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

Summary

Symbol: RT1-Haprovided by RGD
Full Name: RT1 class II, locus Haprovided by RGD
Primary source: RGD:1595921
See related: EnsemblRapid:ENSRNOG00000045908 AllianceGenome:RGD:1595921
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: RT1.Ha
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 type II interferon production. Predicted to be located in cell surface and intracellular membrane-bounded organelle. 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 Crohn's disease; asthma (multiple); hepatitis B; liver disease (multiple); and onchocerciasis. Orthologous to human HLA-DPA1 (major histocompatibility complex, class II, DP alpha 1). [provided by Alliance of Genome Resources, Jan 2025]
Expression: Biased expression in Thymus (RPKM 69.3), Spleen (RPKM 49.1) and 1 other tissue See more
Orthologs: human all
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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 (4762425..4772439, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (4760631..4770662, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (3875478..3885140)

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 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	ISO Inferred from Sequence Orthology 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 antigen processing and presentation of exogenous peptide antigen via MHC class II	ISO Inferred from Sequence Orthology more info
involved_in cellular response to type II interferon	ISO Inferred from Sequence Orthology 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 T cell activation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of T cell proliferation	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 positive regulation of type II interferon production	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	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

General protein information

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Preferred Names: RT1 class II, locus Ha

Names: HLA class II histocompatibility antigen, DP alpha 1 chain-like; RLA class II histocompatibility antigen, DP alpha-1 chain-like; major histocompatibility complex class II H-alpha

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_001008848.2 → NP_001008848.1 RT1 class II, locus Ha precursor

See identical proteins and their annotated locations for NP_001008848.1

Status: VALIDATED

Source sequence(s)

BX883042

UniProtKB/TrEMBL

F7FN89, Q31287, Q6MGB1

Conserved Domains (3) summary

cd05767
Location:111 → 204

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

pfam00993
Location:30 → 107

MHC_II_alpha; Class II histocompatibility antigen, alpha domain

pfam16196
Location:202 → 253

C1-set_C; C1-set C-terminal 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

4762425..4772439 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255916.5 → XP_006255978.2 RT1 class II, locus Ha isoform X1

See identical proteins and their annotated locations for XP_006255978.2

UniProtKB/TrEMBL

Q31287

Related

ENSRNOP00000033818.5, ENSRNOT00000036900.6

Conserved Domains (3) summary

cd05767
Location:153 → 246

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

pfam00993
Location:72 → 149

MHC_II_alpha; Class II histocompatibility antigen, alpha domain

pfam16196
Location:244 → 295

C1-set_C; C1-set C-terminal domain