|
|
major histocompatibility complex, class I, J (pseudogene)
(Previous symbols: HLA-CDA12, D6S203)
| |
Aliases
for HLA-J gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Major Histocompatibility Complex, Class I, J (Pseudogene)1 2 | | CDA121 2 | | D6S2031 2 | | HLA-591 2 | | HLA-CDA121 2 |
Export aliases for HLA-J gene to outside databasesPrevious GC identifers: GC06U990057 GC06M030029 GC06P029857 GC06P029905 GC06P030018 GC06P029908 GC06P029909 GC06P029910 GC06P030082 GC06P030073 GC06P029979 GC06P029984 |
Summaries
for HLA-J gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for HLA-J:
This major histocompatibility complex gene represents a transcribed pseudogene, possibly derived from HLA-A. (providedby RefSeq, May 2010)
|
Genomic Views
for HLA-J gene
(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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000006.11 NC_018917.1 NT_007592.15 NT_113891.2 NT_167244.1 NT_167245.1 NT_167246.1 NT_167247.1
- NT_167248.1 NT_167249.1
Regulatory elements:
 SABiosciences 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
Search SABiosciences Chromatin IP Primers for HLA-J
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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: 6p21.3HLA-J Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 6 GeneLoc Exon Structure GeneLoc location for GC06P029989: 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 |
6/7 alternative locations (see all 7):
| Chr6+,ALT_REF_LOCI_5 29,967,035-29,971,020 | Chr6+,ALT_REF_LOCI_3 29,964,306-29,978,717 | Chr6+,ALT_REF_LOCI_4 29,891,981-29,895,966 | | Chr6+,ALT_REF_LOCI_1 29,910,811-29,922,484 | Chr6+,ALT_REF_LOCI_2 29,963,870-30,006,431 | Chr6+,ALT_REF_LOCI_6 29,963,880-30,002,820 | |
|
Proteins
for HLA-J gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/TrEMBL: Q30175 (See
protein sequence)Recommended Name: MHC class I HLA-J antigen Size: 218 amino acids; 24841 Da |
Protein
Domains /
Families
for HLA-J gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
HLA-J for domains About GeneDecksing
3 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q30175ProtoNet protein and cluster: Q30175 1 Blocks protein family: IPB001039 MHC class I signature
UniProtKB/TrEMBL: Q30175 Similarity: Belongs to the MHC class I family |
Function
for HLA-J gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
Genatlas biochemistry entry for HLA-J:HLA class I-like gene J,5.9 Hind III fragment,see MHC1
Animal Models:
|
Pathways & Interactions
for HLA-J gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
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 Mar 2013 via
Entrez Gene).
About This Section
|
Unified GeneCards pathways About this table 
See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | Ubiquitinated Orc1 is degraded by the proteasome | |
1  BioSystems Pathway for HLA-J
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HLA-J
|
Drugs & Compounds
for HLA-J gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for HLA-J
Search CenterWatch for drugs/clinical trials and news about HLA-J
|
Transcripts
for HLA-J gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 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,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
Sirion Biotech,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
Unigene Cluster for HLA-J: Major histocompatibility complex, class I, J (pseudogene) Hs.720762 [show with all ESTs]Unigene Representative Sequence: NR_0242404 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000469281(uc003nou.4 uc003rtl.4) ENST00000462773(uc003nov.4)
ENST00000495278(uc021yty.1) ENST00000494367
Additional cDNA sequence: BC020891.1 BC062324.1 BC089454.1 NR_024240.1 8 DOTS entries: DT.102843761 DT.99933773 DT.121345683 DT.121345984 DT.91806393 DT.100733440 DT.91783875 DT.95376858 2 AceView cDNA sequences: BC020891 BC062324
GeneLoc Exon Structure
|
Expression
for HLA-J gene
(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™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| HLA-J expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
Genevestigator expression for HLA-J
SOURCE GeneReport for Unigene cluster: Hs.720762
SABiosciences Custom PCR Arrays for HLA-J
Primer
Products: |  | Browse OriGene genome-wide validated SYBR primer pairs
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse / rat HLA-J | | | Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HLA-J | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HLA-J |
Orthologs
for HLA-J gene
(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)
About This Section
|
--
ENSEMBL Gene Tree for HLA-J (if available)
TreeFam Gene Tree for HLA-J (if available) |
Paralogs
for HLA-J gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for HLA-J gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, 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) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 6 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for HLA-J (29973748 - 29977733 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for HLA-J
2 CNVs: 99484 3599
Locus Specific Mutation Databases (LSDB): HLA-J
| SABiosciences Cancer Mutation PCR Assays |
|
Disorders
/ Diseases
for HLA-J gene
(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.)
About This Section
|
HLA-J for disorders About GeneDecksing
1  disease for HLA-J: About MalaCardsmultiple sclerosis
Human Genome Epidemiology (HuGE) Navigator: HLA-J (2813 documents)
Export disorders for HLA-J gene to outside databases
|
Publications
for HLA-J gene (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)
About This Section
|
PubMed articles for HLA-J gene integrated from 9 sources:
(articles sorted by number of sources associating them with HLA-J) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- 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. (1992)
- Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
- A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PubMed id 20593013)1 Cree B.A.... . (2010)
- Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
- 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. (2002)
- A physical map including a new class I gene (cda12) o f the human major histocompatibility complex (A2/B13 haplotype) derived from a monosomy 6 mutant cell line. (PubMed id 2497062)1 Ragoussis J....Ziegler A. (1989)
|
External Searches for HLA-J gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing HLA-J gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing HLA-J gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing HLA-J gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for HLA-J | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| 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
|
Products
for HLA-J gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
About This Section
|
 | |
 |
| | | | |
 |
 |
|  | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat HLA-J | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HLA-J | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HLA-J | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HLA-J | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HLA-J | | | Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HLA-J |
| |
 |  |  |  | |
| | | | Search Tocris compounds for HLA-J |
| |  |  |  |  | | | | |
 |
 |
 |
 | | | | |  |  |  |  | | | | Search ThermoFisher Antibodies for HLA-J |
| | | Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat HLA-J |
| |  | |
|
|
|
