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Gene Detail
histocompatibility 2, class II antigen A, alpha
Synonyms Aalpha, A alpha, H-2Aa, Ia1, Ia-1, I-Aalpha
Feature Type protein coding gene
Genetic Map
Chromosome 17
17.98 cM
Detailed Genetic Map ± 1 cM

Mapping data(6)
Sequence Map
Chr17:34282744-34287827 bp, - strand
From VEGA annotation of GRCm38

  5084 bp   ±  kb flank

VEGA Genome Browser | Ensembl Genome Browser | UCSC Browser | NCBI Map Viewer

Mouse Genome Browser
HomoloGene:123820  Vertebrate Homology Class
1 human; 1 mouse; 1 rat; 1 chimpanzee; 2 rhesus macaque; 1 cattle

Gene Tree: H2-Aa

Human Homolog HLA-DQA1, major histocompatibility complex, class II, DQ alpha 1
NCBI Gene ID 3117
neXtProt AC  NX_P01909
Human Synonyms  CD, CELIAC1, DQ-A1, GSE, HLA-DQA
Human Chr (Location)  6p21.3; chr6:32637392-32654685 (+)  GRCh38
Disease Associations  (1) Diseases Associated with Human HLA-DQA1
alleles, and
All mutations/alleles(3) : Targeted(3)
Incidental mutations (data from APF )
Mice homozygous for a knock-out allele lack cell surface expression of MHC class II molecules on macrophages and show decreased CD4-positive T cell number, increased CD8-positive T cell number, thymus hyperplasia, enlarged lymph nodes, and altered splenocyte response to staphylococcal enterotoxin B.
H2-Aa interacts with 76 markers (Mir7-1, Mir7-2, Mir7b, ...)
Gene Ontology
All GO classifications: (20 annotations)
Process antigen processing and presentation, antigen processing and presentation of exogenous peptide antigen via MHC class II, ...
Component external side of plasma membrane, integral component of membrane, ...
Function peptide antigen binding, protein binding, ...
External Resources: FuncBase
Literature Summary: (4 records)
Data Summary: Results (48)    Tissues (30)    Images (19)
Theiler Stages: 19, 22, 23, 28
Assay TypeResults
RNA in situ 48
cDNA source data(277)
External Resources: Allen Institute   GEO   Expression Atlas
All nucleic(299) Genomic(16) cDNA(278) Primer pair(3) Other(2)
Microarray probesets(5)
Other database
VEGA Gene ModelOTTMUSG00000037121 (Evidence)
Ensembl Gene ModelENSMUSG00000036594 (Evidence)
Entrez Gene14960 (Evidence)
DFCITC1571966, TC1588238, TC1728757, TC1761443
DoTSDT.110551673, DT.495080, DT.91290396, DT.91344507, DT.94412154
NIA Mouse Gene IndexU037709
PDB1D9K, 1F3J, 1IAK, 1IAO, 1K2D, 1LNU, 1MUJ, 1U3H, 2IAD, 2PXY, 3C5Z, 3C6L, 3CUP, 3MBE, 3RDT, 4P5T, 1ES0, 1JL4, 2P24, 2Z31, 3C60, 4P23, 4P46
Consensus CDS ProjectCCDS28645.1
International Mouse Knockout Project StatusH2-Aa
Representative SequencesLengthStrain/SpeciesFlank
genomic OTTMUSG00000037121 VEGA Gene Model | MGI Sequence Detail 5084 C57BL/6J ±  kb
transcript OTTMUST00000095576 VEGA | MGI Sequence Detail 1132 Not Applicable 
polypeptide OTTMUSP00000053329 VEGA | MGI Sequence Detail 256 Not Applicable 

For the selected sequences
All sequences(74) RefSeq(6) UniProt(17)
Polymorphisms All PCR and RFLP(14) : PCR(2) RFLP(12) SNPs within 2kb(350 from dbSNP Build 137)
InterPro IPR003597 Immunoglobulin C1-set
InterPro IPR007110 Immunoglobulin-like domain
InterPro IPR013783 Immunoglobulin-like fold
InterPro IPR003006 Immunoglobulin/major histocompatibility complex, conserved site
InterPro IPR011162 MHC classes I/II-like antigen recognition protein
InterPro IPR014745 MHC class II, alpha/beta chain, N-terminal
InterPro IPR001003 MHC class II, alpha chain, N-terminal
Protein Ontology PR:000002013 MHC class II histocompatibility antigen alpha chain HLA-DQA1
References (Earliest) J:5527 Shreffler DC, et al., The H-2 major histocompatibility complex and the I immune response region: genetic variation, function, and organization. Adv Immunol. 1975;20:125-95
(Latest) J:207898 Daley SR, et al., Rasgrp1 mutation increases naive T-cell CD44 expression and drives mTOR-dependent accumulation of Helios+ T cells and autoantibodies. Elife. 2013;2:e01020
All references(112)
accession IDs
MGD-MRK-10377, MGD-MRK-10490, MGD-MRK-11044, MGD-MRK-11049

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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last database update
MGI 5.19
The Jackson Laboratory