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HLA-DMB Gene(Protein Coding)

Major Histocompatibility Complex, Class II, DM Beta

GCID:
GC06M032903
GIFtS:
58
Genes Participants
UDN Logo

Aliases for HLA-DMB Gene

Aliases for HLA-DMB Gene

  • Major Histocompatibility Complex, Class II, DM Beta 2 3 5
  • Really Interesting New Gene 7 Protein 3 4
  • MHC Class II Antigen DMB 3 4
  • RING7 3 4
  • HLA Class II Histocompatibility Antigen, DM Beta Chain 3
  • Class II Histocompatibility Antigen, M Beta Chain 3
  • MHC Class II Antigen HLA-DM Beta Chain 3
  • MHC Class II HLA-DMB 3
  • D6S221E 3
  • DMB 4

External Ids for HLA-DMB Gene

Previous GeneCards Identifiers for HLA-DMB Gene

  • GC06M032899
  • GC06M032673
  • GC06M032949
  • GC06M033010
  • GC06Mf32973
  • GC06M032644

Summaries for HLA-DMB Gene

Entrez Gene Summary for HLA-DMB Gene

  • HLA-DMB belongs to the HLA class II beta chain paralogues. This class II molecule is a heterodimer consisting of an alpha (DMA) and a beta (DMB) chain, 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 (class II-associated invariant chain peptide) molecule from the peptide binding site. Class II molecules are expressed in antigen presenting cells (APC: B lymphocytes, dendritic cells, macrophages). The beta chain is approximately 26-28 kDa and its gene contains 6 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the two extracellular domains, exon 4 encodes the transmembrane domain and exon 5 encodes the cytoplasmic tail. [provided by RefSeq, Jul 2008]

GeneCards Summary for HLA-DMB Gene

HLA-DMB (Major Histocompatibility Complex, Class II, DM Beta) is a Protein Coding gene. Diseases associated with HLA-DMB include Red-Green Color Blindness and Red Color Blindness. Among its related pathways are ICos-ICosL Pathway in T-Helper Cell and CTLA4 Signaling. GO annotations related to this gene include MHC class II protein complex binding. An important paralog of this gene is ENSG00000248993.

UniProtKB/Swiss-Prot for HLA-DMB 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-DMB Gene

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

Genomics for HLA-DMB Gene

Products:

  1. Regulatory Element

Regulatory Elements for HLA-DMB Gene

Enhancers for HLA-DMB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G033016 1.9 FANTOM5 Ensembl ENCODE dbSUPER 20.3 -77.8 -77798 5.0 PKNOX1 ZNF493 ARID4B SIN3A ZNF2 YY1 ZNF121 GLIS2 ZNF143 KLF7 HCG25 HLA-DQA2 PPT2 HLA-DPB1 HLA-DPA1 RXRB HLA-DQB2 HLA-DMA COL11A2 BRD2
GH06G032940 1.6 FANTOM5 ENCODE dbSUPER 13.1 -3.1 -3127 8.8 HDGF ATF1 WRNIP1 ARID4B SIN3A BRCA1 ZNF2 YY1 ZNF143 ZNF207 HLA-DMA BRD2 PSMB9 TAP1 TAP2 RING1 HLA-DMB ENSG00000223837 HLA-DPA1 ENSG00000250264
GH06G032965 1.5 ENCODE dbSUPER 12.9 -29.6 -29599 10.4 CREB3L1 AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 BRD2 RING1 RXRB VPS52 LEMD2 PPT2 PRRT1 ATF6B HLA-DMA DAXX
GH06G032984 1.5 Ensembl ENCODE dbSUPER 12.8 -43.8 -43818 1.3 HDGF PKNOX1 ATF1 ARID4B SIN3A ZNF2 SLC30A9 GLIS2 ZNF207 ZNF143 HLA-DMB TAP2 ENSG00000250264 TAP1 PSMB9 HSD17B8 RXRB SLC39A7 RNY4P10 MIR219A1
GH06G033026 1.8 FANTOM5 Ensembl ENCODE dbSUPER 9.9 -88.6 -88572 5.5 HDGF PKNOX1 ATF1 WRNIP1 TCF12 ZNF121 ZNF766 ZNF143 ZNF207 FOS HLA-DMA HLA-DQB1 HLA-DPA1 HLA-DPB1 HLA-DQB2 HLA-DQA2 HLA-DOA PSMB8 HLA-DMB TAPBP
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HLA-DMB on UCSC Golden Path with GeneCards custom track

Promoters for HLA-DMB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195728 370 1001 TBP ATF1 TEAD4 BRCA1 ZNF2 RFX5 RFXANK ZBTB48 POLR2A NFYB

Transcription factor binding sites by QIAGEN in the HLA-DMB gene promoter:

Genomic Location for HLA-DMB Gene

Chromosome:
6
Start:
32,934,629 bp from pter
End:
32,941,070 bp from pter
Size:
6,442 bases
Orientation:
Minus strand

Genomic View for HLA-DMB Gene

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

Cytogenetic band:
HLA-DMB 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-DMB Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HLA-DMB Gene

Proteins for HLA-DMB Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    P28068-DMB_HUMAN
    Recommended name:
    HLA class II histocompatibility antigen, DM beta chain
    Protein Accession:
    P28068
    Secondary Accessions:
    • O77936
    • Q13012
    • Q29751
    • Q58ZE2
    • Q5SNZ8
    • Q5STC4
    • Q9XRX2

    Protein attributes for HLA-DMB Gene

    Size:
    263 amino acids
    Molecular mass:
    28943 Da
    Quaternary structure:
    • Heterodimer of an alpha chain (DMA) and a beta chain (DMB).

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

neXtProt entry for HLA-DMB Gene

Protein Expression for HLA-DMB Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for HLA-DMB Gene

  • Glycosylation at posLast=110110
  • Modification sites at PhosphoSitePlus

Other Protein References for HLA-DMB Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for HLA-DMB

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

Domains & Families for HLA-DMB Gene

Gene Families for HLA-DMB Gene

HGNC:

Protein Domains for HLA-DMB Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HLA-DMB Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P28068

UniProtKB/Swiss-Prot:

DMB_HUMAN :
  • The YXXZ (Tyr-Xaa-Xaa-Zaa, where Zaa is a hydrophobic residue) motif mediates the targeting to the lysosomal compartments.
  • Belongs to the MHC class II family.
Domain:
  • The YXXZ (Tyr-Xaa-Xaa-Zaa, where Zaa is a hydrophobic residue) motif mediates the targeting to the lysosomal compartments.
Family:
  • Belongs to the MHC class II family.
genes like me logo Genes that share domains with HLA-DMB: view

Function for HLA-DMB Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for HLA-DMB Gene

GENATLAS Biochemistry:
HLA-DM,beta chain,class II related,expressed in B cell lysosomes,same as RING7
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.

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

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

Animal Model Products

Flow Cytometry Products

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

Localization for HLA-DMB Gene

Subcellular locations from UniProtKB/Swiss-Prot for HLA-DMB 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-DMB gene
Compartment Confidence
plasma membrane 5
lysosome 5
endosome 4
extracellular 3
endoplasmic reticulum 2
golgi apparatus 2
cytoskeleton 1
mitochondrion 1
peroxisome 1

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

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane TAS --
GO:0005768 endosome IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with HLA-DMB: view

Pathways & Interactions for HLA-DMB Gene

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

Interacting Proteins for HLA-DMB Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000398890%0d%0a9606.ENSP00000260363%0d%0a9606.ENSP00000300087%0d%0a9606.ENSP00000320130%0d%0a9606.ENSP00000385000%0d%0a9606.ENSP00000324020%0d%0a
Selected Interacting proteins: P28068-DMB_HUMAN ENSP00000398890 for HLA-DMB Gene via MINT STRING IID

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

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

GO ID Qualified GO term Evidence PubMed IDs
GO:0002399 MHC class II protein complex assembly IMP 8139689
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 --
genes like me logo Genes that share ontologies with HLA-DMB: view

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

Drugs & Compounds for HLA-DMB Gene

Products:

  1. Drug

(1) Additional Compounds for HLA-DMB Gene - From: Novoseek

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

Transcripts for HLA-DMB Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for HLA-DMB Gene

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

Unigene Clusters for HLA-DMB Gene

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

Flow Cytometry Products

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

No ASD Table

Relevant External Links for HLA-DMB Gene

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

Expression for HLA-DMB Gene

Products:

  1. Primer

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

mRNA expression in normal human tissues for HLA-DMB Gene
mRNA expression by BioGPS for HLA-DMB GenemRNA expression by GTEx for HLA-DMB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Spleen (x5.9).

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

This gene is overexpressed in Blymphocyte (25.1) and Lymph node (11.6).

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



SOURCE GeneReport for Unigene cluster for HLA-DMB Gene:

Hs.351279

Evidence on tissue expression from TISSUES for HLA-DMB Gene

  • Blood(4.5)
  • Bone marrow(4.2)
  • Spleen(2.3)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with HLA-DMB: 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-DMB Gene

Orthologs for HLA-DMB Gene

This gene was present in the common ancestor of chordates.

Orthologs for HLA-DMB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PATR-DMB 34 35
  • 99.11 (n)
dog
(Canis familiaris)
 Mammalia DLA-DMB 34
  • 82.45 (n)
-- 35
  • 78 (a)
 OneToMany
cow
(Bos Taurus)
 Mammalia BOLA-DMB 34
  • 79.89 (n)
HLA-DMB 35
  • 74 (a)
 OneToMany
mouse
(Mus musculus)
 Mammalia H2-DMb2 34 16 35
  • 79.08 (n)
H2-DMb1 35
  • 72 (a)
 ManyToMany
oppossum
(Monodelphis domestica)
 Mammalia -- 35
  • 61 (a)
 OneToMany
chicken
(Gallus gallus)
 Aves BMA2 34
  • 54.18 (n)
-- 35
  • 29 (a)
 ManyToMany
-- 35
  • 28 (a)
 ManyToMany
BLB1 35
  • 25 (a)
 ManyToMany
lizard
(Anolis carolinensis)
 Reptilia -- 35
  • 26 (a)
 ManyToMany
tropical clawed frog
(Silurana tropicalis)
 Amphibia LOC100495183 34
  • 47.12 (n)
zebrafish
(Danio rerio)
 Actinopterygii si:zfos-2070c2.3 35
  • 33 (a)
 ManyToMany
mhc2dbb 35
  • 25 (a)
 ManyToMany
si:busm1-228j01.4 35
  • 23 (a)
 ManyToMany
mhc2dab 35
  • 22 (a)
 ManyToMany
wu:fd58b11 35
  • 22 (a)
 ManyToMany
si:busm1-194e12.12 35
  • 21 (a)
 ManyToMany
si:busm1-104n07.3 35
  • 20 (a)
 ManyToMany
si:busm1-228j01.6 35
  • 19 (a)
 ManyToMany
si:dkey-33b17.3 35 35
  • 19 (a)
 ManyToMany
Species where no ortholog for HLA-DMB 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HLA-DMB Gene

ENSEMBL:
Gene Tree for HLA-DMB (if available)
TreeFam:
Gene Tree for HLA-DMB (if available)

Paralogs for HLA-DMB Gene

Paralogs for HLA-DMB Gene

(78) SIMAP similar genes for HLA-DMB Gene using alignment to 11 proteins:

genes like me logo Genes that share paralogs with HLA-DMB: view

Variants for HLA-DMB Gene

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

DMB_HUMAN-P28068
The following alleles of DMB are known: DMB*01:01, DMB*01:02, DMB*01:03, DMB*01:04 (DMB3.4), DMB*01:05, DMB*01:06, and DMB*01:07. The sequence shown is that of DMB*01:01.

Sequence variations from dbSNP and Humsavar for HLA-DMB Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000032892 -- 32,942,435(+) TGTAT(A/T)CTCCT upstream-variant-2KB
rs1000382742 -- 32,942,727(+) GTCAC(A/G)TGTGT upstream-variant-2KB
rs1000987928 -- 32,941,260(+) GGCTG(C/T)CCACT upstream-variant-2KB
rs1001033728 -- 32,938,509(+) CTCAC(A/G)TCAGC intron-variant
rs1001205168 -- 32,942,087(+) CTCCT(A/C)CCATC upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
esv2759417 CNV gain 17122850
esv33619 CNV gain 17666407
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1119076 CNV deletion 24896259
nsv1161376 CNV duplication 26073780
nsv483081 CNV loss 15286789
nsv819732 CNV loss 19587683
nsv830633 CNV loss 17160897

Variation tolerance for HLA-DMB Gene

Residual Variation Intolerance Score: 77.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.57; 56.04% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HLA-DMB Gene

Human Gene Mutation Database (HGMD)
HLA-DMB
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HLA-DMB

Disorders for HLA-DMB Gene

MalaCards: The human disease database

(4) MalaCards diseases for HLA-DMB Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
red-green color blindness
  • deutan defect
red color blindness
  • protan defect
nodular medulloblastoma
  • medulloblastoma, with extensive nodularity
rheumatoid arthritis
  • rheumatoid arthritis, progression of
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for HLA-DMB

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

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

Publications for HLA-DMB Gene

  1. HLA-DM polymorphism and risk of trichloroethylene induced medicamentosa-like dermatitis. (PMID: 18348411) Yue F. … Chen X.M. (Biomed. Environ. Sci. 2007) 3 22 46 64
  2. Association of HLA-DM polymorphism with the production of antiphospholipid antibodies. (PMID: 15547089) Sanchez M.L. … Khamashta M.A. (Ann. Rheum. Dis. 2004) 3 22 46 64
  3. Association of TAP and HLA-DM genes with psoriasis in Koreans. (PMID: 12648225) Pyo C.W. … Kim T.G. (J. Invest. Dermatol. 2003) 3 22 46 64
  4. Polymorphisms of TAP, LMP and HLA-DM genes in the Chinese. (PMID: 11775239) Zhu X. … Wang F. (Chin. Med. J. 2000) 3 22 46 64
  5. A new human HLA class II-related locus, DM. (PMID: 1922365) Kelly A.P. … Trowsdale J. (Nature 1991) 2 3 4 64

Products for HLA-DMB Gene

Sources for HLA-DMB Gene

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