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KCNQ1OT1 KCNQ1 opposite strand/antisense transcript 1 [ Homo sapiens (human) ]

Gene ID: 10984, updated on 25-Jan-2022


Official Symbol
KCNQ1OT1provided by HGNC
Official Full Name
KCNQ1 opposite strand/antisense transcript 1provided by HGNC
Primary source
See related
Ensembl:ENSG00000269821 MIM:604115; AllianceGenome:HGNC:6295
Gene type
RefSeq status
Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LIT1; Kncq1; KvDMR1; KCNQ10T1; KCNQ1-AS2; KvLQT1-AS; NCRNA00012
Human chromosomal region 11p15.5 contains two clusters of epigenetically-regulated genes that are expressed from only one chromosome in a parent-of-origin manner. Each cluster, or imprinted domain, is regulated by a functionally independent imprinting control region (ICR). The human CDKN1C/KCNQ1OT1 domain is regulated by an ICR located in an intron of KCNQ1, and contains at least eight genes that are expressed exclusively or preferentially from the maternally-inherited allele. The DNA of the ICR is specifically methylated on the maternally-inherited chromosome, and unmethylated on the paternally-inherited chromosome. The ICR contains the promoter of the KCNQ1OT1 gene that is exclusively expressed from the paternal allele. The KCNQ1OT1 transcript is the antisense to the KCNQ1 gene and is a unspliced long non-coding RNA. It interacts with chromatin and regulates transcription of multiple target genes through epigenetic modifications. The transcript is abnormally expressed from both chromosomes in most patients with Beckwith-Wiedemann syndrome, and the transcript also plays an important role in colorectal carcinogenesis. [provided by RefSeq, Apr 2012]
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Genomic context

See KCNQ1OT1 in Genome Data Viewer
Exon count:
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (2608328..2699998, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (2629558..2721228, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene transient receptor potential cation channel subfamily M member 5 Neighboring gene potassium voltage-gated channel subfamily Q member 1 Neighboring gene Sharpr-MPRA regulatory region 10946 Neighboring gene nonconserved acetylation island sequence 52 enhancer Neighboring gene cytochrome c oxidase subunit 6C pseudogene 18

Genomic regions, transcripts, and products


GeneRIFs: Gene References Into Functions

What's a GeneRIF?


Associated conditions

Description Tests
Beckwith-Wiedemann syndrome Compare labs

Copy number response

Copy number response

Little evidence for dosage pathogenicity (Last evaluated 2012-03-22)

ClinGen Genome Curation PagePubMed

Some evidence for dosage pathogenicity (Last evaluated 2012-03-22)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Genome-wide association study identifies 8 novel loci associated with blood pressure responses to interventions in Han Chinese.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies in african americans provides insights into the genetic architecture of type 2 diabetes.
EBI GWAS Catalog
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.
EBI GWAS Catalog


Products Interactant Other Gene Complex Source Pubs Description

General gene information


Other Names

  • KCNQ1 antisense RNA 2 (non-protein coding)
  • KCNQ1 opposite strand/antisense transcript 1 (non-protein coding)
  • KCNQ1 overlapping transcript 1 (non-protein coding)
  • long QT intronic transcript 1

Clone Names

  • FLJ41078

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables miRNA binding IDA
Inferred from Direct Assay
more info
Component Evidence Code Pubs
located_in nucleolus IEA
Inferred from Electronic Annotation
more info

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.


  1. NG_016178.2 RefSeqGene

    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1052


  1. NR_002728.3 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC021424, AC124055

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly


  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    2608328..2699998 complement
    GenBank, FASTA, Sequence Viewer (Graphics)
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