Free for academic non-profit institutions. Other users need a Commercial license

Aliases for KCNQ1OT1 Gene

Subcategory (RNA class) for KCNQ1OT1 Gene


Quality Score for this RNA gene is


Aliases for KCNQ1OT1 Gene

  • KCNQ1 Opposite Strand/Antisense Transcript 1 2 3 5
  • 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
  • Long QT Intronic Transcript 1 3
  • Non-Protein Coding RNA 12 2
  • NCRNA00012 3
  • KCNQ1-AS2 3
  • KvLQT1-AS 3
  • KCNQ10T1 3
  • KvDMR1 3
  • Kncq1 3
  • LIT1 3

External Ids for KCNQ1OT1 Gene

ORGUL Members 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 antisense RNA class. Diseases associated with KCNQ1OT1 include Beckwith-Wiedemann Syndrome and Hemihyperplasia, Isolated.

Gene Wiki entry for KCNQ1OT1 Gene

Additional gene information for KCNQ1OT1 Gene

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

Genomics for KCNQ1OT1 Gene

GeneHancer (GH) Regulatory Elements for KCNQ1OT1 Gene

Promoters and enhancers for KCNQ1OT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J002696 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 600.7 -1.6 -1575 10.2 SP1 ZFX ELF3 MNT ZNF148 NKRF POLR2A MLLT1 GTF2F1 ZNF687 KCNQ1OT1 TSSC4 OSBPL5 ENSG00000235027 KCNQ1 TRPM5 ENSG00000276015 COX6CP18
GH11J001849 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.7 +847.2 847194 6.3 SP1 NKRF POLR2A ZNF687 RELA CREM MLLT1 ZBED1 IKZF1 BACH1 LSP1 KCNQ1OT1 TNNI2 TNNT3 H19 C11orf21 TSPAN32 IGF2 GC11P001831
GH11J002881 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 11 -184.3 -184308 5.7 ZFX ZNF148 MLLT1 ZNF121 ZSCAN21 MAFK ZBTB7A TRIM24 SP7 EGR1 CDKN1C PHLDA2 TRPM5 KCNQ1OT1 RNU1-91P SLC22A18 ENSG00000274740
GH11J002724 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 12.8 -28.4 -28398 7.6 ELF3 RERE TFE3 HNF1A PPARG SP5 KAT8 HMG20B SOX13 PRDM10 KCNQ1OT1 KCNQ1DN TSSC4 COX6CP18 KCNQ1
GH11J002732 Enhancer 1.1 ENCODE dbSUPER 12.8 -32.6 -32618 0.4 ELF3 CEBPG AHR TFE3 PPARG SP5 ZNF644 KAT8 HMG20B SOX13 KCNQ1OT1 COX6CP18 KCNQ1
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for KCNQ1OT1 Gene

Genomic Locations for KCNQ1OT1 Gene
91,671 bases
Minus strand
91,671 bases
Minus strand

Genomic View for KCNQ1OT1 Gene

Genes around KCNQ1OT1 on UCSC Golden Path with GeneCards custom track

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

Graphical View of Domain Structure for InterPro Entry

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

No data available for Protein Domains , Suggested Antigen Peptide Sequences 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

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
nucleus 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

Interacting Proteins for KCNQ1OT1 Gene

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 and SIGNOR curated interactions for KCNQ1OT1 Gene

Drugs & Compounds for KCNQ1OT1 Gene

No Compound Related Data Available

Transcripts for KCNQ1OT1 Gene

mRNA/cDNA for KCNQ1OT1 Gene

(4) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
(2) RNA Central transcripts :

Unigene Clusters for KCNQ1OT1 Gene

KCNQ1 opposite strand/antisense transcript 1 (non-protein coding):
Representative Sequences:

CRISPR Products

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

No ASD Table

Relevant External Links for KCNQ1OT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for KCNQ1OT1 Gene

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

NURSA nuclear receptor signaling pathways regulating expression of KCNQ1OT1 Gene:


SOURCE GeneReport for Unigene cluster for KCNQ1OT1 Gene:


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

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • outer ear
  • skull
  • tongue
  • tooth
  • chest wall
  • clavicle
  • diaphragm
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • abdominal wall
  • adrenal gland
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • stomach
  • ovary
  • pelvis
  • penis
  • testicle
  • ureter
  • urinary bladder
  • vagina
  • 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
  • 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

Gene Tree for KCNQ1OT1 (if available)
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 from dbSNP and Humsavar for KCNQ1OT1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1060503982 likely-benign, Long QT syndrome 2,662,013(-) C/T non_coding_transcript_variant
rs114030398 benign, short QT syndrome, Romano-Ward syndrome, Long QT syndrome, Jervell and Lange-Nielsen syndrome, Familial atrial fibrillation 2,616,965(-) T/G non_coding_transcript_variant
rs12577654 benign, Cardiac arrhythmia 2,662,099(-) C/T non_coding_transcript_variant
rs137887424 benign, Long QT syndrome 2,661,998(-) C/T non_coding_transcript_variant
rs146407692 likely-benign, short QT syndrome, Jervell and Lange-Nielsen syndrome, Familial atrial fibrillation, Romano-Ward syndrome, Long QT syndrome 2,611,500(-) C/G non_coding_transcript_variant

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

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

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

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

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for KCNQ1OT1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 58
  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 58
  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 58
  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 58
  5. Identification of a common genetic substrate underlying postpartum cardiac events in congenital long QT syndrome. (PMID: 15851119) Khositseth A … Ackerman MJ (Heart rhythm 2004) 3 45 58

Products for KCNQ1OT1 Gene

Sources for KCNQ1OT1 Gene

Loading form....