Transcript: KCNQ1OT1:4

Basic information

LNCipedia transcript ID: KCNQ1OT1:4 
LNCipedia gene ID: KCNQ1OT1
Location (hg38): chr11:2675326-2699994
Strand: -
Class: antisense
Sequence Ontology term: antisense_lncRNA
Transcript size: 24669 bp
Exons: 1
Sources: Gencode v13; Ensembl release 68 - Jul 2012
Alternative transcript names: ENST00000557213.1; KCNQ1OT1-001; OTTHUMT00000411275.1
Alternative gene names: ENSG00000258492.1; KCNQ1OT1; OTTHUMG00000171022.1; KvDMR1; KCNQ1-AS2; KvLQT1-AS; LIT1; NCRNA00012


RNA sequence:

Structure:

Protein coding potential

Metric Raw result Interpretation
PRIDE reprocessing 2.0 0 non-coding 
Lee translation initiation sites 0 non-coding 
PhyloCSF score 4.1844 non-coding 
CPAT coding probability 10.75% non-coding 
Bazzini small ORFs 0 non-coding 

In stringent set: yes

Locus conservation

Locus conservation?
KCNQ1OT1:4 no no no no

Available literature

  1. Kanduri (2016), Long noncoding RNAs: Lessons from genomic imprinting., Biochim. Biophys. Acta
  2. Liu (2016), The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster., Nucleic Acids Res.
  3. Miano (2016), Luminal long non-coding RNAs regulated by estrogen receptor alpha in a ligand-independent manner show functional roles in breast cancer., Oncotarget
  4. Zhang (2016), Long non-coding RNA chromogenic in situ hybridisation signal pattern correlation with breast tumour pathology., J. Clin. Pathol.
  5. Bao (2015), The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters., Cell Res.
  6. Cajigas (2015), Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling., Development
  7. Chen (2015), Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity., Sci Rep
  8. Chen (2015), Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA., Sci Rep
  9. Engelhardt (2015), Evolution of the unspliced transcriptome., BMC Evol. Biol.
  10. Fan (2015), Long non-coding RNA ROR decoys gene-specific histone methylation to promote tumorigenesis., Genome Biol.
  11. Fan (2015), Erratum to: Long non-coding RNA ROR decoys gene-specific histone methylation to promote tumorigenesis., Genome Biol.
  12. He (2015), LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis., Bioinformatics
  13. Quek (2015), lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs., Nucleic Acids Res.
  14. Schultz (2015), Enhancers compete with a long non-coding RNA for regulation of the Kcnq1 domain., Nucleic Acids Res.
  15. Smolle (2015), Long Non-Coding RNAs in Endometrial Carcinoma., Int J Mol Sci
  16. Tantai (2015), Combined identification of long non-coding RNA XIST and HIF1A-AS1 in serum as an effective screening for non-small cell lung cancer., Int J Clin Exp Pathol
  17. Wang (2015), Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer., Nucleic Acids Res.
  18. Wang (2015), Upregulated lncRNA-UCA1 contributes to progression of lung cancer and is closely related to clinical diagnosis as a predictive biomarker in plasma., Int J Clin Exp Med
  19. Werner (2015), Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes., Cell Rep
  20. Yang (2015), The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation., Genome Biol.
  21. Chalei (2014), The long non-coding RNA Dali is an epigenetic regulator of neural differentiation., Elife
  22. Cordeiro (2014), Relevance of genomic imprinting in intrauterine human growth expression of CDKN1C, H19, IGF2, KCNQ1 and PHLDA2 imprinted genes., J. Assist. Reprod. Genet.
  23. Guallar (2014), RNA-binding proteins in pluripotency, differentiation, and reprogramming., Front Biol (Beijing)
  24. Li (2014), Comparison of long non‑coding RNAs, microRNAs and messenger RNAs involved in initiation and progression of esophageal squamous cell carcinoma., Mol Med Rep
  25. Li (2014), [Long noncoding RNAs in gene expression control]., Zhong Nan Da Xue Xue Bao Yi Xue Ban
  26. Pestell (2014), Long and noncoding RNAs (lnc-RNAs) determine androgen receptor dependent gene expression in prostate cancer growth in vivo., Asian J. Androl.
  27. Skroblin (2014), "Going long": long non-coding RNAs as biomarkers., Circ. Res.
  28. Su (2014), Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes., Oncotarget
  29. Sun (2014), A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies., Nucleic Acids Res.
  30. Vausort (2014), Long noncoding RNAs in patients with acute myocardial infarction., Circ. Res.
  31. Beato (2013), A new role for an old player: steroid receptor RNA Activator (SRA) represses hormone inducible genes., Transcription
  32. Du (2013), Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer., Nat. Struct. Mol. Biol.
  33. Kapusta (2013), Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs., PLoS Genet.
  34. Kobayashi (2013), Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc., Epigenetics
  35. Nelissen (2013), Placentas from pregnancies conceived by IVF/ICSI have a reduced DNA methylation level at the H19 and MEST differentially methylated regions., Hum. Reprod.
  36. Niemczyk (2013), Imprinted chromatin around DIRAS3 regulates alternative splicing of GNG12-AS1, a long noncoding RNA., Am. J. Hum. Genet.
  37. Papait (2013), Long noncoding RNA: a new player of heart failure?, J Cardiovasc Transl Res
  38. St Laurent (2013), VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer., Genome Biol.
  39. Vallot (2013), Long non-coding RNAs and human X-chromosome regulation: a coat for the active X chromosome., RNA Biol
  40. Wan (2013), Long non-coding RNA ANRIL (CDKN2B-AS) is induced by the ATM-E2F1 signaling pathway., Cell. Signal.
  41. Wan (2013), A novel tetranucleotide repeat polymorphism within KCNQ1OT1 confers risk for hepatocellular carcinoma., DNA Cell Biol.
  42. Chiesa (2012), The KCNQ1OT1 imprinting control region and non-coding RNA: new properties derived from the study of Beckwith-Wiedemann syndrome and Silver-Russell syndrome cases., Hum. Mol. Genet.
  43. Clark (2012), Genome-wide analysis of long noncoding RNA stability., Genome Res.
  44. Li (2012), AS1DHRS4, a head-to-head natural antisense transcript, silences the DHRS4 gene cluster in cis and trans., Proc. Natl. Acad. Sci. U.S.A.
  45. Lipovich (2012), Activity-dependent human brain coding/noncoding gene regulatory networks., Genetics
  46. Miyagawa (2012), Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles., RNA
  47. Morán (2012), Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes., Cell Metab.
  48. Sati (2012), Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci., Nucleic Acids Res.
  49. Tilgner (2012), Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs., Genome Res.
  50. Troy (2012), Genetic "lnc"-age of noncoding RNAs to human disease., J. Clin. Invest.
  51. Vizoso (2012), The activatory long non-coding RNA DBE-T reveals the epigenetic etiology of facioscapulohumeral muscular dystrophy., Cell Res.
  52. Al-Khtib (2011), Vitrification at the germinal vesicle stage does not affect the methylation profile of H19 and KCNQ1OT1 imprinting centers in human oocytes subsequently matured in vitro., Fertil. Steril.
  53. Golding (2011), Depletion of Kcnq1ot1 non-coding RNA does not affect imprinting maintenance in stem cells., Development
  54. Jones (2011), An extended domain of Kcnq1ot1 silencing revealed by an imprinted fluorescent reporter., Mol. Cell. Biol.
  55. Kanduri (2011), Kcnq1ot1: a chromatin regulatory RNA., Semin. Cell Dev. Biol.
  56. Lin (2011), Nonallelic transcriptional roles of CTCF and cohesins at imprinted loci., Mol. Cell. Biol.
  57. Nakagawa (2011), eXIST with matrix-associated proteins., Trends Cell Biol.
  58. Saxena (2011), Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs., Bioessays
  59. Mohammad (2010), Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1., Development
  60. Zhao (2010), Genome-wide identification of polycomb-associated RNAs by RIP-seq., Mol. Cell
  61. Redrup (2009), The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing., Development
  62. Mohammad (2008), Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region., Mol. Cell. Biol.
  63. Pandey (2008), Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation., Mol. Cell
  64. Terranova (2008), Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos., Dev. Cell
  65. Fitzpatrick (2007), Allele-specific binding of CTCF to the multipartite imprinting control region KvDMR1., Mol. Cell. Biol.
  66. Murakami (2007), Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1., J. Hum. Genet.
  67. Higashimoto (2006), Imprinting disruption of the CDKN1C/KCNQ1OT1 domain: the molecular mechanisms causing Beckwith-Wiedemann syndrome and cancer., Cytogenet. Genome Res.
  68. Mancini-Dinardo (2006), Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes., Genes Dev.
  69. Nakano (2006), Expression profile of LIT1/KCNQ1OT1 and epigenetic status at the KvDMR1 in colorectal cancers., Cancer Sci.
  70. Paulsen (2005), Evolution of the Beckwith-Wiedemann syndrome region in vertebrates., Genome Res.
  71. Pandey (2004), NF-Y regulates the antisense promoter, bidirectional silencing, and differential epigenetic marks of the Kcnq1 imprinting control region., J. Biol. Chem.
  72. Thakur (2004), An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region., Mol. Cell. Biol.
  73. Umlauf (2004), Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes., Nat. Genet.
  74. Gicquel (2003), In vitro fertilization may increase the risk of Beckwith-Wiedemann syndrome related to the abnormal imprinting of the KCN1OT gene., Am. J. Hum. Genet.
  75. DeBaun (2002), Epigenetic alterations of H19 and LIT1 distinguish patients with Beckwith-Wiedemann syndrome with cancer and birth defects., Am. J. Hum. Genet.
  76. Horike (2000), Targeted disruption of the human LIT1 locus defines a putative imprinting control element playing an essential role in Beckwith-Wiedemann syndrome., Hum. Mol. Genet.
  77. Lee (1999), Loss of imprinting of a paternally expressed transcript, with antisense orientation to KVLQT1, occurs frequently in Beckwith-Wiedemann syndrome and is independent of insulin-like growth factor II imprinting., Proc. Natl. Acad. Sci. U.S.A.
  78. Mitsuya (1999), LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using monochromosomal hybrids., Hum. Mol. Genet.
  79. Smilinich (1999), A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith-Wiedemann syndrome., Proc. Natl. Acad. Sci. U.S.A.


LNCipedia transcript ID history

LNCipedia version LNCipedia transcript ID
3.1 lnc-CDKN1C-3:2
4.0 KCNQ1OT1:4
4.1 KCNQ1OT1:4
5.0 KCNQ1OT1:4
5.1 KCNQ1OT1:4
5.2 KCNQ1OT1:4