Human Gene HLA-DMA (uc011hfo.1) 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 :: BC011447.1, X62744.1 [ECO:0000332] RNAseq introns :: single sample supports all introns ERS025087, ERS025093 [ECO:0000348] ##Evidence-Data-END##
Transcript (Including UTRs)
   Position: chr6_mann_hap4:4,373,602-4,378,111 Size: 4,510 Total Exon Count: 5 Strand: -
Coding Region
   Position: chr6_mann_hap4:4,373,855-4,378,025 Size: 4,171 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDMicroarray
RNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated: 2013-06-14

+  Sequence and Links to Tools and Databases
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-  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, 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 Ig-like C1-type (immunoglobulin-like) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database: 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

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

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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GNF Expression Atlas 1 Human Data on Affy U95 Chips

      
    
     
      
    
    
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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 -91.60253-0.362 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_dom
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:
PF00047 - Immunoglobulin domain
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
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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    
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-  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.
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.
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: uc011hfo.1
RefSeq Accession: NM_006120
Protein: Q31604

-  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.