RT1-B (RT1 class II, locus B) - Rat Genome Database

Name: RT1-B
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: RT1-B (RT1 class II, locus B) Rattus norvegicus

Analyze

No known orthologs.

Symbol:

RT1-B

Name:

RT1 class II, locus B

RGD ID:

3467

Description:

Predicted to enable MHC class II protein complex binding activity. Predicted to be involved in 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 integral component of membrane. Predicted to be part of MHC class II protein complex. Human ortholog(s) of this gene implicated in several diseases, including allergic disease (multiple); autoimmune disease (multiple); bacterial infectious disease (multiple); hematologic cancer (multiple); and liver disease (multiple). Orthologous to human HLA-DQB1 (major histocompatibility complex, class II, DQ beta 1).

Type:

protein-coding

Previously known as:

rano class II histocompatibility antigen, A beta chain; RT1 class II histocompatibility antigen, A beta chain; RT1 region, class II (B); RT1 region, class II, locus B

RGD Orthologs

Alliance Genes

More Info

homologs ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Other homologs ²				less info ...
Homo sapiens (human):	HLA-DQB1 (major histocompatibility complex, class II, DQ beta 1)	HGNC	Panther
Homo sapiens (human):	HLA-DQB2 (major histocompatibility complex, class II, DQ beta 2)	HGNC	Panther
Alliance orthologs ³
Homo sapiens (human):	HLA-DQB1 (major histocompatibility complex, class II, DQ beta 1)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	H2-Ab1 (histocompatibility 2, class II antigen A, beta 1)	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	si:busm1-228j01.6	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	mhc2dbb (major histocompatibility complex class II DBB gene)	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	si:zfos-2070c2.3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	si:busm1-104n07.3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	mhc2dab (major histocompatibility complex class II DAB gene)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	si:ch73-158p21.3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	mhc2dgb	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

NCBI Annotation Information:

Genome Annotation Status: not in current annotation release

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Cytogenetic Map	20		NCBI

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

allergic asthma (ISO)

asthma (ISO)

occupational asthma (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adaptive immune response (IEA)

antigen processing and presentation of exogenous peptide antigen via MHC class II (IBA)

peptide antigen assembly with MHC class II protein complex (IBA)

positive regulation of T cell activation (IBA)

Cellular Component

integral component of membrane (IEA)

MHC class II protein complex (IBA)

Molecular Function

MHC class II protein complex binding (IBA)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Genome-wide association study identifies HLA-DP as a susceptibility gene for pediatric asthma in Asian populations.	Noguchi E, etal., PLoS Genet. 2011 Jul;7(7):e1002170. doi: 10.1371/journal.pgen.1002170. Epub 2011 Jul 21.
3.	GOA pipeline	RGD automated data pipeline
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
5.	Allergic and Nonallergic Asthma Have Distinct Phenotypic and Genotypic Features.	Takejima P, etal., Int Arch Allergy Immunol. 2017;172(3):150-160. doi: 10.1159/000458151. Epub 2017 Apr 6.
6.	Genetic variants in the major histocompatibility complex class I and class II genes are associated with diisocyanate-induced Asthma.	Yucesoy B, etal., J Occup Environ Med. 2014 Apr;56(4):382-7. doi: 10.1097/JOM.0000000000000138.

Additional References at PubMed

PMID:3865896	PMID:19740318	PMID:20356827	PMID:25672758

Genomics

Position Markers

D20Rhw1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	157,756 - 157,908 (+)	MAPPER	mRatBN7.2
Rnor_6.0	20	303,758 - 303,909	NCBI	Rnor6.0
Rnor_5.0	20	297,840 - 297,991	UniSTS	Rnor5.0
RGSC_v3.4	20	74,938 - 75,089	UniSTS	RGSC3.4
Celera	20	1,029,929 - 1,030,080	UniSTS
Cytogenetic Map	20	p12	UniSTS

Expression

Sequence

Nucleotide Sequences


GenBank Nucleotide	AH003181	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Protein Sequences


GenBank Protein	AAA74477	(Get FASTA)	NCBI Sequence Viewer
	P06341	(Get FASTA)	NCBI Sequence Viewer

Protein Domains

Ig-like C1-type

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P06341-F1-model_v2	AlphaFold	P06341	1-233	view protein structure

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3467	AgrOrtholog
Gene3D-CATH	2.60.40.10	UniProtKB/Swiss-Prot
	3.10.320.10	UniProtKB/Swiss-Prot
InterPro	Ig-like_dom	UniProtKB/Swiss-Prot
	Ig-like_dom_sf	UniProtKB/Swiss-Prot
	Ig-like_fold	UniProtKB/Swiss-Prot
	Ig/MHC_CS	UniProtKB/Swiss-Prot
	Ig_C1-set	UniProtKB/Swiss-Prot
	MHC_I/II-like_Ag-recog	UniProtKB/Swiss-Prot
	MHC_II_a/b_N	UniProtKB/Swiss-Prot
	MHC_II_b_N	UniProtKB/Swiss-Prot
NCBI Gene	24738	ENTREZGENE
Pfam	C1-set	UniProtKB/Swiss-Prot
	MHC_II_beta	UniProtKB/Swiss-Prot
PhenoGen	RT1-B	PhenoGen
PROSITE	IG_LIKE	UniProtKB/Swiss-Prot
	IG_MHC	UniProtKB/Swiss-Prot
SMART	IGc1	UniProtKB/Swiss-Prot
	MHC_II_beta	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF48726	UniProtKB/Swiss-Prot
	SSF54452	UniProtKB/Swiss-Prot
UniProt	HB2A_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2009-09-15	RT1-B	RT1 class II, locus B	RT1-B	RT1 region, class II (B)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-02-11	RT1-2.5	RT1 region, class II (B)	RT1-B	RT1 region, class II, locus B	Name updated	625702	APPROVED
2002-06-10	RT1-B	RT1 region, class II, locus B			Symbol and Name status set to approved	70586	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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