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Aliases for HLA-DMA Gene

Aliases for HLA-DMA Gene

  • Major Histocompatibility Complex, Class II, DM Alpha 2 3 5
  • Really Interesting New Gene 6 Protein 3 4
  • MHC Class II Antigen DMA 3 4
  • RING6 3 4
  • DMA 3 4
  • HLA Class II Histocompatibility Antigen, DM Alpha Chain 3
  • Class II Histocompatibility Antigen, M Alpha Chain 3
  • D6S222E 3
  • HLADM 3

External Ids for HLA-DMA Gene

Previous GeneCards Identifiers for HLA-DMA Gene

  • GC06M032913
  • GC06M032687
  • GC06M032963
  • GC06M033024
  • GC06M032917
  • GC06M032918
  • GC06M032658
  • GC06M032919
  • GC06M032924

Summaries for HLA-DMA Gene

Entrez Gene Summary for HLA-DMA Gene

  • HLA-DMA belongs to the HLA class II alpha chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DMA) and a beta chain (DMB), both anchored in the membrane. It is located in intracellular vesicles. DM plays a central role in the peptide loading of MHC class II molecules by helping to release the CLIP molecule from the peptide binding site. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The alpha chain is approximately 33-35 kDa and its gene contains 5 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and the cytoplasmic tail. [provided by RefSeq, Jul 2008]

GeneCards Summary for HLA-DMA Gene

HLA-DMA (Major Histocompatibility Complex, Class II, DM Alpha) is a Protein Coding gene. Diseases associated with HLA-DMA include Rheumatoid Arthritis and Diabetes Mellitus. Among its related pathways are Rheumatoid arthritis and GPCR Pathway. Gene Ontology (GO) annotations related to this gene include MHC class II protein complex binding. An important paralog of this gene is HLA-DPA1.

UniProtKB/Swiss-Prot for HLA-DMA Gene

  • Plays a critical role in catalyzing the release of class II-associated invariant chain peptide (CLIP) from newly synthesized MHC class II molecules and freeing the peptide binding site for acquisition of antigenic peptides. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO.

Gene Wiki entry for HLA-DMA Gene

Additional gene information for HLA-DMA Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HLA-DMA Gene

Genomics for HLA-DMA Gene

GeneHancer (GH) Regulatory Elements for HLA-DMA Gene

Promoters and enhancers for HLA-DMA Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J032965 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 687.5 -1.6 -1575 10.4 ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 ZNF263 BRD2 HLA-DMA ENSG00000223837 LEMD2 ATF6B VPS52 RXRB DAXX WDR46 HCG25
GH06J032951 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 655.6 +15.2 15249 3.9 HDGF PKNOX1 ATF1 SMAD1 ZNF133 ARID4B SIN3A YY1 ZNF207 ZNF143 HLA-DMA ENSG00000248993 HLA-DOB HLA-DPA1 LYPLA2P1 GC06M032966 GC06M032900
GH06J032940 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 60.2 +24.9 24897 8.8 HDGF ATF1 ARID4B ZNF2 IRF4 BRCA1 YY1 ZNF207 ZNF143 ATF7 HLA-DMA BRD2 PSMB9 TAP1 TAP2 PSMB8 RING1 HLA-DMB HLA-DOB ENSG00000223837
GH06J032837 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 19.4 +126.9 126855 9.8 HDGF PKNOX1 SMAD1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 PSMB9 PSMB8-AS1 PSMB8 TAP2 HLA-DMA BRD2 VPS52 TAP1 DAXX LEMD2
GH06J032982 Enhancer 1.1 Ensembl ENCODE dbSUPER 37.2 -14.4 -14434 1.4 FOXA2 CEBPG BMI1 FEZF1 ZNF664 POLR2A NFATC1 ZSCAN5C PRDM10 BCLAF1 HLA-DMA HLA-DMB TAP2 ENSG00000250264 TAP1 PSMB9 RNY4P10 RXRB SLC39A7 HSD17B8
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HLA-DMA on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HLA-DMA gene promoter:
  • TFIID
  • TBP
  • SRY
  • Max
  • c-Myc
  • IRF-7A
  • deltaCREB

Genomic Locations for HLA-DMA Gene

Genomic Locations for HLA-DMA Gene
chr6:32,948,613-32,969,094
(GRCh38/hg38)
Size:
20,482 bases
Orientation:
Minus strand
chr6:32,916,390-32,936,871
(GRCh37/hg19)
Size:
20,482 bases
Orientation:
Minus strand

Genomic View for HLA-DMA Gene

Genes around HLA-DMA on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HLA-DMA Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HLA-DMA Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for HLA-DMA Gene

  • Protein details for HLA-DMA Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P28067-DMA_HUMAN
    Recommended name:
    HLA class II histocompatibility antigen, DM alpha chain
    Protein Accession:
    P28067
    Secondary Accessions:
    • Q29639
    • Q29640

    Protein attributes for HLA-DMA Gene

    Size:
    261 amino acids
    Molecular mass:
    29194 Da
    Quaternary structure:
    • Heterodimer of an alpha chain (DMA) and a beta chain (DMB).

    Three dimensional structures from OCA and Proteopedia for HLA-DMA Gene

neXtProt entry for HLA-DMA Gene

Post-translational modifications for HLA-DMA Gene

  • Glycosylation at Asn41
  • Modification sites at PhosphoSitePlus

Other Protein References for HLA-DMA Gene

Antibody Products

  • Abcam antibodies for HLA-DMA
  • Boster Bio Antibodies for HLA-DMA

No data available for DME Specific Peptides for HLA-DMA Gene

Domains & Families for HLA-DMA Gene

Gene Families for HLA-DMA Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Graphical View of Domain Structure for InterPro Entry

P28067

UniProtKB/Swiss-Prot:

DMA_HUMAN :
  • Belongs to the MHC class II family.
Family:
  • Belongs to the MHC class II family.
genes like me logo Genes that share domains with HLA-DMA: view

Function for HLA-DMA Gene

Molecular function for HLA-DMA Gene

UniProtKB/Swiss-Prot Function:
Plays a critical role in catalyzing the release of class II-associated invariant chain peptide (CLIP) from newly synthesized MHC class II molecules and freeing the peptide binding site for acquisition of antigenic peptides. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO.
GENATLAS Biochemistry:
HLA-DM,alpha chain,class II related,expressed in B cell lysosomes,same as RING6

Phenotypes From GWAS Catalog for HLA-DMA Gene

Gene Ontology (GO) - Molecular Function for HLA-DMA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 9768757
GO:0023026 MHC class II protein complex binding IDA 22733780
genes like me logo Genes that share ontologies with HLA-DMA: view
genes like me logo Genes that share phenotypes with HLA-DMA: view

Animal Models for HLA-DMA Gene

MGI Knock Outs for HLA-DMA:

Animal Model Products

CRISPR Products

miRNA for HLA-DMA Gene

miRTarBase miRNAs that target HLA-DMA

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HLA-DMA

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HLA-DMA Gene

Localization for HLA-DMA Gene

Subcellular locations from UniProtKB/Swiss-Prot for HLA-DMA Gene

Late endosome membrane; Single-pass type I membrane protein. Lysosome membrane; Single-pass type I membrane protein. Note=Localizes to late endocytic compartment. Associates with lysosome membranes.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HLA-DMA gene
Compartment Confidence
plasma membrane 5
extracellular 5
lysosome 5
endosome 5
endoplasmic reticulum 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HLA-DMA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane TAS --
GO:0005768 endosome IEA --
GO:0009986 cell surface IDA 22247549
GO:0016020 membrane IEA,HDA 19946888
genes like me logo Genes that share ontologies with HLA-DMA: view

Pathways & Interactions for HLA-DMA Gene

genes like me logo Genes that share pathways with HLA-DMA: view

Interacting Proteins for HLA-DMA Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000363976%0d%0a9606.ENSP00000260363%0d%0a9606.ENSP00000324020%0d%0a9606.ENSP00000307078%0d%0a9606.ENSP00000414982%0d%0a9606.ENSP00000385000%0d%0a
Selected Interacting proteins: ENSP00000363976 P28067-DMA_HUMAN for HLA-DMA Gene via STRING IID MINT

Symbol External ID(s) Details
HLA-B
HLA-A
HLA-C
HLA-DRB1
HLA-DMB

Gene Ontology (GO) - Biological Process for HLA-DMA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002503 peptide antigen assembly with MHC class II protein complex IDA 7606781
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II IEA --
GO:0006955 immune response IEA --
GO:0019882 antigen processing and presentation IEA --
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II TAS --
genes like me logo Genes that share ontologies with HLA-DMA: view

No data available for SIGNOR curated interactions for HLA-DMA Gene

Drugs & Compounds for HLA-DMA Gene

(3) Drugs for HLA-DMA Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for HLA-DMA Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HLA-DMA: view

Transcripts for HLA-DMA Gene

mRNA/cDNA for HLA-DMA Gene

(1) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(565) Selected AceView cDNA sequences:
(9) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HLA-DMA Gene

Major histocompatibility complex, class II, DM alpha:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HLA-DMA

Alternative Splicing Database (ASD) splice patterns (SP) for HLA-DMA Gene

No ASD Table

Relevant External Links for HLA-DMA Gene

GeneLoc Exon Structure for
HLA-DMA
ECgene alternative splicing isoforms for
HLA-DMA

Expression for HLA-DMA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HLA-DMA Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HLA-DMA Gene

This gene is overexpressed in Spleen (x4.2).

Protein differential expression in normal tissues from HIPED for HLA-DMA Gene

This gene is overexpressed in Blymphocyte (20.8), Monocytes (20.0), and Lung (9.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HLA-DMA Gene



SOURCE GeneReport for Unigene cluster for HLA-DMA Gene:

Hs.728759

Evidence on tissue expression from TISSUES for HLA-DMA Gene

  • Lung(3.8)
  • Blood(2.8)
  • Spleen(2.7)
  • Lymph node(2.2)
genes like me logo Genes that share expression patterns with HLA-DMA: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HLA-DMA Gene

Orthologs for HLA-DMA Gene

This gene was present in the common ancestor of chordates.

Orthologs for HLA-DMA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia MAMU-DMA 33
  • 98.72 (n)
HLA-DMA 34
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia BOLA-DMA 34 33
  • 83.53 (n)
OneToOne
mouse
(Mus musculus)
Mammalia H2-DMa 16 34 33
  • 79.95 (n)
dog
(Canis familiaris)
Mammalia DLA-DMA 34
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia MODO-DMA 34
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves BMA1 33
  • 53.54 (n)
DMA 34
  • 34 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HLA-DMA 34
  • 45 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii si:zfos-2070c2.1 34
  • 25 (a)
ManyToMany
Species where no ortholog for HLA-DMA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HLA-DMA Gene

ENSEMBL:
Gene Tree for HLA-DMA (if available)
TreeFam:
Gene Tree for HLA-DMA (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HLA-DMA: view image

Paralogs for HLA-DMA Gene

Paralogs for HLA-DMA Gene

(12) SIMAP similar genes for HLA-DMA Gene using alignment to 8 proteins:

  • DMA_HUMAN
  • A2AAT8_HUMAN
  • F6S093_HUMAN
  • H0Y732_HUMAN
  • O77837_HUMAN
  • Q29878_HUMAN
  • Q5SP00_HUMAN
  • Q6ICR9_HUMAN
genes like me logo Genes that share paralogs with HLA-DMA: view

Variants for HLA-DMA Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for HLA-DMA Gene

DMA_HUMAN-P28067
The following alleles of DMA are known: DMA*01:01, DMA*01:02, DMA*01:03 (DMA3.2) and DMA*01:04 (DMA3.4). The sequence shown is that of DMA*01:01.

Sequence variations from dbSNP and Humsavar for HLA-DMA Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000984337 -- 32,954,725(-) C/A upstream_transcript_variant
rs1001306239 -- 32,948,507(-) C/T downstream_transcript_variant
rs1001472439 -- 32,948,504(-) T/G downstream_transcript_variant
rs1001503678 -- 32,948,921(-) T/G intron_variant
rs1001864641 -- 32,954,053(-) C/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HLA-DMA Gene

Variant ID Type Subtype PubMed ID
esv2759417 CNV gain 17122850
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1119076 CNV deletion 24896259
nsv1161376 CNV duplication 26073780
nsv483081 CNV loss 15286789
nsv830633 CNV loss 17160897

Variation tolerance for HLA-DMA Gene

Residual Variation Intolerance Score: 81.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.92; 74.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HLA-DMA Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HLA-DMA

Disorders for HLA-DMA Gene

MalaCards: The human disease database

(2) MalaCards diseases for HLA-DMA Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
rheumatoid arthritis
  • ra
diabetes mellitus
  • diabetes
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HLA-DMA

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HLA-DMA: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HLA-DMA Gene

Publications for HLA-DMA Gene

  1. [HLA-DM polymorphisms in Guizhou Han individuals]. (PMID: 18779172) Jiang HM … Wang Y (Yi chuan = Hereditas 2008) 3 22 44 58
  2. HLA-DM polymorphism and risk of trichloroethylene induced medicamentosa-like dermatitis. (PMID: 18348411) Yue F … Chen XM (Biomedical and environmental sciences : BES 2007) 3 22 44 58
  3. [HLA-DM gene polymorphism in Cantonese with condyloma acuminata]. (PMID: 16864101) Yang WL … Ye T (Nan fang yi ke da xue xue bao = Journal of Southern Medical University 2006) 3 22 44 58
  4. HLA-DMA*0103 and HLA-DMB*0104 alleles as novel prognostic factors in rheumatoid arthritis. (PMID: 15547082) Morel J … Combe B (Annals of the rheumatic diseases 2004) 3 22 44 58
  5. Association of HLA-DM polymorphism with the production of antiphospholipid antibodies. (PMID: 15547089) Sanchez ML … Khamashta MA (Annals of the rheumatic diseases 2004) 3 22 44 58

Products for HLA-DMA Gene

Sources for HLA-DMA Gene

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