RT1-Db2 RT1 class II, locus Db2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: RT1-Db2provided by RGD
Official Full Name: RT1 class II, locus Db2provided by RGD
Primary source: RGD:1595922
See related: EnsemblRapid:ENSRNOG00000030431 AllianceGenome:RGD:1595922
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
Also known as: Db2
Summary: Predicted to enable MHC class II protein complex binding activity and peptide antigen binding activity. Predicted to be involved in several processes, including antigen processing and presentation of exogenous peptide antigen via MHC class II; peptide antigen assembly with MHC class II protein complex; and positive regulation of T cell activation. 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); HLA-DRB3 (major histocompatibility complex, class II, DR beta 3); and HLA-DRB4 (major histocompatibility complex, class II, DR beta 4). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 144.4), Thymus (RPKM 73.4) and 7 other tissues See more
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Genomic context

Location:: 20p12

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (4521929..4541654, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4520723..4539724, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (4106136..4126103)

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
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?

our findings suggest that the H2-E2 or RT1-D2 molecules could function as Ag-presenting molecules for a particular class of Ags, as modulators of Ag presentation like nonclassical nonpolymorphic class II molecules
Title: The Forgotten: Identification and Functional Characterization of MHC Class II Molecules H2-Eb2 and RT1-Db2.

Submit: New GeneRIF Correction

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

Process	Evidence Code	Pubs
involved_in adaptive immune response	IEA Inferred from Electronic Annotation 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 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 immune response	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of MHC class II protein complex	IBA Inferred from Biological aspect of Ancestor 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

General protein information

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Preferred Names: RT1 class II, locus Db2

Names: MHC class II beta 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_001164826.1 → NP_001158298.1 RT1 class II, locus Db2 precursor

Status: PROVISIONAL

Source sequence(s)

BX883043

UniProtKB/TrEMBL

A0A023IKG1

Conserved Domains (2) summary

pfam00969
Location:42 → 115

MHC_II_beta; Class II histocompatibility antigen, beta domain

cl11960
Location:125 → 218

Ig; Immunoglobulin domain

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

4521929..4541654 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255911.5 → XP_006255973.2 RT1 class II, locus Db2 isoform X1

UniProtKB/TrEMBL

A0A023IKG1, A0A023IKK2, A0A0G2JZX8, D3ZT06

Related

ENSRNOP00000071225.2, ENSRNOT00000083085.4

Conserved Domains (2) summary

pfam00969
Location:42 → 115

MHC_II_beta; Class II histocompatibility antigen, beta domain

cl11960
Location:125 → 218

Ig; Immunoglobulin domain
XM_039098428.2 → XP_038954356.1 RT1 class II, locus Db2 isoform X2

Conserved Domains (2) summary

cd00096
Location:29 → 37

Ig; Ig strand A [structural motif]

cl11960
Location:27 → 122

Ig; Immunoglobulin domain