RT1-M3-1 RT1 class Ib, locus M3, gene 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: RT1-M3-1provided by RGD
Official Full Name: RT1 class Ib, locus M3, gene 1provided by RGD
Primary source: RGD:3494
See related: EnsemblRapid:ENSRNOG00000000763 AllianceGenome:RGD:3494
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: H2-M3; RT1-M3; RanoM3; 4B2/3.7; RanoM301; RanoM302
Summary: Predicted to enable CD8 receptor binding activity; peptide antigen binding activity; and protein homodimerization activity. Predicted to be involved in several processes, including positive regulation of cytokine production; regulation of leukocyte differentiation; and regulation of lymphocyte mediated immunity. Predicted to act upstream of or within several processes, including antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent; positive regulation of biosynthetic process; and response to bacterium. Predicted to be located in cis-Golgi network membrane; early endosome; and plasma membrane. Predicted to be part of 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 Stevens-Johnson syndrome; 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, Oct 2024]
Expression: Biased expression in Spleen (RPKM 155.4), Thymus (RPKM 151.8) and 9 other tissues See more
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Genomic context

Location:: 20p12

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (1329227..1333394, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (1323976..1328126, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (1814661..1833033, 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:

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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 CD8 receptor binding	ISO Inferred from Sequence Orthology more info
enables identical protein 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 protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables signaling receptor binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within alpha-beta T cell activation involved in immune response	ISO Inferred from Sequence Orthology more info
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation of endogenous peptide antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within antigen processing and presentation of endogenous peptide antigen via MHC class Ib	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 exogenous peptide antigen via MHC class Ib	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within defense response to bacterium	ISO Inferred from Sequence Orthology more info
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in immune response-inhibiting cell surface receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of G0 to G1 transition	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of T cell mediated cytotoxicity	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 angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of dendritic cell differentiation	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 negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISO Inferred from Sequence Orthology more info
acts_upstream_of nitric oxide biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in peripheral B cell tolerance induction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor 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 tolerance induction	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cellular senescence	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endothelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-12 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of macrophage cytokine production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of natural killer cell cytokine production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of natural killer cell mediated cytotoxicity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of nitric oxide biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of regulatory T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tolerance induction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of type II interferon 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 protein homotrimerization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to molecule of bacterial origin	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of MHC class Ib protein complex	ISO Inferred from Sequence Orthology more info
located_in cis-Golgi network membrane	ISO Inferred from Sequence Orthology more info
located_in early endosome	ISO Inferred from Sequence Orthology more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in external side of plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: RT1 class Ib, locus M3-1

Names: MHC class I antigen; MHC class I-b antigen M3; histocompatibility 2, M region locus 3

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_022921.2 → NP_075210.2 RT1 class Ib, locus M3-1 precursor

See identical proteins and their annotated locations for NP_075210.2

Status: VALIDATED

Source sequence(s)

BX883052

UniProtKB/TrEMBL

A6KR51, G3V627, Q62708

Related

ENSRNOP00000000990.4, ENSRNOT00000000990.7

Conserved Domains (2) summary

pfam00129
Location:25 → 203

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

cd07698
Location:207 → 298

IgC1_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain, alpha3 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

1329227..1333394 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_008772688.4 → XP_008770910.2 RT1 class Ib, locus M3-1 isoform X2

UniProtKB/TrEMBL

A6KR51, G3V627, Q62708

Related

ENSRNOP00000104526.1, ENSRNOT00000148018.1

Conserved Domains (2) summary

pfam00129
Location:25 → 203

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

cd07698
Location:207 → 298

IgC1_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains
XM_063278959.1 → XP_063135029.1 RT1 class Ib, locus M3-1 isoform X1

UniProtKB/TrEMBL

A0A8I5ZTS2

Related

ENSRNOP00000112747.1, ENSRNOT00000158710.1