RT1-M6-2 RT1 class I, locus M6, gene 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: RT1-M6-2provided by RGD
Official Full Name: RT1 class I, locus M6, gene 2provided by RGD
Primary source: RGD:1595815
See related: EnsemblRapid:ENSRNOG00000040052 AllianceGenome:RGD:1595815
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable peptide antigen binding activity and signaling receptor binding activity. Predicted to be involved in several processes, including antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent; antigen processing and presentation of endogenous peptide antigen via MHC class Ib; and positive regulation of T cell mediated cytotoxicity. Predicted to be located in lumenal side of endoplasmic reticulum membrane and phagocytic vesicle membrane. Predicted to be part of MHC class I 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 human 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, Dec 2024]
Expression: Biased expression in Spleen (RPKM 129.2), Lung (RPKM 124.0) 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 (1588501..1592333)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (1583267..1587099)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (2075796..2079183)

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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables peptide antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables signaling receptor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
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
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of MHC class I protein complex	IEA Inferred from Electronic Annotation more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor 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

General protein information

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Preferred Names: RT1 class I, locus M6, gene 2

Names: MHC class Ib antigen

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_001008853.1 → NP_001008853.1 RT1 class I, locus M6, gene 2 precursor

See identical proteins and their annotated locations for NP_001008853.1

Status: PROVISIONAL

Source sequence(s)

BX883052

UniProtKB/TrEMBL

A8U3J6, Q6MFY3

Related

ENSRNOP00000107851.1, ENSRNOT00000041500.5

Conserved Domains (3) summary

cd07698
Location:191 → 284

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

cd12087
Location:288 → 319

TM_EGFR-like; Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases

cl08246
Location:29 → 187

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

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

1588501..1592333

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017601696.2 → XP_017457185.2 RT1 class I, locus M6, gene 2 isoform X2

UniProtKB/TrEMBL

Q0GC73, Q0PKT3, Q6JV21

Conserved Domains (3) summary

cd00096
Location:213 → 222

Ig; Ig strand A [structural motif]

cl08246
Location:29 → 208

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

cl11960
Location:209 → 307

Ig; Immunoglobulin domain
XM_063279325.1 → XP_063135395.1 RT1 class I, locus M6, gene 2 isoform X1