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HLA-DRB6 Gene

pseudogene   GIFtS: 26
GCID: GC06M032520

Major Histocompatibility Complex, Class II, DR Beta 6 (Pseudogene)

  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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Aliases
Major Histocompatibility Complex, Class II, DR Beta 6 (Pseudogene)1 2

External Ids:    HGNC: 49541   Entrez Gene: 31282   Ensembl: ENSG000002293917   UniProtKB: O779664   

Export aliases for HLA-DRB6 gene to outside databases

Previous GC identifers: GC06U990052 GC06M032291 GC06Md32591 GC06Md32628 GC06M032628


(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 HLA-DRB6 Gene:
HLA-DRB6 (major histocompatibility complex, class II, DR beta 6 (pseudogene)) is a pseudogene. Diseases associated with HLA-DRB6 include gestational diabetes, and systemic lupus erythematosus.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the HLA-DRB6 gene promoter:
         NF-1   GR-beta   Evi-1   Roaz   YY1   POU2F1   CP2   POU2F1a   GR-alpha   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for HLA-DRB6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HLA-DRB6


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

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p21.32   HGNC cytogenetic band: 6p21.3

HLA-DRB6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HLA-DRB6 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M032520:  view genomic region     (about GC identifiers)

Start:
32,520,490 bp from pter      End:
32,527,799 bp from pter
Size:
7,310 bases      Orientation:
minus strand

1 alternative location:
Chr6-,NT_167248 3,759,009-3,789,826     

(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/TrEMBL: O77966 (See protein sequence)
Recommended Name: MHC class II antigen  
Size: 34 amino acids; 4086 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:
HLA: Histocompatibility complex

ProtoNet protein and cluster: O77966


(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 HLA-DRB6:
HLA-DR,beta 6 pseudogene,found on DR1,DR2 and DR10 haplotypes

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 HLA-DRB6
Interactions:

    Search GeneGlobe Interaction Network for HLA-DRB6

(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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4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000411500(uc003obm.1 uc003obn.1) ENST00000437183 ENST00000437650(uc003obo.1)
ENST00000440876
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5 AceView cDNA sequences:

AF005487 L76566 NR_001298 L76565 U33547 

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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HLA-DRB6 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
HLA-DRB6 Expression
About this image

HLA-DRB6 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
    Custom PCR Arrays for HLA-DRB6
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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 HLA-DRB6 (if available)
TreeFam Gene Tree for HLA-DRB6 (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 HLA-DRB6 (see all 80)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1883005301,2
--32520000(+) TTGATA/GCTGAC 1 -- ds50010--------
rs1479439851,2
C--32520010(+) CTCTC-/AGAT  
        
AGAAT
1 -- ds50010--------
rs1140310161,2
C,F--32520035(+) CCCTCC/TATCTT 1 -- ds50013Minor allele frequency- T:0.14WA NA EA 358
rs1130678451,2
C,F--32520170(+) AGAAAA/GAGTTC 1 -- ds50013Minor allele frequency- G:0.11WA NA EA 358
rs1811269961,2
--32520190(+) TGCTGA/GCTGGT 1 -- ds50010--------
rs680818811,2
C--32520206(+) ATCTC-/AATGTT 1 -- ds50010--------
rs1165933501,2
F--32520361(+) AGTGTG/AAAATG 1 -- ds50012Minor allele frequency- A:0.08NA EA 240
rs717801901,2
C--32520388(+) TAACA-/TGTGCAT 1 -- ds50010--------
rs680381821,2
C--32520539(+) CAATG-/TGTT  
        
TGTGG
1 -- nc-transcript-variant0--------
rs1850795711,2
--32520557(+) AGGGGA/GATACA 1 -- nc-transcript-variant0--------

HapMap Linkage Disequilibrium report for HLA-DRB6 (32520490 - 32527799 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for HLA-DRB6 (see all 106):    About this table    
Variant IDTypeSubtypePubMed ID
esv2731847CNV Deletion23290073
dgv1100e199CNV Deletion23128226
dgv1107e199CNV Deletion23128226
esv2731848CNV Deletion23290073
dgv1106e199CNV Deletion23128226
dgv1108e199CNV Deletion23128226
dgv1105e199CNV Deletion23128226
esv2671539CNV Deletion23128226
esv2422111CNV Deletion20811451
dgv1045e201CNV Deletion23290073

Locus Specific Mutation Databases (LSDB): HLA-DRB6

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing HLA-DRB6
DNA2.0 Custom Variant and Variant Library Synthesis for HLA-DRB6

(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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5 diseases for HLA-DRB6:    
About MalaCards
gestational diabetes    systemic lupus erythematosus    lupus erythematosus    diabetes mellitus
multiple sclerosis


HLA-DRB6 for disorders           About GeneDecksing

Genetic Association Database (GAD): HLA-DRB6
Human Genome Epidemiology (HuGE) Navigator: HLA-DRB6 (2 documents)

Export disorders for HLA-DRB6 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 HLA-DRB6 gene integrated from 10 sources:
(articles sorted by number of sources associating them with HLA-DRB6)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Complete cDNA sequences of the DRB6 gene from humans and chimpanzees: a possible model of a stop codon readingthrough mechanism in primates. (PubMed id 10436177)1, 3 Moreno-Pelayo M.A....Arnaiz-Villena A. (Immunogenetics 1999)
  2. Nomenclature for factors of the HLA system, 1991. WHO Nomenclature Committee for factors of the HLA system. (PubMed id 1529427)1, 3 Bodmer J.G....Sasazuki T. (Tissue Antigens 1992)
  3. Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles. (PubMed id 23472185)1 Mero I.L....SA ( 2013)
  4. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. (PubMed id 23535732)1 Eeles R.A....Easton D.F. (Nat. Genet. 2013)
  5. Antinuclear antibodies and HLA class II alleles in Jamaican patients with systemic lupus erythematosus. (PubMed id 17910142)1 Christian N....Barton E.N. (West Indian Med J 2007)
  6. [Study on the gestational diabetes mellitus and histocompatibility human leukocyte antigen DRB allele polymorphism]. (PubMed id 12133402)1 Song D....Jiao S. (Zhonghua Fu Chan Ke Za Zhi 2002)
  7. Cytokine gene polymorphisms and acute human liver graft rejection. (PubMed id 12089714)1 WarlAc M.C....Bouma G.J. (Liver Transpl. 2002)
  8. Transcription and weak expression of HLA-DRB6: a gene with anomalies in exon 1 and other regions. (PubMed id 9601939)1 Fernandez-Soria V.M.... Arnaiz-Villena A. (Immunogenetics 1998)
  9. Primate DRB6 pseudogenes: clue to the evolutionary origin of the HLA-DR2 haplotype. (PubMed id 1937579)1 Figueroa F....Klein J. (Immunogenetics 1991)

(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: 3128 HGNC: 4954 AceView: HLA-DRB6 Ensembl:ENSG00000229391 euGenes: HUgn3128
ECgene: HLA-DRB6 H-InvDB: HLA-DRB6

(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 HLA-DRB6 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 HLA-DRB6 gene:
Search GeneIP for patents involving HLA-DRB6

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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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