RT1-Db1 RT1 class II, locus Db1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: RT1-Db1provided by RGD
Official Full Name: RT1 class II, locus Db1provided by RGD
Primary source: RGD:1593282
See related: EnsemblRapid:ENSRNOG00000033215 AllianceGenome:RGD:1593282
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: Db1; RT1-Db; RT1-Db1n
Summary: Predicted to enable several functions, including MHC class II receptor activity; peptide antigen binding activity; and signaling receptor binding activity. Involved in response to dexamethasone. Predicted to be located in external side of plasma membrane and immunological synapse. 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 several diseases, including asthma (multiple); autoimmune disease (multiple); bacterial infectious disease (multiple); eye disease (multiple); and sarcoidosis (multiple). Orthologous to several human genes including HLA-DRB1 (major histocompatibility complex, class II, DR beta 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 2046.1), Thymus (RPKM 1063.0) and 7 other tissues See more
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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 (4550594..4560182, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4548664..4558237, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (4087621..4097190)

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 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 CD4 receptor binding	ISO Inferred from Sequence Orthology more info
enables MHC class II protein complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables MHC class II receptor activity	ISO Inferred from Sequence Orthology 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 T cell receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in T-helper 1 type immune response	ISO Inferred from Sequence Orthology more info
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
involved_in humoral immune response	ISO Inferred from Sequence Orthology more info
involved_in immune response	ISO Inferred from Sequence Orthology more info
involved_in inflammatory response to antigenic stimulus	ISO Inferred from Sequence Orthology more info
involved_in macrophage differentiation	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 negative regulation of T cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of inflammatory response to antigenic stimulus	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of type II interferon production	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 DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of ERK1 and ERK2 cascade	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of MAPK cascade	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 T cell mediated immune response to tumor cell	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of insulin secretion involved in cellular response to glucose stimulus	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of kinase activity	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 positive regulation of monocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of viral entry into host cell	ISO Inferred from Sequence Orthology more info
involved_in protein tetramerization	ISO Inferred from Sequence Orthology more info
involved_in regulation of T-helper cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of interleukin-10 production	ISO Inferred from Sequence Orthology more info
involved_in regulation of interleukin-4 production	ISO Inferred from Sequence Orthology more info
involved_in response to dexamethasone	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to type II interferon	ISO Inferred from Sequence Orthology more info
involved_in signal transduction	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	IEA Inferred from Electronic Annotation 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

General protein information

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Preferred Names: rano class II histocompatibility antigen, D-1 beta chain

Names: MHC class II RT1D beta1 chain antigen; RT1 class II histocompatibility antigen, D-1 beta chain; RT1-D beta

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.