H2-Ea histocompatibility 2, class II antigen E alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: H2-Eaprovided by MGI
Official Full Name: histocompatibility 2, class II antigen E alphaprovided by MGI
Primary source: MGI:MGI:95900
See related: Ensembl:ENSMUSG00000036322 AllianceGenome:MGI:95900
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Ia3; Ia-3; H-2Ea; H2-Ea-ps; I-Ealpha; E-alpha-f; MHC-H2-Ea
Summary: This locus belongs to the class II major histocompatibility complex (MHC) family of genes, which encode immune response (Ia) antigens that function in the T-cell-dependent immune response. This family member has multiple haplotypes, some of which result in the production of an E-alpha subunit that combines with an E-beta subunit to form a functional E complex at the cell surface. Other haplotypes, including that of the reference genome allele, contain mutations and they thus represent polymorphic pseudogenes that do not produce functional products. These mutations include frameshifting indels, nonsense mutations, and deletions of larger regions. The reference genome haplotype contains a deletion at the 5' end of the gene, including the core promoter region and the transcription start site, and therefore no transcripts result from this haplotype. [provided by RefSeq, Aug 2011]
Annotation information: Note: Genetic polymorphisms result in both protein coding and non-coding alleles of this gene.
Expression: Low expression observed in reference dataset See more
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Genomic context

Location:: 17 B1; 17 17.98 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (34560926..34563619, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (34341952..34344645, complement)

Chromosome 17 - NC_000083.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A computational method for mapping phenotypic traits was used to map an allele-specific, YY1 binding element regulating H2-Ealpha gene expression to the first intron of the H2-Ealpha gene.
Title: In silico genetics: identification of a functional element regulating H2-Ealpha gene expression.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D17Rua10 (e-PCR), detects polymorphism
- UniSTS:142160

D17Rua2 (e-PCR), detects polymorphism
- UniSTS:142161

AI323765 (e-PCR)
- UniSTS:166051

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables MHC class II protein complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables T cell receptor binding	ISO Inferred from Sequence Orthology more info
enables peptide antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables peptide antigen binding	ISO Inferred from Sequence Orthology more info
enables polysaccharide binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class II	ISO Inferred from Sequence Orthology more info
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within antigen processing and presentation of exogenous peptide antigen via MHC class II	IDA Inferred from Direct Assay more info	PubMed
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II	ISO Inferred from Sequence Orthology more info
involved_in antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	ISO Inferred from Sequence Orthology more info
involved_in cognition	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within immunoglobulin mediated immune response	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within immunoglobulin mediated immune response	IGI Inferred from Genetic Interaction more info	PubMed
involved_in myeloid dendritic cell antigen processing and presentation	ISO Inferred from Sequence Orthology more info
involved_in peptide antigen assembly with MHC class II protein complex	IBA Inferred from Biological aspect of Ancestor more info
involved_in peptide antigen assembly with MHC class II protein complex	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of CD4-positive, alpha-beta T cell activation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell activation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of T cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of immune response	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of immune response	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of immune response	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of memory T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of T-helper cell differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of MHC class II protein complex	IBA Inferred from Biological aspect of Ancestor more info
part_of MHC class II protein complex	ISO Inferred from Sequence Orthology more info
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in external side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in immunological synapse	ISO Inferred from Sequence Orthology more info
is_active_in late endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome membrane	ISO Inferred from Sequence Orthology more info
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: histocompatibility 2, class II antigen E alpha

Names: H-2 class II histocompatibility antigen, E-D alpha chain; H-2 class II histocompatibility antigen, E-K alpha chain; H-2 class II histocompatibility antigen, E-U alpha chain; H2-IE-alpha; I-E alpha MHC class II; MHC class II H2-E alpha chain; MHC class II alpha chain; MHC class II antigen E alpha; MHC class II antigen IEk-alpha; MHC class II protein; histocompatibility 2, class II antigen E alpha, pseudogene

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_010381.3 → NP_034511.3 histocompatibility 2, class II antigen E alpha precursor

Status: VALIDATED

Source sequence(s)

BC106107

UniProtKB/Swiss-Prot

P04224

UniProtKB/TrEMBL

A0A0R7FDL7, A0A290WGA7

Conserved Domains (2) summary

cd05767
Location:111 → 204

IgC_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain

pfam00993
Location:29 → 107

MHC_II_alpha; Class II histocompatibility antigen, alpha domain

RNA

NR_164196.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

CR974457

Related

ENSMUST00000134042.4

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000083.7 Reference GRCm39 C57BL/6J

Range

34560926..34563619 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein	Strain
Heading	Accession and Version	Protein	Strain

Protein Accession	Links
Protein Accession	GenPept Link	UniProtKB Link
P01904.2	GenPept	UniProtKB/Swiss-Prot:P01904
P04224.1	GenPept	UniProtKB/Swiss-Prot:P04224
P14439.2	GenPept	UniProtKB/Swiss-Prot:P14439