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

Summary

Official Symbol: RT1-Baprovided by RGD
Official Full Name: RT1 class II, locus Baprovided by RGD
Primary source: RGD:1595867
See related: EnsemblRapid:ENSRNOG00000000451 AllianceGenome:RGD:1595867
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: BA1
Summary: Predicted to enable MHC class II protein complex binding activity and peptide antigen binding activity. Involved in cellular response to glucocorticoid stimulus and negative regulation of T cell proliferation. Predicted to be located in external side of plasma membrane and lysosome. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Used to study uveitis. Human ortholog(s) of this gene implicated in several diseases, including autoimmune disease (multiple); gastrointestinal system cancer (multiple); glomerulonephritis (multiple); hematologic cancer (multiple); and systemic scleroderma (multiple). Orthologous to human HLA-DQA1 (major histocompatibility complex, class II, DQ alpha 1) and HLA-DQA2 (major histocompatibility complex, class II, DQ alpha 2). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 2568.6), Thymus (RPKM 1746.6) and 6 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 (4577057..4581650)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4575134..4579727)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (4066133..4070726, 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?

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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	IBA Inferred from Biological aspect of Ancestor more info
enables peptide antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables peptide antigen binding	IEA Inferred from Electronic Annotation more info
enables peptide antigen binding	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed

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
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class II	IEA Inferred from Electronic Annotation 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 antigen processing and presentation of peptide antigen	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 cellular response to glucocorticoid stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in negative regulation of T cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in peptide antigen assembly with MHC class II protein complex	IBA Inferred from Biological aspect of Ancestor 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 differentiation	IEA Inferred from Electronic Annotation 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 immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of T cell activation	IEA Inferred from Electronic Annotation more info
involved_in regulation of leukocyte cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in response to type II interferon	IEA Inferred from Electronic Annotation 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 external side of plasma membrane	IEA Inferred from Electronic Annotation more info
located_in external side of plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in late endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in lysosomal membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: rano class II histocompatibility antigen, B alpha chain

Names: MHC class I antigen; MHC class II antigen RT1.B alpha chain; RT1 class II antigen, Ba chain; RT1-B alpha; activated B cell RT1Bl alpha chain

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_001008831.3 → NP_001008831.1 rano class II histocompatibility antigen, B alpha chain precursor

See identical proteins and their annotated locations for NP_001008831.1

Status: VALIDATED

Source sequence(s)

BC086448, BX883043

UniProtKB/TrEMBL

A0A023ILS4, A6JJD5, Q6MGA0, Q8VI32

Related

ENSRNOP00000000523.1, ENSRNOT00000000523.6

Conserved Domains (3) summary

cd05767
Location:112 → 205

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

pfam00993
Location:31 → 108

MHC_II_alpha; Class II histocompatibility antigen, alpha domain

pfam16196
Location:203 → 254

C1-set_C; C1-set C-terminal domain