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

Summary

Symbol: RT1-DMaprovided by RGD
Full Name: RT1 class II, locus DMaprovided by RGD
Primary source: RGD:735053
See related: EnsemblRapid:ENSRNOG00000066773 AllianceGenome:RGD:735053
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: DMA1; RT1.Ma; RT1.DMa
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; peptide antigen assembly with MHC class II protein complex; and positive regulation of immune response. Predicted to act upstream of or within several processes, including chaperone cofactor-dependent protein refolding; positive regulation of T cell differentiation; and positive thymic T cell selection. Predicted to be located in cell surface; endosome; and lysosome. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Orthologous to human HLA-DMA (major histocompatibility complex, class II, DM alpha). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 165.6), Spleen (RPKM 165.6) and 9 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 (4708932..4712335, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4707028..4710432, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (3935512..3938915)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Complementary DNA sequence encoding the multimammate rat MHC class II DQ alpha chain and cross-species sequence comparison in rodents are reported.
Title: Complementary DNA sequences encoding the multimammate rat MHC class II DQ alpha and beta chains and cross-species sequence comparison in rodents.

Submit: New GeneRIF Correction

General gene information

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Markers

D20Yum76 (e-PCR)
- UniSTS:526109

RH136915 (e-PCR)
- UniSTS:219004

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 MHC class II protein complex binding	ISO Inferred from Sequence Orthology more info
enables peptide antigen binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within antigen processing and presentation	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
acts_upstream_of_or_within chaperone cofactor-dependent protein refolding	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within immunoglobulin mediated immune response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear development	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 T cell activation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of germinal center formation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of humoral immune response	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
acts_upstream_of_or_within positive thymic T cell selection	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein-containing complex assembly	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 endosome membrane	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in late endosome	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 multivesicular body	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: RT1 class II, DM alpha

Names: MHC class II-like alpha chain; class II histocompatibility antigen, M alpha chain; major histocompatibility complex, class II, DM 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.