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
-
Kanduri
(2016),
Long noncoding RNAs: Lessons from genomic imprinting.,
Biochim. Biophys. Acta
-
Liu
(2016),
The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster.,
Nucleic Acids Res.
-
Miano
(2016),
Luminal long non-coding RNAs regulated by estrogen receptor alpha in a ligand-independent manner show functional roles in breast cancer.,
Oncotarget
-
Zhang
(2016),
Long non-coding RNA chromogenic in situ hybridisation signal pattern correlation with breast tumour pathology.,
J. Clin. Pathol.
-
Bao
(2015),
The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters.,
Cell Res.
-
Cajigas
(2015),
Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling.,
Development
-
Chen
(2015),
Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity.,
Sci Rep
-
Chen
(2015),
Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA.,
Sci Rep
-
Engelhardt
(2015),
Evolution of the unspliced transcriptome.,
BMC Evol. Biol.
-
Fan
(2015),
Long non-coding RNA ROR decoys gene-specific histone methylation to promote tumorigenesis.,
Genome Biol.
-
Fan
(2015),
Erratum to: Long non-coding RNA ROR decoys gene-specific histone methylation to promote tumorigenesis.,
Genome Biol.
-
He
(2015),
LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis.,
Bioinformatics
-
Quek
(2015),
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs.,
Nucleic Acids Res.
-
Schultz
(2015),
Enhancers compete with a long non-coding RNA for regulation of the Kcnq1 domain.,
Nucleic Acids Res.
-
Smolle
(2015),
Long Non-Coding RNAs in Endometrial Carcinoma.,
Int J Mol Sci
-
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
-
Wang
(2015),
Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer.,
Nucleic Acids Res.
-
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
-
Werner
(2015),
Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes.,
Cell Rep
-
Yang
(2015),
The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation.,
Genome Biol.
-
Chalei
(2014),
The long non-coding RNA Dali is an epigenetic regulator of neural differentiation.,
Elife
-
Cordeiro
(2014),
Relevance of genomic imprinting in intrauterine human growth expression of CDKN1C, H19, IGF2, KCNQ1 and PHLDA2 imprinted genes.,
J. Assist. Reprod. Genet.
-
Guallar
(2014),
RNA-binding proteins in pluripotency, differentiation, and reprogramming.,
Front Biol (Beijing)
-
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
-
Li
(2014),
[Long noncoding RNAs in gene expression control].,
Zhong Nan Da Xue Xue Bao Yi Xue Ban
-
Pestell
(2014),
Long and noncoding RNAs (lnc-RNAs) determine androgen receptor dependent gene expression in prostate cancer growth in vivo.,
Asian J. Androl.
-
Skroblin
(2014),
"Going long": long non-coding RNAs as biomarkers.,
Circ. Res.
-
Su
(2014),
Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes.,
Oncotarget
-
Sun
(2014),
A novel antisense long noncoding RNA within the IGF1R gene locus is imprinted in hematopoietic malignancies.,
Nucleic Acids Res.
-
Vausort
(2014),
Long noncoding RNAs in patients with acute myocardial infarction.,
Circ. Res.
-
Beato
(2013),
A new role for an old player: steroid receptor RNA Activator (SRA) represses hormone inducible genes.,
Transcription
-
Du
(2013),
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.,
Nat. Struct. Mol. Biol.
-
Kapusta
(2013),
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.,
PLoS Genet.
-
Kobayashi
(2013),
Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc.,
Epigenetics
-
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.
-
Niemczyk
(2013),
Imprinted chromatin around DIRAS3 regulates alternative splicing of GNG12-AS1, a long noncoding RNA.,
Am. J. Hum. Genet.
-
Papait
(2013),
Long noncoding RNA: a new player of heart failure?,
J Cardiovasc Transl Res
-
St Laurent
(2013),
VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer.,
Genome Biol.
-
Vallot
(2013),
Long non-coding RNAs and human X-chromosome regulation: a coat for the active X chromosome.,
RNA Biol
-
Wan
(2013),
Long non-coding RNA ANRIL (CDKN2B-AS) is induced by the ATM-E2F1 signaling pathway.,
Cell. Signal.
-
Wan
(2013),
A novel tetranucleotide repeat polymorphism within KCNQ1OT1 confers risk for hepatocellular carcinoma.,
DNA Cell Biol.
-
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.
-
Clark
(2012),
Genome-wide analysis of long noncoding RNA stability.,
Genome Res.
-
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.
-
Lipovich
(2012),
Activity-dependent human brain coding/noncoding gene regulatory networks.,
Genetics
-
Miyagawa
(2012),
Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles.,
RNA
-
Morán
(2012),
Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes.,
Cell Metab.
-
Sati
(2012),
Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci.,
Nucleic Acids Res.
-
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.
-
Troy
(2012),
Genetic "lnc"-age of noncoding RNAs to human disease.,
J. Clin. Invest.
-
Vizoso
(2012),
The activatory long non-coding RNA DBE-T reveals the epigenetic etiology of facioscapulohumeral muscular dystrophy.,
Cell Res.
-
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.
-
Golding
(2011),
Depletion of Kcnq1ot1 non-coding RNA does not affect imprinting maintenance in stem cells.,
Development
-
Jones
(2011),
An extended domain of Kcnq1ot1 silencing revealed by an imprinted fluorescent reporter.,
Mol. Cell. Biol.
-
Kanduri
(2011),
Kcnq1ot1: a chromatin regulatory RNA.,
Semin. Cell Dev. Biol.
-
Lin
(2011),
Nonallelic transcriptional roles of CTCF and cohesins at imprinted loci.,
Mol. Cell. Biol.
-
Nakagawa
(2011),
eXIST with matrix-associated proteins.,
Trends Cell Biol.
-
Saxena
(2011),
Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs.,
Bioessays
-
Mohammad
(2010),
Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1.,
Development
-
Zhao
(2010),
Genome-wide identification of polycomb-associated RNAs by RIP-seq.,
Mol. Cell
-
Redrup
(2009),
The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing.,
Development
-
Mohammad
(2008),
Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region.,
Mol. Cell. Biol.
-
Pandey
(2008),
Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation.,
Mol. Cell
-
Terranova
(2008),
Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos.,
Dev. Cell
-
Fitzpatrick
(2007),
Allele-specific binding of CTCF to the multipartite imprinting control region KvDMR1.,
Mol. Cell. Biol.
-
Murakami
(2007),
Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1.,
J. Hum. Genet.
-
Higashimoto
(2006),
Imprinting disruption of the CDKN1C/KCNQ1OT1 domain: the molecular mechanisms causing Beckwith-Wiedemann syndrome and cancer.,
Cytogenet. Genome Res.
-
Mancini-Dinardo
(2006),
Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes.,
Genes Dev.
-
Nakano
(2006),
Expression profile of LIT1/KCNQ1OT1 and epigenetic status at the KvDMR1 in colorectal cancers.,
Cancer Sci.
-
Paulsen
(2005),
Evolution of the Beckwith-Wiedemann syndrome region in vertebrates.,
Genome Res.
-
Pandey
(2004),
NF-Y regulates the antisense promoter, bidirectional silencing, and differential epigenetic marks of the Kcnq1 imprinting control region.,
J. Biol. Chem.
-
Thakur
(2004),
An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region.,
Mol. Cell. Biol.
-
Umlauf
(2004),
Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes.,
Nat. Genet.
-
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.
-
DeBaun
(2002),
Epigenetic alterations of H19 and LIT1 distinguish patients with Beckwith-Wiedemann syndrome with cancer and birth defects.,
Am. J. Hum. Genet.
-
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.
-
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.
-
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.
-
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 |