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HCG4B Gene

RNA gene   GIFtS: 21
GCID: GC06M030015

HLA Complex Group 4B (Non-Protein Coding)

(Previous name: HLA complex group 4 pseudogene 6)
(Previous symbol: HCG4P6)
  Search for HCG4B
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 4B (Non-Protein Coding)1 2     HCGIV-62
HCG4P61 2     HCGIV.52
HCGIV-6 Pseudogene1     bCX67J3.32
HLA Complex Group 4 Pseudogene 61     bPG309N1.12
HCGIV-062     bQB90C11.32

External Ids:    HGNC: 229191   Entrez Gene: 808682   Ensembl: ENSG000002272627   
ORGUL members:         

Export aliases for HCG4B gene to outside databases

Previous GC identifers: GC06M029898 GC06M029906 GC06M029921 GC06M029934 GC06M029954


(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 HCG4B Gene:
HCG4B (HLA complex group 4B (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class.


(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_167244.2  NT_167245.2  NT_167246.2  NT_167248.2  
NT_167249.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for HCG4B
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HCG4B


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

HCG4B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HCG4B gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M030015:  view genomic region     (about GC identifiers)

Start:
29,892,369 bp from pter      End:
29,893,428 bp from pter
Size:
1,060 bases      Orientation:
minus strand

Selected alternative locations (see all 7):
Chr6-,NT_167248 1,187,016-1,188,075      Chr6-,NT_167246 1,186,623-1,187,678      Chr6-,NT_167244 1,134,224-1,135,287     
Chr6- 29,893,760-29,894,750      Chr6-,NT_167249 1,223,623-1,224,684      Chr6-,NT_113891.2 1,406,088-1,407,151     

(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,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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, 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 HCG4B
Interactions:

    Search GeneGlobe Interaction Network for HCG4B

(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 HCG4B



(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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Unigene Cluster for HCG4B:

HLA complex group 4B (non-protein coding)
Hs.661198  [show with all ESTs]
Unigene Representative Sequence: AF036973
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000450128
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Additional mRNA sequence: 

NR_001317.1 X81005.1 

1 DOTS entry:

DT.91806393 

1 AceView cDNA sequence:

AK097625 

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 HCG4B:none

HCG4B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
HCG4B Expression
About this image

HCG4B Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.661198
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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 HCG4B (if available)
TreeFam Gene Tree for HCG4B (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 HCG4B (see all 212)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs16114181,2
C,A--29891907(+) tcttaC/Gaactg 1 -- ds50017Minor allele frequency- G:0.21NA WA 248
rs16114191,2
C,F--29891984(+) GGGAAG/TCCCGG 1 -- ds500111Minor allele frequency- T:0.24NA WA EA 506
rs92598011,2
C,F--29892029(+) TGACTA/CAGGTA 1 -- ds50011Minor allele frequency- C:0.03NA 120
rs25177851,2
C,F,A,H--29892104(-) cagctT/Cctcag 1 -- ds50019Minor allele frequency- C:0.48NA WA CSA EA 370
rs16114201,2
C,F--29892107(+) AGGAGC/TTGACA 1 -- ds50016Minor allele frequency- T:0.29NA WA EA 364
rs1400515181,2
--29892132(+) GCATCC/TAGGAA 1 -- ds50010--------
rs16114211,2
C,F--29892137(+) CAGGAA/C/GTTTGA 1 -- ds50016NA WA EA 364
rs92598021,2
C,F--29892151(+) CAGCCA/GAGATC 1 -- ds50011Minor allele frequency- G:0.03NA 120
rs556762271,2
C,F--29892163(+) AACAGT/CGAGAC 1 -- ds50012Minor allele frequency- C:0.10NA EA 240
rs25177841,2
C,F,A,H--29892196(-) ccagcA/Taatta 1 -- ds50019Minor allele frequency- T:0.46NA WA CSA EA 370

HapMap Linkage Disequilibrium report for HCG4B (29892369 - 29893428 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for HCG4B (see all 64):    About this table    
Variant IDTypeSubtypePubMed ID
dgv7e195CNV Deletion20811451
esv2670487CNV Deletion23128226
dgv1039e201CNV Deletion23290073
esv2665698CNV Deletion23128226
esv3124CNV Deletion18987735
dgv1087e199CNV Deletion23128226
dgv1088e199CNV Deletion23128226
dgv1086e199CNV Deletion23128226
esv2659548CNV Deletion23128226
nsv820564CNV Deletion20802225

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing HCG4B
DNA2.0 Custom Variant and Variant Library Synthesis for HCG4B

(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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  --

(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 HCG4B gene integrated from 10 sources:
(articles sorted by number of sources associating them with HCG4B)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. Rapid evolution of major histocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity. (PubMed id 16702430)1 Shiina T.... Bahram S. (Genetics 2006)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)

(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: 80868 HGNC: 22919 AceView: HCG4P6 Ensembl:ENSG00000227262 euGenes: HUgn80868
ECgene: HCG4B H-InvDB: HCG4B

(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 HCG4B 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 HCG4B gene:
Search GeneIP for patents involving HCG4B

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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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