RT1-DOa RT1 class II, locus DOa [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: RT1-DOaprovided by RGD
Official Full Name: RT1 class II, locus DOaprovided by RGD
Primary source: RGD:3477
See related: EnsemblRapid:ENSRNOG00000026762 AllianceGenome:RGD:3477
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: H2-Oa
Summary: Predicted to enable MHC class II protein complex binding activity and peptide antigen binding activity. Predicted to be involved in several processes, including antigen processing and presentation of exogenous peptide antigen via MHC class II; negative regulation of antigen processing and presentation of peptide antigen via MHC class II; and peptide antigen assembly with MHC class II protein complex. Predicted to act upstream of or within antigen processing and presentation and regulation of T cell differentiation. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Human ortholog(s) of this gene implicated in occupational asthma. Orthologous to human HLA-DOA (major histocompatibility complex, class II, DO alpha). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 126.7), Thymus (RPKM 60.3) and 3 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (4755287..4758491, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4753587..4756590, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (3889106..3892360)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables MHC class II protein complex binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within antigen processing and presentation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within antigen processing and presentation of exogenous peptide antigen via MHC class II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of antigen processing and presentation of peptide antigen via MHC class II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of T cell differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of MHC class II protein complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: RT1 class II, locus DOa

Names: histocompatibility 2, O region alpha locus

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_183051.2 → NP_898874.2 RT1 class II, locus DOa precursor

Status: VALIDATED

Source sequence(s)

BX883042

UniProtKB/TrEMBL

A6JJF2, F7F5V5, Q31289, Q6MGB0

Conserved Domains (2) summary

cd05767
Location:112 → 205

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

pfam00993
Location:30 → 108

MHC_II_alpha; Class II histocompatibility antigen, alpha domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086038.1 Reference GRCr8

Range

4755287..4758491 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017601546.3 → XP_017457035.1 RT1 class II, locus DOa isoform X2

UniProtKB/TrEMBL

Q31289
XM_006255914.5 → XP_006255976.1 RT1 class II, locus DOa isoform X1

UniProtKB/TrEMBL

A6JJF2, F7F5V5, Q31289, Q6MGB0

Related

ENSRNOP00000098018.2, ENSRNOT00000120328.2

Conserved Domains (2) summary

cd05767
Location:112 → 205

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

pfam00993
Location:30 → 108

MHC_II_alpha; Class II histocompatibility antigen, alpha domain