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 lea... See more...

Aliases for KCNQ1OT1 Gene

Subcategory (RNA class) for KCNQ1OT1 Gene

lncRNA

Number of RNA Genes sources:

3 / 17

Aliases for KCNQ1OT1 Gene

  • KCNQ1 Opposite Strand/Antisense Transcript 1 2 3 5
  • KCNQ1OT1 2 5 165
  • KCNQ1 Opposite Strand/Antisense Transcript 1 (Non-Protein Coding) 2 3
  • KCNQ1 Overlapping Transcript 1 (Non-Protein Coding) 2 3
  • KCNQ1 Antisense RNA 2 (Non-Protein Coding) 2 3
  • NCRNA00012 2 3
  • KCNQ1-AS2 2 3
  • KvLQT1-AS 2 3
  • KvDMR1 2 3
  • LIT1 2 3
  • Long QT Intronic Transcript 1 3
  • Non-Protein Coding RNA 12 2
  • NONHSAG007431.2 91
  • HSALNG0082237 164
  • HSALNG0082235 164
  • HSALNG0082236 164
  • KCNQ10T1 3
  • Kncq1 3

External Ids for KCNQ1OT1 Gene

Previous GeneCards Identifiers for KCNQ1OT1 Gene

  • GC11U990199
  • GC11M002674
  • GC11M002450

Summaries for KCNQ1OT1 Gene

Entrez Gene Summary for KCNQ1OT1 Gene

  • 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]

GeneCards Summary for KCNQ1OT1 Gene

KCNQ1OT1 (KCNQ1 Opposite Strand/Antisense Transcript 1) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with KCNQ1OT1 include Beckwith-Wiedemann Syndrome and Hemihyperplasia, Isolated.

Gene Wiki entry for KCNQ1OT1 Gene

Rfam classification for KCNQ1OT1 Gene

  • KCNQ1 overlapping transcript 1 conserved region 5
  • KCNQ1 overlapping transcript 1 conserved region 3
  • KCNQ1 overlapping transcript 1 conserved region 2
  • KCNQ1 overlapping transcript 1 conserved region 1

Additional gene information for KCNQ1OT1 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary and piRNA Summary for KCNQ1OT1 Gene

Genomics for KCNQ1OT1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for KCNQ1OT1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KCNQ1OT1 on the GeneHancer Hub at the UCSC Golden Path

Top Transcription factor binding sites by QIAGEN in the KCNQ1OT1 gene promoter:
  • MyoD

Genomic Locations for KCNQ1OT1 Gene

Genomic Locations for KCNQ1OT1 Gene
chr11:2,597,114-2,699,998
(GRCh38/hg38)
Size:
102,885 bases
Orientation:
Minus strand
chr11:2,629,558-2,721,228
(GRCh37/hg19)
Size:
91,671 bases
Orientation:
Minus strand

Genomic View for KCNQ1OT1 Gene

Genes around KCNQ1OT1 on UCSC Golden Path with GeneCards custom track
KCNQ1OT1 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Cytogenetic band:
KCNQ1OT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KCNQ1OT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KCNQ1OT1 Gene

Proteins for KCNQ1OT1 Gene

Post-translational modifications for KCNQ1OT1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for KCNQ1OT1 Gene

Domains & Families for KCNQ1OT1 Gene

Gene Families for KCNQ1OT1 Gene

genes like me logo Genes that share domains with KCNQ1OT1: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for KCNQ1OT1 Gene

Function for KCNQ1OT1 Gene

Molecular function for KCNQ1OT1 Gene

GENATLAS Biochemistry:
intronic transcript 1,embedded in intron 9 (and 10) of KCNQ1,in opposite orientation,expressed in most tissues from the paternal allele,the maternal allele being imprinted through a specific methylation of a CpG island,abnormally expressed from both paternal and maternal alleles in patients with Beckwith-Wiedemann syndrome,independently of IGF2 imprinting,normally imprinted in Wilms tumor

Phenotypes From GWAS Catalog for KCNQ1OT1 Gene

Human Phenotype Ontology for KCNQ1OT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for KCNQ1OT1 Gene

Localization for KCNQ1OT1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KCNQ1OT1 gene
Compartment Confidence
extracellular 2
nucleus 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1

Gene Ontology (GO) - Cellular Components for KCNQ1OT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with KCNQ1OT1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for KCNQ1OT1 Gene

Pathways & Interactions for KCNQ1OT1 Gene

PathCards logo

SuperPathways for KCNQ1OT1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for KCNQ1OT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006342 chromatin silencing IEA --
genes like me logo Genes that share ontologies with KCNQ1OT1: view

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for KCNQ1OT1 Gene

Drugs & Compounds for KCNQ1OT1 Gene

No Compound Related Data Available

Transcripts for KCNQ1OT1 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for KCNQ1OT1 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS0000759CF4_9606 lncRNA 91671 4

HGNC: 6295,

RefSeq: NR_002728,

LNCipedia: KCNQ1OT1:2,

NONCODE: NONHSAT017523.2,

URS00000CE0D1_9606 lncRNA 91667 2

Ensembl: ENST00000597346 (view in UCSC) ,

LNCipedia: KCNQ1OT1:5,

URS00008BF727_9606 lncRNA 581 3

LncBook: HSALNT0171219,

LNCipedia: KCNQ1OT1:6,

NONCODE: NONHSAT017526.2,

URS00008BDF93_9606 lncRNA 380 2

LncBook: HSALNT0171216,

LNCipedia: KCNQ1OT1:7,

URS00009B2601_9606 lncRNA 373 2

LncBook: HSALNT0171217,

NONCODE: NONHSAT160020.1,

KCNQ1OT1 in the GeneCards ncRNA compendium hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for KCNQ1OT1 Gene

4 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for KCNQ1OT1 Gene

No ASD Table

Relevant External Links for KCNQ1OT1 Gene

GeneLoc Exon Structure for
KCNQ1OT1

Expression for KCNQ1OT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for KCNQ1OT1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for KCNQ1OT1

SOURCE GeneReport for Unigene cluster for KCNQ1OT1 Gene:

Hs.604823

Phenotype-based relationships between genes and organs from Gene ORGANizer for KCNQ1OT1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • outer ear
  • skull
  • tongue
  • tooth
Thorax:
  • chest wall
  • clavicle
  • diaphragm
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
  • adrenal gland
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • stomach
Pelvis:
  • ovary
  • pelvis
  • penis
  • testicle
  • ureter
  • urinary bladder
  • vagina
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with KCNQ1OT1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for KCNQ1OT1 Gene

Orthologs for KCNQ1OT1 Gene

Evolution for KCNQ1OT1 Gene

ENSEMBL:
Gene Tree for KCNQ1OT1 (if available)
TreeFam:
Gene Tree for KCNQ1OT1 (if available)

No data available for Orthologs for KCNQ1OT1 Gene

Paralogs for KCNQ1OT1 Gene

No data available for Paralogs for KCNQ1OT1 Gene

Variants for KCNQ1OT1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for KCNQ1OT1 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
666841 Uncertain Significance: not specified 2,662,065(-) A/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
671951 Benign: not provided 2,662,237(-) C/G NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
676027 Likely Benign: not provided 2,661,920(-) G/C NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
735812 Likely Benign: not provided 2,662,079(-) A/C NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
800846 Uncertain Significance: Autosomal dominant KCNQ1-related disease 2,665,371(-) A/G NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for KCNQ1OT1 Gene

Structural Variations from Database of Genomic Variants (DGV) for KCNQ1OT1 Gene

Variant ID Type Subtype PubMed ID
esv1004234 CNV insertion 20482838
esv2744010 CNV deletion 23290073
esv2744011 CNV deletion 23290073
esv3625128 CNV loss 21293372
esv991030 CNV deletion 20482838
nsv1037537 CNV gain 25217958
nsv1047967 CNV loss 25217958
nsv467652 CNV loss 19166990
nsv517065 CNV gain 19592680
nsv951291 CNV deletion 24416366

Additional Variant Information for KCNQ1OT1 Gene

Human Gene Mutation Database (HGMD)
KCNQ1OT1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KCNQ1OT1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for KCNQ1OT1 Gene

Disorders for KCNQ1OT1 Gene

MalaCards: The human disease database

(35) MalaCards diseases for KCNQ1OT1 Gene - From: LncRNADisease, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for KCNQ1OT1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with KCNQ1OT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for KCNQ1OT1 Gene

Publications for KCNQ1OT1 Gene

  1. Clone- and gene-specific aberrations of parental imprinting in human induced pluripotent stem cells. (PMID: 19711451) Pick M … Benvenisty N (Stem cells (Dayton, Ohio) 2009) 3 23
  2. Dynamic CpG methylation of the KCNQ1OT1 gene during maturation of human oocytes. (PMID: 18762571) Khoueiry R … Lefèvre A (Journal of medical genetics 2008) 3 23
  3. Expression profile of LIT1/KCNQ1OT1 and epigenetic status at the KvDMR1 in colorectal cancers. (PMID: 16965397) Nakano S … Oshimura M (Cancer science 2006) 3 23
  4. ZAC, LIT1 (KCNQ1OT1) and p57KIP2 (CDKN1C) are in an imprinted gene network that may play a role in Beckwith-Wiedemann syndrome. (PMID: 15888726) Arima T … Wake N (Nucleic acids research 2005) 3 23
  5. Microdeletion of LIT1 in familial Beckwith-Wiedemann syndrome. (PMID: 15372379) Niemitz EL … Feinberg AP (American journal of human genetics 2004) 3 23

Products for KCNQ1OT1 Gene

Sources for KCNQ1OT1 Gene