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HLA-J Gene

pseudogene   GIFtS: 32
GCID: GC06P030190

Major Histocompatibility Complex, Class I, J (Pseudogene)


(Previous symbols: HLA-CDA12, D6S203)
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(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Major Histocompatibility Complex, Class I, J (Pseudogene)1 2
D6S2031 2
HLA-CDA121 2
CDA122
HLA-592

External Ids:    HGNC: 49671   Entrez Gene: 31372   Ensembl: ENSG000002046227   UniProtKB: Q301754   
ORGUL members:         

Export aliases for HLA-J gene to outside databases

Previous GC identifers: GC06U990057 GC06M030029 GC06P029857 GC06P029905 GC06P030018 GC06P029908 GC06P029909 GC06P029910 GC06P030082 GC06P030073 GC06P029979 GC06P029984 GC06P029989 GC06P029998


(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 HLA-J Gene:
This major histocompatibility complex gene represents a transcribed pseudogene, possibly derived from HLA-A.
(provided by RefSeq, May 2010)

GeneCards Summary for HLA-J Gene:
HLA-J (major histocompatibility complex, class I, J (pseudogene)) is a pseudogene, 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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Regulatory elements:
   Regulatory transcription factor binding sites in the HLA-J gene promoter:
         ER-alpha   GATA-3   p53   HSF1 (long)   E4BP4   HEN1   HSF2   HSF1short   ATF6   
         Other transcription factors

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

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


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

Entrez Gene cytogenetic band: 6p21.31   Ensembl cytogenetic band:  6p22.1   HGNC cytogenetic band: 6p21.3

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

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P030190:  view genomic region     (about GC identifiers)

Start:
29,973,748 bp from pter      End:
29,977,733 bp from pter
Size:
3,986 bases      Orientation:
plus strand

Selected alternative locations (see all 7):
Chr6+,NT_167244 1,213,596-1,217,581      Chr6+,NT_167246 1,272,322-1,276,307      Chr6+,NT_167249 1,303,076-1,307,061     
Chr6+,NT_167247 1,355,612-1,359,597      Chr6+,NT_167248 1,266,664-1,270,636      Chr6+,NT_113891.2 1,485,462-1,489,447     

(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, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/TrEMBL: Q30175 (See protein sequence)
Recommended Name: MHC class I HLA-J antigen  
Size: 218 amino acids; 24841 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

4 InterPro protein domains:
 IPR011162 MHC_I/II-like_Ag-recog
 IPR011161 MHC_I-like_Ag-recog
 IPR001039 MHC_I_a_a1/a2
 IPR027648 MHC_I_a

Graphical View of Domain Structure for InterPro Entry Q30175

ProtoNet protein and cluster: Q30175

1 Blocks protein domain: IPB001039 MHC class I signature

UniProtKB/TrEMBL: Q30175
Similarity: Belongs to the MHC class I family


Find genes that share domains with HLA-J           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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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Molecular Function:
     Genatlas biochemistry entry for HLA-J:
HLA class I-like gene J,5.9 Hind III fragment,see MHC1

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for HLA-J

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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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular3
cytosol1
peroxisome1

(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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SuperPaths for HLA-J About    
See pathways by source

SuperPathContained pathways About
1CDK-mediated phosphorylation and removal of Cdc6
Proteasome Degradation0.57


1 BioSystems Pathway for HLA-J
    Proteasome Degradation


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Interactions:

    Search GeneGlobe Interaction Network for HLA-J

(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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for HLA-J



(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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4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000469281(uc003nou.4 uc003rtl.4) ENST00000462773(uc003nov.4)
ENST00000495278(uc021yty.1) ENST00000494367
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2 AceView cDNA sequences:

BC062324 BC020891 

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

HLA-J Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

HLA-J Protein Expression
    Custom PCR Arrays for HLA-J
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HLA-J

(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-J (if available)
TreeFam Gene Tree for HLA-J (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for HLA-J gene
Selected SIMAP similar genes for HLA-J using alignment to 1 protein entry:     Q30175_HUMAN(see all similar genes):
HLA G locus    HLA C*    HLA-G    EA2.1    HLA-A24AK    HLA-B*35KM
HLA-B35    HLA-A*24    HLA-A*2410    HLA-B41    HLA-DQB1    HLA-A*03
HLA-Cw*15P    HLA-A*01    HLA-A*31    HLA-A*33    HLA-B*27    HLA-B*3512

Find genes that share paralogs with HLA-J           About GenesLikeMe



(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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Structural Variations
     Database of Genomic Variants (DGV) 7 variations for HLA-J:    About this table    
Variant IDTypeSubtypePubMed ID
esv2641340CNV Deletion19546169
esv2731777CNV Deletion23290073
dgv1088e199CNV Deletion23128226
dgv1040e201CNV Deletion23290073
esv2731778CNV Deletion23290073
nsv508398CNV Loss20534489
dgv1910e1CNV Complex17122850

Locus Specific Mutation Databases (LSDB): HLA-J

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

(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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Find genes that share disorders with HLA-J           About GenesLikeMe

Genetic Association Database (GAD): HLA-J
Human Genome Epidemiology (HuGE) Navigator: HLA-J (2813 documents)

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

  1. 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)
  2. HLA-J, a second inactivated class I HLA gene related to HLA-G and HLA-A. Implications for the evolution of the HLA-A-related genes. (PubMed id 1602142)1, 3 Messer G....Girdlestone J. (J. Immunol. 1992)
  3. Paradoxical downregulation of HLA-A expression by IFNI^ associated with schizophrenia and noncoding genes. (PubMed id 23083632)1 Gu S....Wank R. (Immunobiology 2013)
  4. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
  5. Identification of independent risk loci for Graves' disease within the MHC in the Japanese population. (PubMed id 21900946)1 Nakabayashi K....Shirasawa S. (J. Hum. Genet. 2011)
  6. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  7. 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)
  8. A physical map including a new class I gene (cda12) of the human major histocompatibility complex (A2/B13 haplotype) derived from a monosomy 6 mutant cell line. (PubMed id 2497062)1 Ragoussis J....Ziegler A. (Genomics 1989)

(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: 3137 HGNC: 4967 AceView: HLA-J Ensembl:ENSG00000204622 euGenes: HUgn3137
ECgene: HLA-J H-InvDB: HLA-J

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

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, 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
Advanced Cell Diagnostics, Animal models from genOway)
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