RT1-DMb (RT1 class II, locus DMb)

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

Analyze

Symbol:

RT1-DMb

Name:

RT1 class II, locus DMb

RGD ID:

735096

Description:

Predicted to enable MHC class II protein complex binding activity. Predicted to be involved in peptide antigen assembly with MHC class II protein complex; positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell; and positive regulation of T cell proliferation. Predicted to act upstream of or within antigen processing and presentation of exogenous peptide antigen via MHC class II and chaperone cofactor-dependent protein refolding. Predicted to be located in late endosome membrane; lysosomal membrane; and multivesicular body. Predicted to be part of MHC class II protein complex. Orthologous to human HLA-DMB (major histocompatibility complex, class II, DM beta); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; asthma pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 3,3',5,5'-tetrabromobisphenol A.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

class II histocompatibility antigen, M beta 1 chain; DMb; Hla-dmb; LOC108348139; major histocompatibility complex, class II, DM beta; MHC class II-like beta chain; RT1 class II, DM beta; RT1.DMb; RT1.Mb

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Is Marker For:

Strains: DA.AS2-(Tesb-RT1-DMb) DA.KHW-(RT1-Db1-RT1-DMb) DA.E3-(Btnl2-RT1-DMb)
QTLs: Tcs2

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	4,693,102 - 4,700,340 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	4,693,103 - 4,700,340 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	20	5,445,432 - 5,452,711 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	20	4,807,175 - 4,814,454 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	20	5,288,598 - 5,295,865 (-)	NCBI	Rnor_WKY
Rnor_6.0	20	3,945,383 - 3,952,838 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	3,945,601 - 3,952,846 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0 Ensembl	20	5,227,045 - 5,234,290 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	20	7,288,114 - 7,295,355 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	4,829,535 - 4,836,772 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	20	4,829,762 - 4,836,902 (-)	NCBI
Celera	20	6,293,763 - 6,301,000 (-)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Behcet's disease (ISO)

Experimental Liver Cirrhosis (EXP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (EXP,ISO)

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

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

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

3,3',5,5'-tetrabromobisphenol A (EXP)

3-methylcholanthrene (ISO)

3H-1,2-dithiole-3-thione (EXP)

4,4'-diaminodiphenylmethane (EXP)

4-hydroxyphenyl retinamide (ISO)

acrylamide (ISO)

albendazole (ISO)

ampicillin (EXP)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

belinostat (ISO)

benzene (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

Benzo[ghi]perylene (ISO)

Benzo[k]fluoranthene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

bortezomib (ISO)

buspirone (EXP)

cadmium dichloride (EXP)

calcitriol (ISO)

carbon nanotube (ISO)

cisplatin (ISO)

clofibrate (ISO)

cobalt atom (ISO)

cobalt dichloride (ISO)

dexamethasone (ISO)

dichloromethane (EXP)

diethyl malate (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

entinostat (ISO)

epoxiconazole (ISO)

ethosuximide (ISO)

ethyl methanesulfonate (ISO)

ethylbenzene (EXP)

famotidine (ISO)

fenthion (ISO)

flutamide (EXP)

formaldehyde (ISO)

gentamycin (EXP)

glafenine (EXP)

hexachlorobenzene (EXP)

lead diacetate (ISO)

lead(0) (ISO)

lead(2+) (ISO)

levobunolol (ISO)

lidocaine (EXP)

mercury dibromide (ISO)

methyl methanesulfonate (ISO)

metronidazole (EXP)

N,N-diethyl-m-toluamide (EXP)

N-nitrosodiethylamine (ISO)

N-nitrosodimethylamine (EXP)

naproxen (ISO)

neomycin (EXP)

nickel atom (ISO)

nimesulide (EXP)

nitrofen (EXP)

ozone (ISO)

panobinostat (ISO)

paracetamol (EXP,ISO)

PCB138 (ISO)

perfluorooctane-1-sulfonic acid (EXP)

permethrin (EXP)

phenylmercury acetate (ISO)

phorbol 13-acetate 12-myristate (ISO)

piperacillin (ISO)

pirinixic acid (ISO)

piroxicam (ISO)

pregnenolone 16alpha-carbonitrile (EXP)

protein kinase inhibitor (ISO)

resveratrol (EXP)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium dichromate (ISO)

Soman (EXP)

streptozocin (EXP)

tamibarotene (ISO)

tamoxifen (ISO)

temozolomide (ISO)

tert-butyl hydroperoxide (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

topiramate (ISO)

trichloroethene (EXP)

Tungsten carbide (ISO)

valdecoxib (ISO)

valproic acid (EXP,ISO)

vancomycin (EXP,ISO)

vinclozolin (EXP)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adaptive immune response (IEA)

antigen processing and presentation (ISO)

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

chaperone cofactor-dependent protein refolding (ISO)

MHC class II protein complex assembly (ISO)

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

positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (ISO)

positive regulation of T cell proliferation (ISO)

Cellular Component

endosome membrane (ISO)

intracellular membrane-bounded organelle (ISO)

late endosome (ISO)

late endosome membrane (ISO)

lysosomal membrane (ISO)

lysosome (ISO)

membrane (ISO)

MHC class II protein complex (ISO)

multivesicular body (ISO)

Molecular Function

MHC class II protein complex binding (ISO)

protein 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.	The major histocompatibility complex of the rat (Rattus norvegicus).	Gunther E and Walter L, Immunogenetics 2001 Sep;53(7):520-42.
3.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
4.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
5.	GOA pipeline	RGD automated data pipeline
6.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
7.	HLA-DMA and HLA-DMB genotyping in patients with rheumatic diseases.	Yen JH, etal., Kaohsiung J Med Sci. 1999 May;15(5):263-7.

Additional References at PubMed

PMID:7584146	PMID:7590989	PMID:7606781	PMID:8139689	PMID:11027433	PMID:11148202	PMID:11854359	PMID:12477932	PMID:19691639	PMID:22247549	PMID:22733780	PMID:24586191

Genomics

Comparative Map Data

RT1-DMb
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	20	4,693,102 - 4,700,340 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	4,693,103 - 4,700,340 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	20	5,445,432 - 5,452,711 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	20	4,807,175 - 4,814,454 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	20	5,288,598 - 5,295,865 (-)	NCBI	Rnor_WKY
Rnor_6.0	20	3,945,383 - 3,952,838 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	3,945,601 - 3,952,846 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0 Ensembl	20	5,227,045 - 5,234,290 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	20	7,288,114 - 7,295,355 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	20	4,829,535 - 4,836,772 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	20	4,829,762 - 4,836,902 (-)	NCBI
Celera	20	6,293,763 - 6,301,000 (-)	NCBI		Celera
Cytogenetic Map	20	p12	NCBI

HLA-DMB
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	32,934,636 - 32,941,028 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	6	32,934,629 - 32,941,028 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	32,902,413 - 32,908,805 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	33,010,393 - 33,016,795 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	6	33,010,392 - 33,016,795	NCBI
Celera	6	34,451,309 - 34,457,750 (-)	NCBI		Celera
Cytogenetic Map	6	p21.32	NCBI
HuRef	6	32,644,839 - 32,651,376 (-)	NCBI		HuRef
CHM1_1	6	32,903,201 - 32,909,642 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	32,755,985 - 32,762,378 (-)	NCBI		T2T-CHM13v2.0

H2-DMb1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	34,372,165 - 34,379,203 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	34,372,046 - 34,379,204 (+)	Ensembl		GRCm39 Ensembl
GRCm38	17	34,153,191 - 34,160,229 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	34,153,072 - 34,160,230 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	34,290,136 - 34,297,174 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	17	33,755,892 - 33,762,211 (+)	NCBI		MGSCv36	mm8
Celera	17	35,203,417 - 35,204,017 (+)	NCBI		Celera
Cytogenetic Map	17	B1	NCBI
cM Map	17	17.98	NCBI

LOC102023521
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955437	1,541,491 - 1,551,159 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955437	1,544,906 - 1,551,412 (-)	NCBI	ChiLan1.0	ChiLan1.0

MHC-DMB
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	6	33,619,511 - 33,625,956 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	33,619,870 - 33,625,685 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	32,504,074 - 32,510,669 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3

LOC101959667
(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	38,108,261 - 38,113,614 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936476	25,846,630 - 25,851,409 (+)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936476	25,846,653 - 25,852,006 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLA-DMB
(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	25,119,139 - 25,128,236 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	25,119,278 - 25,125,089 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	29,485,890 - 29,491,702 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3
Pig Cytomap	7	q1.1	NCBI

MHC-DMB
(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	39,153,744 - 39,161,029 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	39,154,850 - 39,161,090 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666044	32,723,053 - 32,730,236 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

LOC101701356
(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	23,773,934 - 23,779,952 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624754	23,774,013 - 23,779,851 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in RT1-DMb
169 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	393
Count of miRNA genes:	143
Interacting mature miRNAs:	165
Transcripts:	ENSRNOT00000073474, ENSRNOT00000075342
Prediction methods:	Microtar, 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 (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
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	24159021	Rat
1600382	Edcs3	Endometrial carcinoma susceptibility QTL3	3.5	0.003	uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	20	1	25159026	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	27339237	Rat
1641893	Alcrsp7	Alcohol response QTL 7			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	20	1	27339237	Rat
8694189	Bw153	Body weight QTL 153	3.13	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	20	1	29191651	Rat
9590275	Scort15	Serum corticosterone level QTL 15	3.48	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	29191651	Rat
7411650	Foco23	Food consumption QTL 23	20.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	29191651	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	29191651	Rat
9589155	Insul32	Insulin level QTL 32	6.38	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	20	1	29191651	Rat
6893685	Bw111	Body weight QTL 111	2.7	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	20	1	32578807	Rat
7411668	Foco32	Food consumption QTL 32	8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	20	1	36600972	Rat
9590252	Scort12	Serum corticosterone level QTL 12	20.46	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	20	1	36600972	Rat
2305926	Iddm37	Insulin dependent diabetes mellitus QTL 37	6		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	20	1527842	46527842	Rat
2306850	Pia40	Pristane induced arthritis QTL 40		0.0001	joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	1527959	5304575	Rat
1641915	Colcr9	Colorectal carcinoma resistance QTL 9	2.97	0.0024	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	20	1530655	46530655	Rat
1598816	Memor12	Memory QTL 12	2.4		exploratory behavior trait (VT:0010471)	average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)	20	2606836	47606836	Rat
2317057	Aia27	Adjuvant induced arthritis QTL 27	2.83		joint integrity trait (VT:0010548)	right rear ankle joint diameter (CMO:0002150)	20	2892597	26381954	Rat
1300152	Bp195	Blood pressure QTL 195	3.46		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	20	3621649	9243559	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	3621649	10078919	Rat
61432	Cia1	Collagen induced arthritis QTL 1			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	3621656	14101050	Rat
7175099	Tcs2	T cell selection QTL 2			T cell selection	expression	20	4502557	4693102	Rat
61474	Eae1	Experimental allergic encephalomyelitis QTL 1	3		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	20	4606607	6691706	Rat
4889857	Pur27	Proteinuria QTL 27	12.2	0.001	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	20	4606607	17617956	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	4606607	17617956	Rat

Related Rat Strains

The following Strains have been annotated to RT1-DMb

DA.AS2-(Tesb-RT1-DMb)

DA.E3-(Btnl2-RT1-DMb)

DA.KHW-(RT1-Db1-RT1-DMb)

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	1				2
Low	2	1	5		16				1	2	1	8
Below cutoff	2	15	33	23	6	23	3	5	8	19	17	5	3

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_198740	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017601577	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC098547	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC091108	(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
	FM108008	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ226840	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ227160	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233093	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233373	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000324	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222897	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222898	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222899	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222900	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222901	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U31599	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	Z49762	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000073474 ⟹ ENSRNOP00000065741

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	4,693,600 - 4,698,489 (-)	Ensembl
Rnor_6.0 Ensembl	20	5,227,045 - 5,234,290 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000075342 ⟹ ENSRNOP00000066169

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	4,693,103 - 4,700,340 (-)	Ensembl
Rnor_6.0 Ensembl	20	3,945,601 - 3,952,846 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000078309

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	4,693,600 - 4,698,861 (-)	Ensembl
Rnor_6.0 Ensembl	20	5,227,161 - 5,230,034 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000079111

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	3,952,269 - 3,952,838 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000086240 ⟹ ENSRNOP00000074293

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	5,227,053 - 5,227,620 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000087321

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	3,952,061 - 3,952,838 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000087520

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	5,227,053 - 5,227,830 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000087782

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	5,230,949 - 5,231,561 (-)	Ensembl

RefSeq Acc Id:

NM_198740 ⟹ NP_942035

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	20	4,693,102 - 4,700,340 (-)	NCBI
Rnor_6.0	20	3,945,601 - 3,952,838 (+)	NCBI
Rnor_5.0	20	7,288,114 - 7,295,355 (-)	NCBI
RGSC_v3.4	20	4,829,535 - 4,836,772 (-)	RGD
Celera	20	6,293,763 - 6,301,000 (-)	RGD

Sequence:

show sequence

GGATTTGGTTGAGTTAGTGGGTGCAACTTTAAGATCTAAGGAGGGGCTGAGTGACCTGGGGCCA
CATCGGCAGCAAGGAGCAAGGGACCTGAACAACAAGTACCGTCTTTACCTCAGCGTGGGAAAAT
CATTTGTCCAAGCTGGGGCAGGAGAGGTCCCGAGGCCCCTGCGTGAGGTGGCCCAGGAGCCTGA
CCTTCCTGCACCTTCAGAGAGTGGAACATGGCTGCACTATGGCCGCTGCTGCTGGCCCTGAGTC
TGGGTTGTATAGGAGCAGGTGGCTTTGTGGCTCATGTGGAAAGCACGTGCTTGCTGGATGATGA
AGGGACCCCAATGGACTTCACATACTGTATTTCCTTCAACAAAGATCTGCTGGCCTGCTGGGAT
CCAGAGGAGGGACAAATAGTCCCCTGTGAATATGGGGTCCTGTTTAAGTTGGCCGAATTCATTT
CAAATATCCTCAACAAGGAAGAAGGCCTGATCCAGCGCTTGAAAAATGGGCTTCAGGACTGTTC
CACACACACCCAGCCCTTCTGGAACGCGCTGACCCACAGAACCAGAACGCCATCTGTCCAAGTA
GCCCAAACCGCTCCTTTTAACACAAGGGAGCCTGTGATGCTGGCCTGCTACGTCTGGGGCTTCT
ATCCGGCGGATGTGACCGTCGTGTGGATGAAGAACGGGCAGCTTGTTACTTCCCACAGCAACAA
GGAGAAGACGGCTCAGCCTAATGGGGACTGGACATACCAGACCGTCTCCTACCTAGCCTTAACC
CCTTCCTACTGGGACATCTACACCTGCGTGGTACAGCACAGCGGGACCCCTGAGCCCATCCGCG
CGAACTGGACACCCGGGCTGTCCCCCATCCAGACAGTGAAGGTCTCTGTGTCTGCAGCCACCCT
GGGCCTGGGCTTCATCATCTTCTGTCTTGGCTTCTTCAGATGGCGCAAGTCTCACTCCTCCAGC
TACACTCCTCTCCCTGGATCCACCTACCCGGAAGGACGGCCCTAGAGGGCAGAGCCCCGCGCTG
AGAAGGAGATCCAGACTTTTGATGGTGCCTTCATGCCCCCCAGCATCTTCAGGACACCCCACTT
TCTTGTGTCATAATTCCTCTACTCAGTTCCACTTTCCCATGTAAATATTGGTGGCCTGGGGGGT
ATTCGTAATCAAATCTGCCTCGGGTGTTTTCTGAGGTGAGCTGCTCTGAGGAGGGGGTTCAGTG
CCCTCCTGAAAGCCCCACCTTGTCACAGAAGGCACTGTGTCACGATCACACCTAAGAAATAAAC
TGGTGTGGAATTAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_942035	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB05196	(Get FASTA)	NCBI Sequence Viewer
	AAH91108	(Get FASTA)	NCBI Sequence Viewer
	AGV38994	(Get FASTA)	NCBI Sequence Viewer
	AGV38995	(Get FASTA)	NCBI Sequence Viewer
	AGV38996	(Get FASTA)	NCBI Sequence Viewer
	AGV38997	(Get FASTA)	NCBI Sequence Viewer
	AGV38998	(Get FASTA)	NCBI Sequence Viewer
	CAA89832	(Get FASTA)	NCBI Sequence Viewer
	CAE83939	(Get FASTA)	NCBI Sequence Viewer
	EDL96812	(Get FASTA)	NCBI Sequence Viewer
	EDL96813	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_942035 ⟸ NM_198740
- Peptide Label:	precursor
- UniProtKB:	Q6MGA7 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAALWPLLLALSLGCIGAGGFVAHVESTCLLDDEGTPMDFTYCISFNKDLLACWDPEEGQIVPC EYGVLFKLAEFISNILNKEEGLIQRLKNGLQDCSTHTQPFWNALTHRTRTPSVQVAQTAPFNTR EPVMLACYVWGFYPADVTVVWMKNGQLVTSHSNKEKTAQPNGDWTYQTVSYLALTPSYWDIYTC VVQHSGTPEPIRANWTPGLSPIQTVKVSVSAATLGLGFIIFCLGFFRWRKSHSSSYTPLPGSTY PEGRP hide sequence

RefSeq Acc Id:

ENSRNOP00000074293 ⟸ ENSRNOT00000086240

RefSeq Acc Id:

ENSRNOP00000066169 ⟸ ENSRNOT00000075342

RefSeq Acc Id:

ENSRNOP00000065741 ⟸ ENSRNOT00000073474

Protein Domains

Ig-like

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q6MGA7-F1-model_v2	AlphaFold	Q6MGA7	1-261	view protein structure

Transcriptome

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

Promoters

RGD ID:

13701323

Promoter ID:

EPDNEW_R11845

Type:

initiation region

Name:

LOC108348139_1

Description:

class II histocompatibility antigen, M beta 1 chain

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	3,945,632 - 3,945,692	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:735096	AgrOrtholog
BioCyc Gene	G2FUF-4551	BioCyc
Ensembl Genes	ENSRNOG00000049491	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOG00000051002	Ensembl
Ensembl Protein	ENSRNOP00000065741.2	UniProtKB/TrEMBL
	ENSRNOP00000066169	ENTREZGENE
	ENSRNOP00000066169.1	UniProtKB/TrEMBL
	ENSRNOP00000097489.1	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000073474.3	UniProtKB/TrEMBL
	ENSRNOT00000075342	ENTREZGENE
	ENSRNOT00000075342.3	UniProtKB/TrEMBL
	ENSRNOT00000078309.2	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.10	UniProtKB/TrEMBL
	3.10.320.10	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7380292	IMAGE-MGC_LOAD
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_I/II-like_Ag-recog	UniProtKB/TrEMBL
	MHC_II_a/b_N	UniProtKB/TrEMBL
	MHC_II_b_N	UniProtKB/TrEMBL
KEGG Report	rno:294273	UniProtKB/TrEMBL
MGC_CLONE	MGC:108534	IMAGE-MGC_LOAD
NCBI Gene	294273	ENTREZGENE
Pfam	C1-set	UniProtKB/TrEMBL
	MHC_II_beta	UniProtKB/TrEMBL
PhenoGen	RT1-DMb	PhenoGen
PROSITE	IG_LIKE	UniProtKB/TrEMBL
	IG_MHC	UniProtKB/TrEMBL
SMART	IGc1	UniProtKB/TrEMBL
	MHC_II_beta	UniProtKB/TrEMBL
Superfamily-SCOP	MHC_I/II-like_Ag-recog	UniProtKB/TrEMBL
	SSF48726	UniProtKB/TrEMBL
UniProt	A0A8I6ANG9_RAT	UniProtKB/TrEMBL
	M0R8E5_RAT	UniProtKB/TrEMBL
	Q6MGA7	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2021-03-09	RT1-DMb	RT1 class II, locus DMb	LOC108348139	class II histocompatibility antigen, M beta 1 chain	Data Merged	737654	PROVISIONAL
2016-08-02	LOC108348139	class II histocompatibility antigen, M beta 1 chain			Symbol and Name status set to provisional	70820	PROVISIONAL
2009-09-14	RT1-DMb	RT1 class II, locus DMb	Hla-dmb	major histocompatibility complex, class II, DM beta	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2009-09-14	Hla-dmb	major histocompatibility complex, class II, DM beta	RT1-DMb	RT1 class II, locus DMb	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2009-09-14	RT1-DMb	RT1 class II, locus DMb	Hla-dmb	major histocompatibility complex, class II, DM beta	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Hla-dmb	major histocompatibility complex, class II, DM beta			Symbol and Name status set to approved	1299863	APPROVED
2005-09-30	Hla-dmb				Symbol and Name status set to provisional	70820	PROVISIONAL

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)

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)