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

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Symbol:

RT1-DOb

Name:

RT1 class II, locus DOb

RGD ID:

1595814

Description:

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; negative regulation of antigen processing and presentation of peptide antigen via MHC class II; and peptide antigen assembly with MHC class II protein complex. Predicted to be located in lysosome. Predicted to be part of MHC class II protein complex. Predicted to be active in late endosome membrane and lysosomal membrane. Orthologous to human HLA-DOB (major histocompatibility complex, class II, DO beta); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; asthma pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

DOb; H2-Ob; histocompatibility 2, O region beta locus; RT1 class II, DO beta; RT1 class II, locus DOb (mapped); RT1-Bb2; RT1-DOb_mapped

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	HLA-DOB (major histocompatibility complex, class II, DO beta)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	H2-Ob (histocompatibility 2, O region beta locus)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LOC100970847 (HLA class II histocompatibility antigen, DO beta chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	DLA-DOB (major histocompatibility complex, class II, DO beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	LOC101961309 (HLA class II histocompatibility antigen, DO beta chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SLA-DOB (MHC class II, DO beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	MHC-DOB (major histocompatibility complex, class II, DO beta)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	LOC101702636 (HLA class II histocompatibility antigen, DO beta chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	PRIMPOL (primase and DNA directed polymerase)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	HLA-DOB (major histocompatibility complex, class II, DO beta)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	H2-Ob (histocompatibility 2, O region beta locus)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	si:busm1-228j01.6	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	si:busm1-228j01.6	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoInspector\|SonicParanoid)
Danio rerio (zebrafish):	si:dkey-33b17.3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	mhc2dcb (major histocompatibility complex class II DCB gene)	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoInspector\|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):	mhc2dbb (major histocompatibility complex class II DBB gene)	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoInspector\|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):	mhc2dab (major histocompatibility complex class II DAB gene)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	si:ch73-158p21.3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	mhc2dhb	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)
Danio rerio (zebrafish):	mhc2dgb	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoInspector\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	mhc2-dab (provisional)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	mhc2-dcb	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	20	4,621,336 - 4,627,537 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	20	4,619,694 - 4,627,523 (-)	Ensembl				GRCr8
mRatBN7.2	20	4,619,418 - 4,625,627 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	4,619,816 - 4,625,667 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	20	5,372,193 - 5,377,744 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	20	4,733,934 - 4,739,485 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	20	5,217,240 - 5,222,903 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	20	4,020,273 - 4,026,398 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	4,020,317 - 4,026,346 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	20	6,099,866 - 6,105,845 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	20	4,753,940 - 4,759,648 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	20	6,221,090 - 6,226,692 (-)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (EXP)

17beta-estradiol 3-benzoate (EXP)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2,4,4'-trichlorobiphenyl (ISO)

2-butoxyethanol (ISO)

4,4'-diaminodiphenylmethane (ISO)

acrylamide (EXP)

alpha-Zearalanol (EXP)

ammonium chloride (EXP)

amphetamine (EXP)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

atrazine (EXP)

benzalkonium chloride (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

Benzo[ghi]perylene (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

buta-1,3-diene (ISO)

C60 fullerene (EXP)

cadmium dichloride (EXP)

carbon nanotube (ISO)

chloroprene (ISO)

chrysene (ISO)

dextran sulfate (ISO)

dimethylarsinic acid (ISO)

dioxygen (ISO)

folic acid (ISO)

furan (EXP)

hydralazine (ISO)

hydrazine (ISO)

meropenem (ISO)

methotrexate (ISO)

methylarsonic acid (ISO)

mifepristone (ISO)

nickel atom (ISO)

nitrates (ISO)

okadaic acid (ISO)

ozone (ISO)

PCB138 (ISO)

poly(I:C) (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

testosterone (EXP)

tetraphene (ISO)

thioacetamide (EXP)

trimethoprim (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adaptive immune response (IEA)

antigen processing and presentation (IEA)

antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (IEA)

immune response (IEA)

immune system process (IEA)

negative regulation of antigen processing and presentation of peptide antigen via MHC class II (ISO)

Cellular Component

lysosome (ISO)

membrane (IEA)

MHC class II protein complex (IEA,ISO)

Molecular Function

MHC class II protein complex binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

allograft rejection pathway (IEA)

antigen processing and presentation pathway (IEA)

asthma pathway (IEA)

autoimmune thyroiditis pathway (IEA)

graft-versus-host disease pathway (IEA)

influenza A pathway (IEA)

Leishmaniasis pathway (IEA)

myocarditis pathway (IEA)

phagocytosis pathway (IEA)

rheumatoid arthritis pathway (IEA)

Staphylococcus aureus infection pathway (IEA)

systemic lupus erythematosus pathway (IEA)

toxoplasmosis pathway (IEA)

tuberculosis pathway (IEA)

type 1 diabetes mellitus pathway (IEA)

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.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
3.	GOA pipeline	RGD automated data pipeline
4.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:3865893	PMID:8890155	PMID:9492004	PMID:9601947	PMID:11685465	PMID:22733780	PMID:24586191

Genomics

Comparative Map Data

RT1-DOb
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	20	4,621,336 - 4,627,537 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	20	4,619,694 - 4,627,523 (-)	Ensembl				GRCr8
mRatBN7.2	20	4,619,418 - 4,625,627 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	4,619,816 - 4,625,667 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	20	5,372,193 - 5,377,744 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	20	4,733,934 - 4,739,485 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	20	5,217,240 - 5,222,903 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	20	4,020,273 - 4,026,398 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	4,020,317 - 4,026,346 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	20	6,099,866 - 6,105,845 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	20	4,753,940 - 4,759,648 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	20	6,221,090 - 6,226,692 (-)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

HLA-DOB
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	32,812,763 - 32,817,002 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	32,812,763 - 32,820,466 (-)	Ensembl			hg38	GRCh38
GRCh37	6	32,780,540 - 32,784,779 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	32,888,518 - 32,892,803 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	6	32,888,526 - 32,892,760	NCBI
Celera	6	34,329,595 - 34,333,880 (-)	NCBI		Celera
Cytogenetic Map	6	p21.32	NCBI
HuRef	6	32,522,917 - 32,527,179 (-)	NCBI		HuRef
CHM1_1	6	32,781,544 - 32,785,829 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	32,634,117 - 32,638,355 (-)	NCBI		T2T-CHM13v2.0

H2-Ob
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	34,457,879 - 34,464,882 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	34,457,877 - 34,473,388 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	17	34,238,905 - 34,245,908 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	34,238,903 - 34,254,414 (+)	Ensembl			mm10	GRCm38
MGSCv37	17	34,375,850 - 34,382,853 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	17	33,850,628 - 33,854,100 (+)	NCBI		MGSCv36	mm8
Celera	17	36,980,110 - 36,996,885 (+)	NCBI		Celera
Cytogenetic Map	17	B1	NCBI
cM Map	17	17.98	NCBI

LOC100970847
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	5	47,287,076 - 47,299,056 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	43,158,633 - 43,171,752 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	32,381,463 - 32,387,377 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	33,497,199 - 33,501,542 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	33,497,652 - 33,501,451 (-)	Ensembl			panPan2	panpan1.1

DLA-DOB
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	12	2,376,957 - 2,384,179 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	2,378,126 - 2,432,303 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	2,459,974 - 2,465,584 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	12	2,652,367 - 2,659,185 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	12	2,652,372 - 2,699,034 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	12	2,377,490 - 2,383,108 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	12	2,458,767 - 2,464,390 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	12	2,533,116 - 2,538,741 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

LOC101961309
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404946	38,022,484 - 38,035,492 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936476	25,932,968 - 25,936,593 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936476	25,932,926 - 25,937,024 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLA-DOB
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	25,030,438 - 25,037,962 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	7	25,030,435 - 25,038,196 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	29,242,473 - 29,249,542 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3
Pig Cytomap	7	q1.1	NCBI

MHC-DOB
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	17	39,295,768 - 39,300,032 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	39,295,828 - 39,300,819 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666044	32,593,845 - 32,598,586 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

LOC101702636
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624754	23,839,985 - 23,851,756 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624754	23,846,677 - 23,853,674 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Variants

Variants in RT1-DOb
217 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	40
Count of miRNA genes:	37
Interacting mature miRNAs:	39
Transcripts:	ENSRNOT00000000526
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
4889610	Pancm3	Pancreatic morphology QTL 3	3.75	0.001	pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	20	4189476	49189476	Rat
2306850	Pia40	Pristane induced arthritis QTL 40		0.0001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	1533200	5306452	Rat
1354642	Despr15	Despair related QTL 15		0.0027	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	20	1	24164241	Rat
70154	Insul2	Insulin level QTL 2	3.75		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	1	6693431	Rat
4889857	Pur27	Proteinuria QTL 27	12.2	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	20	1	27341128	Rat
9590109	Sffal8	Serum free fatty acids level QTL 8	5.32	0.01	blood free fatty acid amount (VT:0001553)	plasma free fatty acids level (CMO:0000546)	20	1	29193376	Rat
9590275	Scort15	Serum corticosterone level QTL 15	3.48	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	29193376	Rat
7175099	Tcs2	T cell selection QTL 2			T cell selection trait (VT:0004917)	expression	20	4505932	4695009	Rat
6893685	Bw111	Body weight QTL 111	2.7	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	20	1	32578510	Rat
61474	Eae1	Experimental allergic encephalomyelitis QTL 1	3		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	20	1	6693431	Rat
2317057	Aia27	Adjuvant induced arthritis QTL 27	2.83		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	20	1	26925056	Rat
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	1	33724594	Rat
7387283	Uae44	Urinary albumin excretion QTL 44		0.1712	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	20	1	26128279	Rat
7411668	Foco32	Food consumption QTL 32	8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	36600300	Rat
2305926	Iddm37	Insulin dependent diabetes mellitus QTL 37	6		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	20	1533083	46533083	Rat
1558640	Prcs2	Prostate cancer susceptibility QTL 2	3.3		prostate integrity trait (VT:0010571)	percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)	20	1	34066551	Rat
1331772	Cdexp2	CD45RC expression in CD8 T cells QTL 2	5.7		CD8-positive T cell quantity (VT:0008077)	blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)	20	3626323	10078622	Rat
8694189	Bw153	Body weight QTL 153	3.13	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	20	1	29193376	Rat
1300152	Bp195	Blood pressure QTL 195	3.46		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	20	3626323	9244918	Rat
9589155	Insul32	Insulin level QTL 32	6.38	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	1	29193376	Rat
7411650	Foco23	Food consumption QTL 23	20.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	29193376	Rat
61432	Cia1	Collagen induced arthritis QTL 1			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	1	14100378	Rat
2317851	Alcrsp22	Alcohol response QTL 22	3.2	0.05	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	27341128	Rat
1641893	Alcrsp7	Alcohol response QTL 7			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	27341128	Rat
9590252	Scort12	Serum corticosterone level QTL 12	20.46	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	36600300	Rat

Markers in Region

D20Yum75

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	4,626,203 - 4,626,386 (-)	MAPPER	mRatBN7.2
Rnor_6.0	20	4,019,542 - 4,019,724	NCBI	Rnor6.0
Rnor_5.0	20	6,099,088 - 6,099,270	UniSTS	Rnor5.0
RGSC_v3.4	20	4,760,309 - 4,760,491	UniSTS	RGSC3.4
Celera	20	6,227,353 - 6,227,535	UniSTS
Cytogenetic Map	20	p12	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	11	44	149	81	80	49	92	49	6	306	168	11	120	65	85	31	12	12

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001008846	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_001412194	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005497296	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005497297	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB008110	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC098547	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BX883043	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473988	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000020	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222912	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222913	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222914	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222915	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222916	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222928	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222929	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222930	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222931	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M15561	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000000526 ⟹ ENSRNOP00000000526

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	4,619,939 - 4,625,667 (-)	Ensembl
Rnor_6.0 Ensembl	20	4,020,317 - 4,026,346 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000085724

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	20	4,621,136 - 4,627,523 (-)	Ensembl
mRatBN7.2 Ensembl	20	4,619,816 - 4,625,667 (-)	Ensembl
Rnor_6.0 Ensembl	20	4,023,992 - 4,026,183 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000092127

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	4,020,380 - 4,022,945 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000105085 ⟹ ENSRNOP00000082639

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	4,619,816 - 4,625,603 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000164587 ⟹ ENSRNOP00000098902

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	20	4,619,694 - 4,627,523 (-)	Ensembl

RefSeq Acc Id:

NM_001008846 ⟹ NP_001008846

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	4,621,336 - 4,627,523 (-)	NCBI
mRatBN7.2	20	4,619,418 - 4,625,607 (-)	NCBI
Rnor_6.0	20	4,020,385 - 4,025,987 (+)	NCBI
Rnor_5.0	20	6,099,866 - 6,105,845 (+)	NCBI
RGSC_v3.4	20	4,753,940 - 4,759,648 (-)	RGD
Celera	20	6,221,090 - 6,226,692 (-)	RGD

Sequence:

show sequence

ATGGGTGCTGGGAGGGCCCCCTGGGTGGTGGCTCTGCTAGTGAACCTCATGAGGCCAGATTCCT
TCATGGTTGAAGGCAGAGACTCCCCAGAGGATTTTGTGATTCAGGCGAAGGCAGAGTGTTACTT
CACCAACGGTACAGAAAAGGTCCGCTTCCTGGTCAGGTTCATCTTCAACCTGGAGGAGTACTTA
CATTTCGACAGTGACCTGGGGTTTTTCGTGGCACTGACGGAGCTGGGGGAGGTGGACGCTGATC
AGTGGAACAAACGCCTGGATCTCCTGGAAACAAGTAGAGCTGCTGTGAACATGGTCTGCAGGCA
AGAGTACAAGCTGGGGGCCCCCTTCACCGTGGAGAGAAATGTGCCTCCGGAGGTGACGGTGTAC
CCAGAGAGGACCCCATTGCTGCAGCAGCACAACCTGTTGCTCTGCTCTGTGACAGACTTCTACC
CTGGGGACATAAGTGTCAGGTGGTTCCGGAATGGGCAGGAGGAGAGGTCCGGGGTCATGTCCAC
TGGCCTTGTTAGGAATGGAGACTGGACCTTCCAGACGACGGTAATGCTGGAAATGATCCCAGAG
CTTGGAGACGTCTACAGTTGCCTTGTGGAGCACCCCGGCCTCCTGAGACCTGTTTCTGTGGCAT
GGGTGGCTCAGTCTGAATATTCCTGGGAAAAGATACTGAGTGGAGCTGCAGCATTCCTGCTTGG
GCTGACTGTCTTTCTGGTGGGAGCTGTCATCCACCTCAAGGCTCAGAAAGCGTCCGTGGAGACT
CAGCCTGGCAATGAGGCTTCAAGGGCGCTTCTCCCACCTCACCCCTACTAA

hide sequence

RefSeq Acc Id:

NM_001412194 ⟹ NP_001399123

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	4,621,336 - 4,627,523 (-)	NCBI
mRatBN7.2	20	4,619,418 - 4,625,607 (-)	NCBI

RefSeq Acc Id:

XR_005497296

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	4,621,795 - 4,627,536 (-)	NCBI
mRatBN7.2	20	4,619,599 - 4,625,626 (-)	NCBI

RefSeq Acc Id:

XR_005497297

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	4,621,788 - 4,627,537 (-)	NCBI
mRatBN7.2	20	4,619,599 - 4,625,627 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001008846	(Get FASTA)	NCBI Sequence Viewer
	NP_001399123	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA68203	(Get FASTA)	NCBI Sequence Viewer
	AGV39009	(Get FASTA)	NCBI Sequence Viewer
	AGV39010	(Get FASTA)	NCBI Sequence Viewer
	AGV39011	(Get FASTA)	NCBI Sequence Viewer
	AGV39012	(Get FASTA)	NCBI Sequence Viewer
	AGV39013	(Get FASTA)	NCBI Sequence Viewer
	AGV39025	(Get FASTA)	NCBI Sequence Viewer
	AGV39026	(Get FASTA)	NCBI Sequence Viewer
	AGV39027	(Get FASTA)	NCBI Sequence Viewer
	AGV39028	(Get FASTA)	NCBI Sequence Viewer
	BAA31863	(Get FASTA)	NCBI Sequence Viewer
	CAE83944	(Get FASTA)	NCBI Sequence Viewer
	EDL96804	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000082841
	ENSRNOP00000082841.2
	ENSRNOP00000098902.1

RefSeq Acc Id:	NP_001008846 ⟸ NM_001008846
- Peptide Label:	isoform 1
- UniProtKB:	Q6MGA2 (UniProtKB/TrEMBL), A6JJD8 (UniProtKB/TrEMBL), A0A023IM52 (UniProtKB/TrEMBL), A0A023ILQ6 (UniProtKB/TrEMBL)
- Sequence:	show sequence MGAGRAPWVVALLVNLMRPDSFMVEGRDSPEDFVIQAKAECYFTNGTEKVRFLVRFIFNLEEYL HFDSDLGFFVALTELGEVDADQWNKRLDLLETSRAAVNMVCRQEYKLGAPFTVERNVPPEVTVY PERTPLLQQHNLLLCSVTDFYPGDISVRWFRNGQEERSGVMSTGLVRNGDWTFQTTVMLEMIPE LGDVYSCLVEHPGLLRPVSVAWVAQSEYSWEKILSGAAAFLLGLTVFLVGAVIHLKAQKASVET QPGNEASRALLPPHPY hide sequence

Ensembl Acc Id:

ENSRNOP00000000526 ⟸ ENSRNOT00000000526

Ensembl Acc Id:

ENSRNOP00000082639 ⟸ ENSRNOT00000105085

RefSeq Acc Id:	NP_001399123 ⟸ NM_001412194
- Peptide Label:	isoform 2
- UniProtKB:	A0A023IM57 (UniProtKB/TrEMBL), A0A023ILR5 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSRNOP00000098902 ⟸ ENSRNOT00000164587

Protein Domains

Ig-like

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q6MGA2-F1-model_v2	AlphaFold	Q6MGA2	1-272	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13701327

Promoter ID:

EPDNEW_R11850

Type:

multiple initiation site

Name:

RT1-DOb_1

Description:

RT1 class II, locus DOb

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	20	4,020,321 - 4,020,381	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1595814	AgrOrtholog
BioCyc Gene	G2FUF-4556	BioCyc
Ensembl Genes	ENSRNOG00000000454	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000085724	ENTREZGENE
	ENSRNOT00000085724.4	UniProtKB/TrEMBL
	ENSRNOT00000164587.1	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.10	UniProtKB/TrEMBL
	Class II Histocompatibility Antigen, M Beta Chain, Chain B, domain 1	UniProtKB/TrEMBL
InterPro	Ig-like	UniProtKB/TrEMBL
	Ig-like_dom_sf	UniProtKB/TrEMBL
	Ig-like_fold	UniProtKB/TrEMBL
	Ig/MHC_CS	UniProtKB/TrEMBL
	Ig_C1-set	UniProtKB/TrEMBL
	MHC/Immunoglobulin	UniProtKB/TrEMBL
	MHC_I/II-like_Ag-recog	UniProtKB/TrEMBL
	MHC_II_a/b_N	UniProtKB/TrEMBL
	MHC_II_b_N	UniProtKB/TrEMBL
KEGG Report	rno:365542	UniProtKB/TrEMBL
NCBI Gene	365542	ENTREZGENE
PANTHER	HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DO BETA CHAIN	UniProtKB/TrEMBL
	MHC CLASS II-RELATED	UniProtKB/TrEMBL
Pfam	C1-set	UniProtKB/TrEMBL
	MHC_II_beta	UniProtKB/TrEMBL
PhenoGen	RT1-DOb	PhenoGen
PROSITE	IG_LIKE	UniProtKB/TrEMBL
	IG_MHC	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000000454	RatGTEx
SMART	IGc1	UniProtKB/TrEMBL
	MHC_II_beta	UniProtKB/TrEMBL
Superfamily-SCOP	MHC_I/II-like_Ag-recog	UniProtKB/TrEMBL
	SSF48726	UniProtKB/TrEMBL
UniProt	A0A023ILQ6	ENTREZGENE, UniProtKB/TrEMBL
	A0A023ILR5	ENTREZGENE, UniProtKB/TrEMBL
	A0A023IM52	ENTREZGENE, UniProtKB/TrEMBL
	A0A023IM57	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I5ZVP9_RAT	UniProtKB/TrEMBL
	A0ABK0L4M8_RAT	UniProtKB/TrEMBL
	A6JJD8	ENTREZGENE
	O88189_RAT	UniProtKB/TrEMBL
	Q6MGA2	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	A6JJD8	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2009-09-14	RT1-DOb	RT1 class II, locus DOb	H2-Ob	histocompatibility 2, O region beta locus	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-07	H2-Ob	histocompatibility 2, O region beta locus	RT1-DOb	RT1 class II, locus DOb	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2007-04-12	RT1-DOb	RT1 class II, locus DOb	RT1-DOb_mapped	RT1 class II, locus DOb (mapped)	Data merged from RGD:3478	737654	APPROVED
2006-11-20	RT1-DOb	RT1 class II, locus DOb			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-20	RT1-DOb_mapped	RT1 class II, locus DOb(mapped)	RT1-DOb	RT1 class II, locus DOb	Symbol set to symbol_mapped, name set to name (mapped)	1582166	APPROVED
2004-02-11	RT1-DOb	RT1 class II, locus DOb			Symbol and Name status set to approved	625702	APPROVED
2002-06-10	RT1-DOb	RT1 class II, locus DOb			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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Imported Annotations - KEGG (archival)