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KCNQ1OT1 Gene

RNA gene   GIFtS: 31
GCID: GC11M002661

KCNQ1 Opposite Strand/Antisense Transcript 1 (Non-Protein...

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 5

Aliases
KCNQ1 Opposite Strand/Antisense Transcript 1 (Non-Protein Coding)1 2     KCNQ1-AS22
LIT12 5     KCNQ10T12
KCNQ1 Antisense RNA 2 (Non-Protein Coding)1     KvDMR12
KCNQ1 Overlapping Transcript 1 (Non-Protein Coding)1     KvLQT1-AS2
Non-Protein Coding RNA 121     NCRNA000122

External Ids:    HGNC: 62951   Entrez Gene: 109842   Ensembl: ENSG000002698217   OMIM: 6041155   
ORGUL members:    fRNAdb10:FR071993 FR218253      
NCBI13:AA329719 AA359588    
NONCODE14:n343064    
RNAdb15:LIT1659 LIT1652    

Export aliases for KCNQ1OT1 gene to outside databases

Previous GC identifers: GC11U990199 GC11M002674 GC11M002450


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 lncRNA class. Diseases associated with KCNQ1OT1 include beckwith-wiedemann syndrome due to 11p15 microdeletion, and hemihypertrophy.

Gene Wiki entry for KCNQ1OT1 Gene

fRNAdb sequence ontology for KCNQ1OT1:
antisense_RNA - Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.

View fRNAdb secondary structures for KCNQ1OT1

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000011.10  NC_018922.2  NT_009237.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the KCNQ1OT1 gene promoter:
         MyoD   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KCNQ1OT1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11p15   Ensembl cytogenetic band:  11p15.5   HGNC cytogenetic band: 11p15.5

KCNQ1OT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KCNQ1OT1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M002661:  view genomic region     (about GC identifiers)

Start:
2,629,558 bp from pter      End:
2,721,228 bp from pter
Size:
91,671 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for KCNQ1OT1

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:
     Genatlas biochemistry entry for KCNQ1OT1:
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:
     8 MGI mutant phenotypes (inferred from 9 alleles(MGI details for Kcnq1ot1):
 cellular  embryogenesis  growth/size/body  liver/biliary system  mortality/aging 
 normal  renal/urinary system  respiratory system 

KCNQ1OT1 for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-outs for KCNQ1OT1: Kcnq1ot1tm2Tilg Kcnq1ot1tm1Tilg Kcnq1ot1tm4Tilg Kcnq1ot1tm1.1Mjh

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for KCNQ1OT1
Interactions:

    GeneGlobe Interaction Network for KCNQ1OT1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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2 fRNAdb Secondary structures:


Unigene Cluster for KCNQ1OT1:

KCNQ1 opposite strand/antisense transcript 1 (non-protein coding)
Hs.604823  [show with all ESTs]
Unigene Representative Sequence: BX089392
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000597346(antisense)
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Additional mRNA sequence: AF086011.1 

1 DOTS entry:

DT.309954 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for KCNQ1OT1:RNAdb

KCNQ1OT1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAATATTTAC
KCNQ1OT1 Expression
About this image


KCNQ1OT1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Adipose (Muscoskeletal System)
         Interscapular Brown Adipose Depot
 
 Ovary (Reproductive System)
KCNQ1OT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.604823
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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for KCNQ1OT1 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Kcnq1ot15 KCNQ1 overlapping transcript 1   --   7 (88.15 cM) 143213111 


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

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Structural Variations
     Database of Genomic Variants (DGV) 7 variations for KCNQ1OT1:    About this table    
Variant IDTypeSubtypePubMed ID
esv2744011CNV Deletion23290073
esv991030CNV Deletion20482838
esv1004234CNV Insertion20482838
dgv1004n71CNV Loss21882294
nsv467652CNV Loss19166990
nsv896833CNV Loss21882294
nsv517065CNV Gain19592680

Human Gene Mutation Database (HGMD): KCNQ1OT1
Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 604115OMIM information: 607542    
OMIM disorders: 130650  
4 diseases for KCNQ1OT1:    
About MalaCards
beckwith-wiedemann syndrome due to 11p15 microdeletion    hemihypertrophy    beckwith-wiedemann syndrome due to imprinting defect of 11p15    beckwith-wiedemann syndrome


KCNQ1OT1 for disorders           About GeneDecksing

4 Novoseek inferred disease relationships for KCNQ1OT1 gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
beckwith-wiedemann syndrome 91.7 6 10958646 (1), 15888726 (1), 15372379 (1), 17901045 (1) (see all 5)
embryonal tumor 82.5 1 11751681 (1)
wilms tumor 51.5 3 17686827 (1), 11751681 (1)
tumors 12.1 5 15887271 (2), 11751681 (2), 18668518 (1)

GeneTests: KCNQ1OT1
GeneReviews: KCNQ1OT1
Genetic Association Database (GAD): KCNQ1OT1
Human Genome Epidemiology (HuGE) Navigator: KCNQ1OT1 (1 document)

Export disorders for KCNQ1OT1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for KCNQ1OT1 gene, integrated from 10 sources (see all 66):
(articles sorted by number of sources associating them with KCNQ1OT1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Identification of a common genetic substrate underlying postpartum cardiac events in congenital long QT syndrome. (PubMed id 15851119)1, 4 Khositseth A....Ackerman M.J. (Heart Rhythm 2004)
  2. In vitro fertilization may increase the risk of Beckwith-Wiedemann syndrome related to the abnormal imprinting of the KCN1OT gene. (PubMed id 12772698)1, 3 Gicquel C....Le Bouc Y. (Am. J. Hum. Genet. 2003)
  3. 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. (PubMed id 10220444)1, 3 Lee M.P....Feinberg A.P. (Proc. Natl. Acad. Sci. U.S.A. 1999)
  4. ZAC, LIT1 (KCNQ1OT1) and p57KIP2 (CDKN1C) are in an imprinted gene network that may play a role in Beckwith-Wiedemann syndrome. (PubMed id 15888726)1, 9 Arima T....Wake N. (Nucleic Acids Res. 2005)
  5. Expression profile of LIT1/KCNQ1OT1 and epigenetic status at the KvDMR1 in colorectal cancers. (PubMed id 16965397)1, 9 Nakano S....Oshimura M. (Cancer Sci. 2006)
  6. Microdeletion of LIT1 in familial Beckwith-Wiedemann syndrome. (PubMed id 15372379)1, 9 Niemitz E.L....Feinberg A.P. (Am. J. Hum. Genet. 2004)
  7. Dynamic CpG methylation of the KCNQ1OT1 gene during maturation of human oocytes. (PubMed id 18762571)1, 9 Khoueiry R....LefA"vre A. (J. Med. Genet. 2008)
  8. Clone- and gene-specific aberrations of parental imprinting in human induced pluripotent stem cells. (PubMed id 19711451)1, 9 Pick M....Benvenisty N. (Stem Cells 2009)
  9. A novel tetranucleotide repeat polymorphism within KCNQ1OT1 confers risk for hepatocellular carcinoma. (PubMed id 23984860)1 Wan J....Gao Y. (DNA Cell Biol. 2013)
  10. Abnormal methylation of KCNQ1OT1 and differential methylation of H19 imprinting control regions in human ICSI embryos. (PubMed id 22300968)1 Khoueiry R....LefA"vre A. (Zygote 2013)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Disorders
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 10984 HGNC: 6295 Ensembl:ENSG00000269821 euGenes: HUgn10984 ECgene: KCNQ1OT1
H-InvDB: KCNQ1OT1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for KCNQ1OT1 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for KCNQ1OT1 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for KCNQ1OT1 gene:
Search GeneIP for patents involving KCNQ1OT1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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