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HGC6.3 Gene

RNA gene   GIFtS: 22
GCID: GC06M168377

Uncharacterized LOC100128124


  See HGC6.3-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 2

Aliases
Uncharacterized LOC1001281242
Uncharacterized Protein LOC1001281242

External Ids:    Entrez Gene: 1001281242   Ensembl: ENSG000002359947   UniProtKB: Q9UM084   

Export aliases for HGC6.3 gene to outside databases

Previous GC identifers: GC06U901159 GC06M168120


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for HGC6.3 Gene:
HGC6.3 is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with HGC6.3 include ovarian cancer.


(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_000006.11  NC_018917.2  NT_025741.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the HGC6.3 gene promoter:
         AP-1   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   POU3F2   POU2F1   FOXC1   POU2F1b   POU2F1a   Sox9   POU2F1c   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for HGC6.3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HGC6.3


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

Entrez Gene cytogenetic band: 6q27   Ensembl cytogenetic band:  6q27   

HGC6.3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HGC6.3 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M168377:  view genomic region     (about GC identifiers)

Start:
168,376,604 bp from pter      End:
168,380,456 bp from pter
Size:
3,853 bases      Orientation:
minus 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/TrEMBL: Q9UM08 (See protein sequence)
Recommended Name: HGC6.3 protein  
Size: 171 amino acids; 17220 Da

REFSEQ proteins: NP_001123367.1  

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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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ProtoNet protein and cluster: Q9UM08


(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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Animal Models:
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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 HGC6.3
Interactions:

    Search GeneGlobe Interaction Network for HGC6.3

(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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Browse Tocris compounds for HGC6.3



(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 HGC6.3 gene: 
NM_001129895.2  

Unigene Cluster for HGC6.3:

Uncharacterized LOC100128124
Hs.448059  [show with all ESTs]
Unigene Representative Sequence: AB016902
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000441716(lincRNA) ENST00000538528(lincRNA)(uc010kks.1)
miRNA
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Additional mRNA sequence: AB016902.2 

1 DOTS entry:

DT.91718755 

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 HGC6.3:none

HGC6.3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
HGC6.3 Expression
About this image

HGC6.3 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.448059
    Custom PCR Arrays for HGC6.3
Primer
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In Situ
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HGC6.3

(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 HGC6.3 (if available)
TreeFam Gene Tree for HGC6.3 (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 HGC6.3 (see all 152)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1465940731,2
--165804057(+) TGCTAC/TGTAAA 1 -- ds50010--------
rs1859721221,2
C--165804058(+) GCTACA/GTAAAT 1 -- ds50010--------
rs789652831,2
C,F--165804071(+) GCTTGG/TAAACA 1 -- ds50011Minor allele frequency- T:0.07WA 118
rs1400846291,2
C--165804293(+) TAAATA/TGTGAT 1 -- ds50010--------
rs1903004491,2
C--165804391(+) TTCATA/GCAGCG 1 -- ds50010--------
rs1420117481,2
C--165804516(+) CTGCA-/GTGTGTG 1 -- ds50010--------
rs778679071,2
C--165804532(+) GGGAGG/CAGGAG 1 -- ds50011Minor allele frequency- C:0.50NA 2
rs1429309551,2
--165804605(+) CTGCA-/GTGTGTG 2 A L fra10--------
rs361291721,2
C--165804681(+) GGTCAC/TTCCCC 2 N S mis11Minor allele frequency- T:0.50NA 2
rs1436310111,2
C--165804691(+) CTGCA-/GTGTGTG 2 C TA fra10--------

HapMap Linkage Disequilibrium report for HGC6.3 (168376604 - 168380456 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for HGC6.3 (see all 27):    About this table    
Variant IDTypeSubtypePubMed ID
esv2733267CNV Deletion23290073
esv2733266CNV Deletion23290073
esv2733265CNV Deletion23290073
esv1360911CNV Deletion17803354
esv2667680CNV Deletion23128226
esv2733264CNV Deletion23290073
dgv27e196CNV Duplication17116639
esv2422263CNV Duplication17116639
esv2422479CNV Duplication17116639
nsv5593CNV Insertion18451855

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing HGC6.3
DNA2.0 Custom Variant and Variant Library Synthesis for HGC6.3

(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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1 disease for HGC6.3:    
About MalaCards
ovarian cancer


Find genes that share disorders with HGC6.3           About GenesLikeMe

Genetic Association Database (GAD): HGC6.3

Export disorders for HGC6.3 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 HGC6.3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with HGC6.3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid. (PubMed id 23319000)1 Luykx J.J....Ophoff R.A. (Mol. Psychiatry 2013)
  2. Complete DNA sequence and characterization of a 330-kb VNTR-rich region on chromosome 6q27 that is commonly deleted in ovarian cancer. (PubMed id 10382971)1 Minaguchi T.... Nakamura Y. (DNA Res. 1999)

(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: 100128124 Ensembl:ENSG00000235994 euGenes: HUgn100128124

(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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(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for HGC6.3 gene:
Search GeneIP for patents involving HGC6.3

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, antibodies-online, 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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