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

Summary

Official Symbol: RT1-Daprovided by RGD
Official Full Name: RT1 class II, locus Daprovided by RGD
Primary source: RGD:1593283
See related: EnsemblRapid:ENSRNOG00000032844 AllianceGenome:RGD:1593283
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: DA1; H2-Ea; RT1-u
Summary: Predicted to enable several functions, including MHC class II protein complex binding activity; T cell receptor binding activity; and peptide antigen binding activity. Predicted to be involved in several processes, including antigen processing and presentation of endogenous peptide antigen via MHC class II; antigen processing and presentation of exogenous peptide antigen via MHC class II; and regulation of T cell differentiation. Predicted to act upstream of or within immunoglobulin mediated immune response. Predicted to be located in external side of plasma membrane; immunological synapse; and lysosome. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Biomarker of prediabetes syndrome. Human ortholog(s) of this gene implicated in Parkinson's disease (multiple); allergic disease; asthma; and autoimmune disease (multiple). Orthologous to human HLA-DRA (major histocompatibility complex, class II, DR alpha). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 5146.2), Thymus (RPKM 2676.3) and 6 other tissues See more
Orthologs: human 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 (4515393..4520387)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4513464..4518457)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (4127644..4132616, complement)

Chromosome 20 - NC_086038.1 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: 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?

Peptide binding motif for the MHC class II molecule RT1.Da.
Title: Peptide motif for the rat MHC class II molecule RT1.Da: similarities to the multiple sclerosis-associated HLA-DRB1*1501 molecule.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

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	ISO Inferred from Sequence Orthology more info
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 biological_process	ND No biological Data available more info
involved_in cognition	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within immunoglobulin mediated immune response	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
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: RT1 class II, locus Da

Names: MHC RT1.u-D-alpha chain; MHC class II RT1D alpha chain antigen; MHC class II antigen RT1.D alpha chain; RT1-D alpha; RT1-Du alpha; histocompatibility 2, class II antigen E alpha

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_001008847.2 → NP_001008847.1 RT1 class II, locus Da precursor

See identical proteins and their annotated locations for NP_001008847.1

Status: VALIDATED

Source sequence(s)

BC098677, FM048166

UniProtKB/TrEMBL

A0A023IKG5, A0A023IM59, Q6MG98, Q6T4R6

Related

ENSRNOP00000048774.2, ENSRNOT00000048332.6

Conserved Domains (2) summary

pfam00993
Location:29 → 107

MHC_II_alpha; Class II histocompatibility antigen, alpha domain

cd05767
Location:110 → 204

IgC1_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains

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

4515393..4520387

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039098493.2 → XP_038954421.1 RT1 class II, locus Da isoform X1

UniProtKB/TrEMBL

A0A023IKG5, A0A023IM59, Q6MG98, Q6T4R6

Conserved Domains (2) summary

pfam00993
Location:29 → 107

MHC_II_alpha; Class II histocompatibility antigen, alpha domain

cd05767
Location:110 → 204

IgC1_MHC_II_alpha; Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains