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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 (Non-Protein Coding) 2 3 5
  • 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 (Non-Protein Coding)) 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

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

Regulatory Elements for KCNQ1OT1 Gene

Enhancers for KCNQ1OT1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G002724 1.9 FANTOM5 Ensembl ENCODE dbSUPER 12.8 -28.3 -28313 7.4 PKNOX1 MLX CREB3L1 ARID4B DMAP1 ZNF48 ZNF121 GATA2 ZNF263 SP5 KCNQ1OT1 KCNQ1DN TSSC4 COX6CP18
GH11G002732 1.2 ENCODE dbSUPER 12.8 -32.6 -32618 0.4 FOXA2 MLX ARID4B DMAP1 ZNF48 SP5 NFYC PPARG KAT8 MIER3 KCNQ1OT1 COX6CP18
GH11G002739 1.1 Ensembl ENCODE 11.8 -41.3 -41345 3.4 SOX13 KLF1 PKNOX1 TAL1 ZSCAN9 TEAD3 FOSL1 ZNF157 NCOR1 HSF1 KCNQ1OT1 COX6CP18
GH11G002881 1.1 ENCODE 11 -184.3 -184309 5.7 CREB3L1 SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF207 KLF13 SP5 REST PHLDA2 TRPM5 KCNQ1OT1 RNU1-91P SLC22A18 CDKN1C ENSG00000274740
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around KCNQ1OT1 on UCSC Golden Path with GeneCards custom track

Promoters for KCNQ1OT1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

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

Genomic Location for KCNQ1OT1 Gene

2,608,328 bp from pter
2,699,998 bp from pter
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

Human Phenotype Ontology for KCNQ1OT1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model 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 2

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for KCNQ1OT1 Gene

Pathways & Interactions for KCNQ1OT1 Gene

SuperPathways for KCNQ1OT1 Gene

No Data Available

Interacting Proteins for KCNQ1OT1 Gene

Gene Ontology (GO) - Biological Process for KCNQ1OT1 Gene


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

(3) Additional mRNA sequences :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for KCNQ1OT1 Gene

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

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 Sequence Context AA Info Type
rs397508092 Pathogenic 2,662,080(+) TCTCA(-/CA)GTGAG nc-transcript-variant, reference, frameshift-variant
rs794728558 Pathogenic 2,662,013(+) AGAAC(-/C)AACAG nc-transcript-variant, reference, frameshift-variant
rs878854349 Pathogenic 2,662,047(+) AGGGG(-/G)AGACT nc-transcript-variant, reference, frameshift-variant
rs146407692 Likely benign 2,611,500(+) AGCCA(C/G)TGCAC intron-variant, nc-transcript-variant
rs17215465 Likely benign 2,662,022(+) AGCTT(C/T)GCCGA nc-transcript-variant, reference, synonymous-codon

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

Relevant External Links for KCNQ1OT1 Gene

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

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

(9) MalaCards diseases for KCNQ1OT1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
beckwith-wiedemann syndrome
  • wiedemann-beckwith syndrome
hemihyperplasia, isolated
  • isolated hemihyperplasia
adrenal neuroblastoma
  • neuroblastoma of adrenal gland
beckwith-wiedemann syndrome due to imprinting defect of 11p15
silver-russell syndrome
  • srs
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for KCNQ1OT1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 2009) 3 22 64
  2. Dynamic CpG methylation of the KCNQ1OT1 gene during maturation of human oocytes. (PMID: 18762571) Khoueiry R. … LefA"vre A. (J. Med. Genet. 2008) 3 22 64
  3. Expression profile of LIT1/KCNQ1OT1 and epigenetic status at the KvDMR1 in colorectal cancers. (PMID: 16965397) Nakano S. … Oshimura M. (Cancer Sci. 2006) 3 22 64
  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 Res. 2005) 3 22 64
  5. Microdeletion of LIT1 in familial Beckwith-Wiedemann syndrome. (PMID: 15372379) Niemitz E.L. … Feinberg A.P. (Am. J. Hum. Genet. 2004) 3 22 64

Products for KCNQ1OT1 Gene

Sources for KCNQ1OT1 Gene

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