Human Gene HLA-DMA (uc003ocm.2) Description and Page Index
  Description: Homo sapiens major histocompatibility complex, class II, DM alpha (HLA-DMA), mRNA.
RefSeq Summary (NM_006120): 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]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR5189664.121619.1, SRR5189655.179218.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968540, SAMEA2144333 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000374843.9/ ENSP00000363976.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr6:32,916,391-32,920,899 Size: 4,509 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr6:32,916,641-32,920,813 Size: 4,173 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:32,916,391-32,920,899)mRNA (may differ from genome)Protein (261 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: Q31604_HUMAN
DESCRIPTION: SubName: Full=DMA protein; SubName: Full=HLA-DMA protein; SubName: Full=Major histocompatibility complex class II DM alpha; SubName: Full=Major histocompatibility complex, class II, DM alpha; SubName: Full=Major histocompatibility complex, class II, DM alpha, isoform CRA_c; SubName: Full=cDNA FLJ75740, highly similar to Homo sapiens major histocompatibility complex, class II, DM alpha (HLA-DMA), mRNA;
SIMILARITY: Belongs to the MHC class II family.
SIMILARITY: Contains 1 Ig-like C1-type (immunoglobulin-like) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HLA-DMA
CDC HuGE Published Literature: HLA-DMA
Positive Disease Associations: antiphospholipid syndrome , Body Composition , Heart Rate , lupus erythematosus , rheumatoid arthritis , systemic lupus erythematosus
Related Studies:
  1. antiphospholipid syndrome
    Sanchez, M. L. et al. 2004, Association of HLA-DM polymorphism with the production of antiphospholipid antibodies., Annals of the rheumatic diseases. 2004 Dec;63(12):1645-8. [PubMed 15547089]
    The results suggest that HLA-DMA*0102 or its linked gene(s) form one of the genetic risks for the production of aPL.
  2. Body Composition
    , , . [PubMed 0]
  3. Heart Rate
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: HLA-DMA
Diseases sorted by gene-association score: rheumatoid arthritis (4)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 102.46 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 988.82 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -30.4086-0.353 Picture PostScript Text
3' UTR -91.00250-0.364 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003006 - Ig/MHC_CS
IPR003597 - Ig_C1-set
IPR011162 - MHC_I/II-like_Ag-recog
IPR014745 - MHC_II_a/b_N
IPR001003 - MHC_II_a_N

Pfam Domains:
PF00993 - Class II histocompatibility antigen, alpha domain
PF07654 - Immunoglobulin C1-set domain

SCOP Domains:
48726 - Immunoglobulin
54452 - MHC antigen-recognition domain

ModBase Predicted Comparative 3D Structure on Q31604
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0002376 immune system process
GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0006955 immune response
GO:0019882 antigen processing and presentation

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0042613 MHC class II protein complex
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  X62744 - Human RING6 mRNA for HLA class II alpha chain-like product.
BC026279 - Homo sapiens major histocompatibility complex, class II, DM alpha, mRNA (cDNA clone MGC:23886 IMAGE:4703588), complete cds.
BC011447 - Homo sapiens major histocompatibility complex, class II, DM alpha, mRNA (cDNA clone MGC:13532 IMAGE:4245221), complete cds.
AK291858 - Homo sapiens cDNA FLJ75740 complete cds, highly similar to Homo sapiens major histocompatibility complex, class II, DM alpha (HLA-DMA), mRNA.
JD426091 - Sequence 407115 from Patent EP1572962.
JD354564 - Sequence 335588 from Patent EP1572962.
JD382219 - Sequence 363243 from Patent EP1572962.
AB590209 - Synthetic construct DNA, clone: pFN21AE1343, Homo sapiens HLA-DMA gene for major histocompatibility complex, class II, DM alpha, without stop codon, in Flexi system.
CR450324 - Homo sapiens full open reading frame cDNA clone RZPDo834G061D for gene HLA-DMA, major histocompatibility complex, class II, DM alpha; complete cds; without stopcodon.
DQ892839 - Synthetic construct clone IMAGE:100005469; FLH190182.01X; RZPDo839F0675D major histocompatibility complex, class II, DM alpha (HLA-DMA) gene, encodes complete protein.
DQ896086 - Synthetic construct Homo sapiens clone IMAGE:100010546; FLH190178.01L; RZPDo839F0665D major histocompatibility complex, class II, DM alpha (HLA-DMA) gene, encodes complete protein.
KJ896975 - Synthetic construct Homo sapiens clone ccsbBroadEn_06369 HLA-DMA gene, encodes complete protein.
CU679934 - Synthetic construct Homo sapiens gateway clone IMAGE:100023355 5' read HLA-DMA mRNA.
AK298081 - Homo sapiens cDNA FLJ51553 complete cds, highly similar to HLA class II histocompatibility antigen, DMalpha chain precursor.
AK310162 - Homo sapiens cDNA, FLJ17204.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)
hsa04612 - Antigen processing and presentation
hsa04672 - Intestinal immune network for IgA production
hsa04940 - Type I diabetes mellitus
hsa05140 - Leishmaniasis
hsa05310 - Asthma
hsa05320 - Autoimmune thyroid disease
hsa05322 - Systemic lupus erythematosus
hsa05330 - Allograft rejection
hsa05332 - Graft-versus-host disease
hsa05416 - Viral myocarditis

-  Other Names for This Gene
  Alternate Gene Symbols: DAAP-27A1.5-001, DAMA-147C13.1-001, DAMC-226H3.5-001, DAQB-96B10.1-001, DASS-67H14.8-001, DMA, hCG_2001572, NM_006120, NP_006111, O02966, Q31604, Q31604_HUMAN, Q96FA1
UCSC ID: uc003ocm.2
RefSeq Accession: NM_006120
Protein: Q31604 CCDS: CCDS4761.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006120.3
exon count: 5CDS single in 3' UTR: no RNA size: 1122
ORF size: 786CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1772.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 8
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.