RT1-A2 RT1 class Ia, locus A2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: RT1-A2provided by RGD
Official Full Name: RT1 class Ia, locus A2provided by RGD
Primary source: RGD:1595923
See related: EnsemblRapid:ENSRNOG00000069480 AllianceGenome:RGD:1595923
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: RT1A-2; RT1-A2n; RT1.A2(N)
Summary: Predicted to enable beta-2-microglobulin binding activity; peptide antigen binding activity; and signaling receptor binding activity. Predicted to be involved in several processes, including positive regulation of gene expression; regulation of leukocyte mediated cytotoxicity; and regulation of lymphocyte activation. Predicted to act upstream of or within antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent and inner ear development. Predicted to be located in cell surface and plasma membrane. Predicted to be part of MHC class I protein complex and MHC class Ib protein complex. Predicted to be active in external side of plasma membrane and extracellular space. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); asthma (multiple); autoimmune disease (multiple); eye disease (multiple); and inner ear disease (multiple). Orthologous to several human genes including HLA-B (major histocompatibility complex, class I, B); HLA-C (major histocompatibility complex, class I, C); and HLA-E (major histocompatibility complex, class I, E). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Spleen (RPKM 1261.3), Lung (RPKM 1070.9) and 9 other tissues See more
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Genomic context

Location:: 20p12

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (4872720..4876425)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4870939..4910183)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (5374990..5378536)

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?

RT1-A2 MHC class I antigen is a ligand for the single member of a killer cell lectin-like receptor family, KLRH1.
Title: Identification of an MHC class I ligand for the single member of a killer cell lectin-like receptor family, KLRH1.
Induction of the MHCI antigen processing and presentation pathway in hippocampal neurons and glia may contribute to age-related hippocampal dysfunction by increasing neuroimmune signaling or altering synaptic homeostasis.
Title: Neuroglial expression of the MHCI pathway and PirB receptor is upregulated in the hippocampus with advanced aging.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

H2-K1 (e-PCR), detects polymorphism
- UniSTS:463411

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables MHC class I protein binding	ISO Inferred from Sequence Orthology more info
enables T cell receptor binding	ISO Inferred from Sequence Orthology more info
enables beta-2-microglobulin binding	ISO Inferred from Sequence Orthology more info
enables natural killer cell lectin-like receptor binding	ISO Inferred from Sequence Orthology more info
enables peptide antigen binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in CD8-positive, alpha-beta T cell activation	ISO Inferred from Sequence Orthology more info
acts_upstream_of T cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in adaptive immune response	ISO Inferred from Sequence Orthology more info
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class Ib	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent	ISO Inferred from Sequence Orthology more info
involved_in antigen processing and presentation of exogenous peptide antigen via MHC class Ib	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear development	ISO Inferred from Sequence Orthology more info
involved_in natural killer cell tolerance induction	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 natural killer cell activation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of natural killer cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of CD8-positive, alpha-beta T cell activation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of CD8-positive, alpha-beta T cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of T cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of TRAIL production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of antibody-dependent cellular cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of immunoglobulin production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-13 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-4 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of natural killer cell activation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of natural killer cell cytokine production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of natural killer cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of natural killer cell mediated immunity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of natural killer cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
involved_in protection from natural killer cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
involved_in regulation of natural killer cell mediated immunity	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of MHC class I protein complex	ISO Inferred from Sequence Orthology more info
part_of MHC class Ib protein complex	ISO Inferred from Sequence Orthology more info
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in lumenal side of endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in phagocytic vesicle 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: RT1 class Ia, locus A2

Names: RT1 class I gene (A-2); RT1 class Ia, A2n

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_001008829.2 → NP_001008829.1 RT1 class Ia, locus A2 precursor

See identical proteins and their annotated locations for NP_001008829.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000020

UniProtKB/TrEMBL

F7ERG5, P79602, Q6MGB8, Q95569

Conserved Domains (3) summary

cd07698
Location:205 → 297

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain

pfam00129
Location:23 → 201

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

pfam06623
Location:340 → 365

MHC_I_C; MHC_I C-terminus