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HCG9 Gene

RNA gene   GIFtS: 38
GCID: GC06P030182

HLA Complex Group 9 (Non-Protein Coding)

(Previous name: HLA complex group 9)
  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 3

Aliases
HLA Complex Group 9 (Non-Protein Coding)1 2     HCG IX4
HLA Complex Group 91 4     hcgIX4
HCGIX2 4     HcgIX Protein4
HCGIX42     

External Ids:    HGNC: 212431   Entrez Gene: 102552   Ensembl: ENSG000002046257   UniProtKB: Q930654   
ORGUL members:         

Export aliases for HCG9 gene to outside databases

Previous GC identifers: GC06P029713 GC06P030048 GC06P030050 GC06P029943 GC06P030094


(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 HCG9 Gene:
This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but its
function has not been determined. (provided by RefSeq, Jul 2009)

GeneCards Summary for HCG9 Gene:
HCG9 (HLA complex group 9 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with HCG9 include vitiligo, and bipolar disorder.




(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_000006.12  NC_018917.2  NT_007592.16  NT_113891.3  NT_167245.2  NT_167246.2  NT_167247.2  NT_167248.2  
NT_167249.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the HCG9 gene promoter:
         AML1a   p300   SREBP-1c   HTF   SREBP-1b   AREB6   SREBP-1a   ARP-1   ATF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHCG9 promoter sequence
   Search Chromatin IP Primers for HCG9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HCG9


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

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p22.1   HGNC cytogenetic band: 6p21.3

HCG9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HCG9 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P030182:  view genomic region     (about GC identifiers)

Start:
29,942,889 bp from pter      End:
29,946,183 bp from pter
Size:
3,295 bases      Orientation:
plus strand

6 alternative locations:
Chr6+,NT_167245 1,236,226-1,239,515      Chr6+,NT_167249 1,272,216-1,275,502      Chr6+,NT_167246 1,241,473-1,244,759     
Chr6+,NT_113891.2 1,454,595-1,457,884      Chr6+,NT_167247 1,324,753-1,328,042      Chr6+,NT_167248 1,235,684-1,238,975     
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for HCG9

(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, and/or Cloud-Clone Corp.)
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UniProtKB/TrEMBL: Q93065 (See protein sequence)
Recommended Name: HCG IX  
Size: 77 amino acids; 8694 Da


(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: Q93065


(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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Phenotypes:
     1 GenomeRNAi human phenotype for HCG9:
 Synthetic lethal with Ras 

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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Interactions:

    Search GeneGlobe Interaction Network for HCG9

(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 drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for HCG9



(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,
Conferences by KenesGroup, 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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REFSEQ mRNAs for HCG9 gene: 
NM_005844.2  

Unigene Cluster for HCG9:

HLA complex group 9 (non-protein coding)
Hs.656251  [show with all ESTs]
Unigene Representative Sequence: BX097961
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000376800(lincRNA)(uc003rth.3) ENST00000463275(lincRNA)
miRNA
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Additional mRNA sequence: 

AK289926.1 BC119792.1 NR_028032.1 X95289.1 

2 DOTS entries:

DT.307579  DT.91802280 

2 AceView cDNA sequences:

NM_005844 X95289 

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 HCG9:none

HCG9 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AGCTTCTACC
HCG9 Expression
About this image

HCG9 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.656251
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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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ENSEMBL Gene Tree for HCG9 (if available)
TreeFam Gene Tree for HCG9 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for HCG9 gene
1 SIMAP similar gene for HCG9 using alignment to 1 protein entry:     Q93065_HUMAN:
HCGIX-4

HCG9 for paralogs           About GeneDecksing



(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 HCG9 (see all 320)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1479966071,2
C--29940916(+) TGACAC/TAGGTT 1 -- us2k10--------
rs49590101,2
C,F,H--29940943(+) ggataT/Caacac 1 -- us2k113Minor allele frequency- C:0.28NS EA NA WA 784
rs1892740821,2
C--29940997(+) CAAAAG/TAAAAA 1 -- us2k10--------
rs562891021,2
C,F--29941011(+) TTGAGC/TATTAA 1 -- us2k12Minor allele frequency- T:0.09NA EA 240
rs1808211871,2
--29941047(+) GCAACC/TATTAG 1 -- us2k10--------
rs92608021,2
C,F--29941064(+) AGAAAA/GTATTT 1 -- us2k1 tfbs32Minor allele frequency- G:0.04WA NA 238
rs1156480411,2
C,F--29941167(+) AGAATT/CTGAAT 1 -- us2k11Minor allele frequency- C:0.03WA 118
rs25713761,2
C,F,H--29941184(-) tcttcG/Agagaa 1 -- us2k113Minor allele frequency- A:0.30NS EA NA WA CSA 784
rs117548451,2
C,A,H--29941328(+) cacacG/Acacac 1 -- us2k11Minor allele frequency- A:0.00NA 2
rs287495341,2
C--29941330(+) CACACA/GCACAC 1 -- us2k11Minor allele frequency- G:0.00NA 2

HapMap Linkage Disequilibrium report for HCG9 (29942889 - 29946183 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for HCG9 (see all 18):    About this table    
Variant IDTypeSubtypePubMed ID
esv2731778CNV Deletion23290073
esv2641340CNV Deletion19546169
esv2731775CNV Deletion23290073
dgv1088e199CNV Deletion23128226
esv2670487CNV Deletion23128226
dgv1039e201CNV Deletion23290073
dgv1040e201CNV Deletion23290073
esv2731777CNV Deletion23290073
esv274486CNV Insertion20981092
esv267694CNV Insertion20981092

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for HCG9

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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7 diseases for HCG9:    
About MalaCards
vitiligo    bipolar disorder    systemic lupus erythematosus    multiple sclerosis
lupus erythematosus    ulcerative colitis    hodgkin's lymphoma


HCG9 for disorders           About GeneDecksing

Genetic Association Database (GAD): HCG9
Human Genome Epidemiology (HuGE) Navigator: HCG9 (4 documents)

Export disorders for HCG9 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 HCG9 gene, integrated from 10 sources (see all 15):
(articles sorted by number of sources associating them with HCG9)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy. (PubMed id 22197929)1, 4 Yu X.Q....Liu J.J. (Nat. Genet. 2012)
  2. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PubMed id 20593013)1, 4 Cree B.A.... . (PLoS ONE 2010)
  3. Variant of TYR and autoimmunity susceptibility loci in generalized vitiligo. (PubMed id 20410501)1, 4 Jin Y....Spritz R.A. (N. Engl. J. Med. 2010)
  4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1, 4 Barcellos L.F....Criswell L.A. (PLoS Genet. 2009)
  5. Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region. (PubMed id 10557312)1, 3 Shiina T....Inoko H. (Proc. Natl. Acad. Sci. U.S.A. 1999)
  6. A 356-Kb sequence of the subtelomeric part of the MHC class I region. (PubMed id 10727083)1, 3 Hampe A.... Galibert F. (DNA Seq. 1999)
  7. Genome-wide association study of ulcerative colitis in Koreans suggests extensive overlapping of genetic susceptibility with Caucasians. (PubMed id 23511034)1 Yang S.K....Song K. (Inflamm. Bowel Dis. 2013)
  8. A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder. (PubMed id 21647149)1 Kaminsky Z....Petronis A. (Mol. Psychiatry 2012)
  9. Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with BehAset's disease. (PubMed id 20622878)4 Remmers E.F....GA1l A. (Nat. Genet. 2010)
  10. Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (PubMed id 19010793)4 Baranzini S.E....Oksenberg J.R. (Hum. Mol. Genet. 2009)

(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: 10255 HGNC: 21243 AceView: HCG9 Ensembl:ENSG00000204625 euGenes: HUgn10255
ECgene: HCG9 H-InvDB: HCG9

(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 HCG9 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 HCG9 gene:
Search GeneIP for patents involving HCG9

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



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