controlled by two parallel RNA switches – Tsix for Xa and Jpx for Xi. Tsix represses Xist on Xa.	Mouse	Tsix	NR_002844.2	21029862
450	Tsix	XIST	RNA-RNA	Regulatory	For the active X, the antisense Tsix RNA is an established Xist repressor.	Mouse	Tsix	NR_002844.2	21029862
451	TUG1	IgG	RNA-Protein	binding	binding with IgG shown by RIP-Chip data.	Human	TUG1; TI-227H; LINC00080; NCRNA00080	NR_002323.1	19571010
452	TUG1	p53	DNA-TF	Regulatory	TUG1 is induced by p53, binds to PRC2, and has a role in repressing specific genes involved in cell-cycle regulation.	Human	TUG1; TI-227H; LINC00080; NCRNA00080	NR_002323.1	19571010
453	TUG1	Pc2	DNA-Protein	Regulatory	methylation/demethylation of Polycomb 2 protein (Pc2) controls relocation of growth-control genes between Polycomb bodies (PcGs) and interchromatin granules (ICGs) in response to growth signals. This movement is the consequence of binding of methylated and unmethylated Pc2 to the ncRNAs TUG1 and MALAT1/NEAT2.	Human	TUG1; TI-227H; LINC00080; NCRNA00080	NR_002323.1	22078878
454	TUG1	PRC2	RNA-Protein	Binding	TUG1 is induced by p53, binds to PRC2, and has a role in repressing specific genes involved in cell-cycle regulation.	Human	TUG1; TI-227H; LINC00080; NCRNA00080	NR_002323.1	19571010
455	TUG1	PRC2	RNA-Protein	binding	binding with PRC2 shown by RIP-Chip data.	Human	TUG1; TI-227H; LINC00080; NCRNA00080	NR_002323.1	19571010
456	TUG1	PRC2	RNA-Protein	Binding	Required for the proper formation of photoreceptors in the developing retina. Tug1 associates with PRC2 and represses a number of cell cycle genes.	Human	TUG1; TI-227H; LINC00080; NCRNA00080	NR_002323.1	21256239
457	Tug-1	PRC2	RNA-Protein	binding	Numerous lincRNAs are physically associated with PRC2.	Mouse	Tug1; AI316828	NR_002321.1	19571010
458	Vax2OS	Crx	DNA-TF	Regulatory	Vax2OS was independently identified as a transcriptional target of both Crx and Nrl in a recent microarray-based screen.	Mouse	Vax2os1; Vax2os	NR_002873.2	19191220
459	Vax2OS	Nrl	DNA-TF	Regulatory	Vax2OS was independently identified as a transcriptional target of both Crx and Nrl in a recent microarray-based screen.	Mouse	Vax2os1; Vax2os	NR_002873.2	19191220
460	WRAP53	TP53	RNA-RNA	Regulatory	Wrap53 regulates p53 via Wrap53/p53 RNA interaction.	Human	WRAP53; DKCB3; TCAB1; WDR79	NM_001143990.1	19250907
461	WRAP53	TP53	RNA-RNA	Regulatory	Wrap53 is a natural antisense transcript of p53 that regulates endogenous p53 mRNA levels and is furthermore required for induction of p53 protein by targeting the 5'untranslated region of p53 mRNA.	Human	WRAP53; DKCB3; TCAB1; WDR79	NM_001143990.1	19571673
462	Xist	Ezh2	RNA-Protein	binding	Ezh2 interacts with HOTAIR and Xist.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	21123648
463	Xist	EZH2	RNA-Protein	Binding	HOTAIR, Kcnq1ot and Xist all mediate their effects by interacting with the Polycomb-repressive complex 2 (PRC2) component Ezh2 (enhancer of zeste homolog 2 (Drosophila)) and modulating histone methylation.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	21936910
464	Xist	H3	RNA-Protein	Regulatory	The concentration of PRC2 at the 59 end of Xist is intriguing because recruitment of PRC2 and H3-K27me3 are two of the earliest changes to occur on the X following Xist up-regulation.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	19684108
465	Xist	HNRNPU	RNA-Protein	binding	Xist RNA and hnRNP U interact and upon depletion of hnRNP U, Xist RNA is detached from the Xi and diffusely localized into the nucleoplasm.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	20833368
466	Xist	HNRNPU	RNA-Protein	binding	Xist RNA and hnRNP U interact, and depletion of hnRNP U causes Xist to detach from the Xi and to localize diffusely in the nucleoplasm.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	21925379
467	Xist	PRC2	RNA-Protein	binding	The concentration of PRC2 at the 59 end of Xist is intriguing because recruitment of PRC2 and H3-K27me3 are two of the earliest changes to occur on the X following Xist up-regulation.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	19684108
468	XIST	PRC2	RNA-Protein	binding	A large noncoding RNA encoded within the 5  of XIST that can target PRC2 to the inactive X chromosome.	Human	XIST; SXI1; swd66; DXS1089; DXS399E; LINC00001; NCRNA00001	NR_001564.2	19571010
469	Xist	PRC2	RNA-Protein	binding	During female development, Xist RNA is expressed from the inactive X and coats the X chromosome from which it is transcribed, leading to recruitment of Polycomb repressive complex 2 (PRC2), which trimethylates histone H3 at lysine 27 to silence transcription.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	21496640
470	Xist	PRC2	RNA-Protein	binding	X chromosome inactivation requires Xist, an ncRNA that coats the X and recruits Polycomb proteins.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	21029862
471	Xist	PRC2	RNA-Protein	binding	CDK1 and CDK2 phosphorylate EZH2 at threonine 350 (T350) and that T350 phosphorylation is important for the binding of EZH2 to PRC2 recruiters, such as noncoding RNAs (ncRNAs) HOTAIR and XIST.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	21278485
472	Xist	PRC2	RNA-Protein	Binding	Tsix represses Xist induction by several means, including altering the chromatin state of Xist, deploying Dnmt3a’s DNA methyltransferase activity, recruiting the RNAi machinery, and interfering with the ability of Xist and RepA RNA to engage Polycomb proteins.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	21029862
473	Xist	Rnf12	RNA-RNA	Co-expression	Overexpression of Rnf12 ectopically induces Xist expression in XY cells.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	21029862
474	Xist	SAF-A	RNA-Protein	binding	SAF-A is a plausible candidate for an anchor point of the Xist nrRNA to inactive X-chromosomes.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	20940252
475	XIST	TAP/NXF1	RNA-Protein	binding	The export factor TAP/NXF1 binds poorly to XIST RNA in comparison to exported mRNAs, suggesting that reduced TAP/NFX1 binding may contribute to nuclear retention of XIST RNA.	Human	XIST; SXI1; swd66; DXS1089; DXS399E; LINC00001; NCRNA00001	NR_001564.2	17333237
476	Xist	YY1	RNA-Protein	binding	Here, we define the nucleation center for Xist RNA and show that YY1 docks Xist particles onto the X chromosome.	Mouse	Xist; AI314753; A430022B11	NR_001463.3	21729784
477	Xite	Oct4	RNA-Protein	binding	Oct4 directly binds Tsix and Xite, two regulatory noncoding RNA genes of the X-inactivation centre, and also complexes with XCI trans-factors, Ctcf and Yy1.	Mouse	Xite; Xca; Xce	N/A	19536159
478	alpha-280/250	RPS14	RNA-DNA	Regulatory	Regulates RPS14 transcription in humans.	Human	N/A	N/A	7867928