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KCNQ1DN Gene

RNA gene   GIFtS: 33
GCID: GC11P002847

KCNQ1 Downstream Neighbor (Non-Protein Coding)

(Previous name: KCNQ1 downstream neighbor)
  See KCNQ1DN-related disease
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 3

Aliases
KCNQ1 Downstream Neighbor (Non-Protein Coding)1 2
BWRT2 3
KCNQ1 Downstream Neighbor1
HSA4046172
Beckwith-Wiedemann Region Transcript Protein3

External Ids:    HGNC: 133351   Entrez Gene: 555392   Ensembl: ENSG000002379417   OMIM: 6109805   UniProtKB: Q9H4783   
ORGUL members:         

Export aliases for KCNQ1DN gene to outside databases

Previous GC identifers: GC11P002856 GC11P002679


(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 KCNQ1DN Gene:
Imprinting is a phenomenon in which epigenetic modifications lead to expression or suppression of alleles of some
genes based on their parental origin. Wilms tumor-2 (WT2; MIM 194071) is defined by maternal-specific loss of
heterozygosity of a critical region on chromosome 11p15.5 that includes several imprinted genes. KCNQ1DN is an
imprinted gene located within the WT2 critical region that is expressed from the maternal allele (Xin et al.,
2000 (PubMed 11056398)).(supplied by OMIM, Mar 2008)

GeneCards Summary for KCNQ1DN Gene:
KCNQ1DN (KCNQ1 downstream neighbor (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with KCNQ1DN include wilms tumor.

Gene Wiki entry for KCNQ1DN Gene


(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 at NCBI GenBank:
NC_000011.9  NC_018922.2  NT_009237.19  NT_187585.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the KCNQ1DN gene promoter:
         Sox5   STAT1   HOXA3   MyoD   STAT1beta   C/EBPalpha   STAT1alpha   AREB6   CP2   FOXO4   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KCNQ1DN


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

Entrez Gene cytogenetic band: 11p15.4|11p15.5   Ensembl cytogenetic band:  11p15.4   HGNC cytogenetic band: 11p15.5

KCNQ1DN Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KCNQ1DN gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P002847:  view genomic region     (about GC identifiers)

Start:
2,891,263 bp from pter      End:
2,893,335 bp from pter
Size:
2,073 bases      Orientation:
plus strand

(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, Cloud-Clone Corp., and/or eBioscience,
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UniProtKB/Swiss-Prot: KCQ1D_HUMAN, Q9H478 (See protein sequence)
Recommended Name: KCNQ1 downstream neighbor protein  
Size: 68 amino acids; 7384 Da

Explore the universe of human proteins at neXtProt for KCNQ1DN: NX_Q9H478


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(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

ProtoNet protein and cluster: Q9H478


(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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003674molecular_function ND--
     
Find genes that share ontologies with KCNQ1DN           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for KCNQ1DN:
 Increased gamma-H2AX phosphory 

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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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Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005575cellular_component ND--

Find genes that share ontologies with KCNQ1DN           About GenesLikeMe


(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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Interactions:

    Search GeneGlobe Interaction Network for KCNQ1DN

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008150biological_process ND--

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(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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for KCNQ1DN gene: 
NM_018722.2  

Unigene Cluster for KCNQ1DN:

KCNQ1 downstream neighbor (non-protein coding)
Hs.127821  [show with all ESTs]
Unigene Representative Sequence: AB039920
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000441418(antisense)
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Additional mRNA sequence: 

AB039920.1 AJ404617.2 BC098159.1 BC098256.1 BC098319.1 BC098344.1 NR_024627.1 

1 DOTS entry:

DT.40127092 

8 AceView cDNA sequences:

AI732937 AA828167 AB039920 AI791256 NM_018722 AJ404617 AW181922 AW182106 

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 KCNQ1DN:none

KCNQ1DN expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGACCCCAAA
KCNQ1DN Expression
About this image

KCNQ1DN Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.127821

UniProtKB/Swiss-Prot: KCQ1D_HUMAN, Q9H478
Tissue specificity: Shows reduced expression in Wilms' tumor samples

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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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  --

ENSEMBL Gene Tree for KCNQ1DN (if available)
TreeFam Gene Tree for KCNQ1DN (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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Selected SNPs for KCNQ1DN (see all 90)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1883077901,2
--2889397(+) CCTGCA/GAGGAG 1 -- us2k10--------
rs556882991,2
C,F--2889428(+) CGTTTC/TCATTG 1 -- us2k11Minor allele frequency- T:0.50NA 2
rs1924059451,2
--2889616(+) CGCCCC/TGCCTG 1 -- us2k10--------
rs734213731,2
C--2889650(+) GGGGGG/AGCGCA 1 -- us2k11Minor allele frequency- A:0.50WA 2
rs1417639511,2
C--2889820(+) AGGCT-/GGTTTT 1 -- us2k10--------
rs1834592761,2
--2889866(+) ATTGTC/TCCCAC 1 -- us2k10--------
rs575357371,2
C,F--2889971(+) AACTCA/GGAAGG 1 -- us2k10--------
rs1461319951,2
C--2890007(+) CTGGGC/TTGGGG 1 -- us2k10--------
rs1143509501,2
C,F--2890023(+) GCGAGC/TCAGAC 1 -- us2k11Minor allele frequency- T:0.07WA 118
rs122819521,2
C,F--2890320(+) ACCCCG/AGCCCA 1 -- us2k12Minor allele frequency- A:0.05WA NA 238

HapMap Linkage Disequilibrium report for KCNQ1DN (2891263 - 2893335 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for KCNQ1DN (see all 12):    About this table    
Variant IDTypeSubtypePubMed ID
nsv467655CNV Loss19166990
nsv832050CNV Loss17160897
dgv1006n71CNV Loss21882294
nsv469930CNV Loss18288195
dgv1009n71CNV Loss21882294
dgv1007n71CNV Loss21882294
dgv1008n71CNV Loss21882294
nsv896842CNV Loss21882294
dgv1005n71CNV Loss21882294
nsv825715CNV Gain20364138

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 610980    OMIM disorders: --

1 disease for KCNQ1DN:    
About MalaCards
wilms tumor


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Genetic Association Database (GAD): KCNQ1DN

Export disorders for KCNQ1DN 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 KCNQ1DN gene integrated from 10 sources:
(articles sorted by number of sources associating them with KCNQ1DN)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A novel imprinted gene, KCNQ1DN, within the WT2 critical region of human chromosome 11p15.5 and its reduced expression in Wilms' tumors. (PubMed id 11056398)1, 2, 3, 9 Xin Z.... Mukai T. (J. Biochem. 2000)
  2. Sequence and functional comparison in the Beckwith-Wiedemann region: implications for a novel imprinting centre and extended imprinting. (PubMed id 11063728)1, 2, 3 Engemann S.... Walter J. (Hum. Mol. Genet. 2000)
  3. Epigenetic-aging-signature to determine age in different tissues. (PubMed id 22067257)1, 3 Koch C.M. and Wagner W. (Aging (Albany NY) 2011)
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  5. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (Nature 2006)
  6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
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: 55539 HGNC: 13335 AceView: KCNQ1DN Ensembl:ENSG00000237941 euGenes: HUgn55539
ECgene: KCNQ1DN H-InvDB: KCNQ1DN

(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 KCNQ1DN Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for KCNQ1DN gene:
Search GeneIP for patents involving KCNQ1DN

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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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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 , 21 Aug 2014 , 8 Sep 2014

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