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

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Symbol:

RT1-DMa

Name:

RT1 class II, locus DMa

RGD ID:

735053

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; peptide antigen assembly with MHC class II protein complex; and positive regulation of immune response. Predicted to act upstream of or within several processes, including immunoglobulin mediated immune response; positive regulation of T cell differentiation; and positive thymic T cell selection. Predicted to be located in cell surface; endosome; and 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-DMA (major histocompatibility complex, class II, DM alpha); PARTICIPATES IN allograft rejection pathway; antigen processing and presentation pathway; asthma pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-diaminodiphenylmethane.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

class II histocompatibility antigen, M alpha chain; DMA1; Hla-dma; LOC108348072; major histocompatibility complex, class II, DM alpha; MHC class II-like alpha chain; RT1 class II, DM alpha; RT1.DMa; RT1.Ma

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Is Marker For:

Strains: DA.KHW-(RT1-DMa-Mln) DA.E3-(RT1-DMa-Ggnbp1)

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	4,708,932 - 4,712,335 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	20	4,708,933 - 4,712,335 (-)	Ensembl				GRCr8
mRatBN7.2	20	4,707,028 - 4,710,432 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	4,707,028 - 4,710,432 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	20	5,459,571 - 5,462,978 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	20	4,821,312 - 4,824,719 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	20	5,302,578 - 5,305,996 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	20	3,935,512 - 3,938,915 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	5,240,975 - 5,244,386 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	20	7,302,036 - 7,305,439 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	20	4,843,458 - 4,846,861 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	20	6,307,688 - 6,311,091 (-)	NCBI		Celera
RGSC_v3.1	20	4,843,691 - 4,847,054 (-)	NCBI
Cytogenetic Map	20	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Behcet's disease (ISO)

contact dermatitis (ISO)

Diabetic Nephropathies (ISO)

Experimental Liver Cirrhosis (EXP)

occupational dermatitis (ISO)

proteasome-associated autoinflammatory syndrome 1 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

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

2,4-dibromophenyl 2,4,5-tribromophenyl ether (ISO)

2-butoxyethanol (ISO)

2-hydroxypropanoic acid (ISO)

4,4'-diaminodiphenylmethane (EXP)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (ISO)

acrylamide (ISO)

aflatoxin B1 (ISO)

alachlor (EXP)

aldehydo-D-glucose (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

atrazine (EXP,ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (EXP)

carbon nanotube (ISO)

CGP 52608 (ISO)

chloroprene (ISO)

cisplatin (ISO)

clobetasol (ISO)

coumarin (EXP)

cyclosporin A (ISO)

D-glucose (ISO)

dexamethasone (ISO)

dextran sulfate (ISO)

diethylstilbestrol (ISO)

diquat (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

entinostat (ISO)

epoxiconazole (ISO)

fonofos (ISO)

fructose (ISO)

fulvestrant (ISO)

genistein (ISO)

glucose (ISO)

glyphosate (ISO)

hexachlorobenzene (EXP)

isoprenaline (ISO)

lead(0) (ISO)

mercury dibromide (ISO)

methimazole (EXP)

methyl methanesulfonate (ISO)

N-nitrosodiethylamine (EXP)

N-nitrosodimethylamine (EXP)

N-nitrosomorpholine (EXP)

nickel sulfate (ISO)

nitrates (ISO)

omeprazole (ISO)

ozone (ISO)

panobinostat (ISO)

paracetamol (EXP,ISO)

parathion (ISO)

perfluorooctane-1-sulfonic acid (EXP,ISO)

perfluorooctanoic acid (EXP)

pirinixic acid (EXP,ISO)

pregnenolone 16alpha-carbonitrile (EXP)

quercetin (ISO)

rac-lactic acid (ISO)

resveratrol (EXP)

rifampicin (ISO)

SB 431542 (ISO)

silicon dioxide (EXP,ISO)

simvastatin (EXP)

sodium arsenite (ISO)

sodium dichromate (ISO)

Soman (EXP)

streptozocin (EXP)

sulforaphane (ISO)

tamibarotene (ISO)

temozolomide (ISO)

terbufos (ISO)

thapsigargin (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trichloroethene (EXP)

trichostatin A (ISO)

triphenyl phosphate (ISO)

Triptolide (ISO)

triptonide (ISO)

tunicamycin (ISO)

valdecoxib (ISO)

valproic acid (EXP,ISO)

vinclozolin (EXP)

vorinostat (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adaptive immune response (IEA)

antigen processing and presentation (IEA,ISO)

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

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

immune response (IEA)

immune system process (IEA)

immunoglobulin mediated immune response (ISO)

inner ear development (ISO)

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

positive regulation of germinal center formation (ISO)

positive regulation of humoral immune response (ISO)

positive regulation of immune response (IBA,ISO)

positive regulation of T cell activation (IBA)

positive regulation of T cell differentiation (ISO)

positive thymic T cell selection (ISO)

protein folding (ISO)

protein transport (ISO)

protein-containing complex assembly (ISO)

regulation of immune system process (IEA)

Cellular Component

cell surface (IEA,ISO)

endosome membrane (ISO)

late endosome (ISO)

late endosome membrane (IBA,IEA,ISO)

lysosomal membrane (IBA,IEA,ISO)

lysosome (ISO)

membrane (IEA)

MHC class II protein complex (IBA,IEA,ISO)

multivesicular body (ISO)

Molecular Function

MHC class II protein complex binding (IBA,IEA,ISO)

peptide antigen binding (IBA)

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.	The impact of H2-DM on humoral immune responses.	Alfonso C, etal., J Immunol 2001 Dec 1;167(11):6348-55.
2.	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.
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.
8.	Integrated Analysis of Multiple Microarray Studies to Identify Core Gene-Expression Signatures Involved in Tubulointerstitial Injury in Diabetic Nephropathy.	Zhou H, etal., Biomed Res Int. 2022 May 10;2022:9554658. doi: 10.1155/2022/9554658. eCollection 2022.

Additional References at PubMed

PMID:7584146	PMID:7590989	PMID:7606781	PMID:7985028	PMID:8598040	PMID:8598041	PMID:8638109	PMID:8890155	PMID:9432982	PMID:9492004	PMID:11027433	PMID:11148202
PMID:11685465	PMID:11854359	PMID:12477932	PMID:16435885	PMID:19691639	PMID:19946888	PMID:21795542	PMID:22247549	PMID:22733780	PMID:23376485	PMID:24586191

Genomics

Comparative Map Data

RT1-DMa
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	20	4,708,932 - 4,712,335 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	20	4,708,933 - 4,712,335 (-)	Ensembl				GRCr8
mRatBN7.2	20	4,707,028 - 4,710,432 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	20	4,707,028 - 4,710,432 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	20	5,459,571 - 5,462,978 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	20	4,821,312 - 4,824,719 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	20	5,302,578 - 5,305,996 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	20	3,935,512 - 3,938,915 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	20	5,240,975 - 5,244,386 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	20	7,302,036 - 7,305,439 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	20	4,843,458 - 4,846,861 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	20	6,307,688 - 6,311,091 (-)	NCBI		Celera
RGSC_v3.1	20	4,843,691 - 4,847,054 (-)	NCBI
Cytogenetic Map	20	p12	NCBI

HLA-DMA
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	32,948,618 - 32,953,097 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	32,948,613 - 32,969,094 (-)	Ensembl			hg38	GRCh38
GRCh37	6	32,916,395 - 32,920,874 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	33,024,373 - 33,028,831 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	6	33,024,373 - 33,028,831	NCBI
Celera	6	34,465,294 - 34,469,805 (-)	NCBI		Celera
Cytogenetic Map	6	p21.32	NCBI
HuRef	6	32,658,920 - 32,663,431 (-)	NCBI		HuRef
CHM1_1	6	32,917,186 - 32,921,697 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	32,769,955 - 32,774,437 (-)	NCBI		T2T-CHM13v2.0

H2-DMa
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	34,338,667 - 34,358,075 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	34,338,515 - 34,358,075 (+)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	17	34,119,693 - 34,139,101 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	34,119,541 - 34,139,101 (+)	Ensembl			mm10	GRCm38
MGSCv37	17	34,272,616 - 34,275,480 (+)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	17	33,746,082 - 33,749,555 (+)	NCBI		MGSCv36	mm8
Celera	17	36,887,536 - 36,890,397 (+)	NCBI		Celera
Cytogenetic Map	17	B1	NCBI
cM Map	17	17.98	NCBI

LOC102023843
(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	1,558,911 - 1,562,162 (-)	Ensembl
ChiLan1.0	NW_004955437	1,558,806 - 1,562,294 (-)	NCBI	ChiLan1.0	ChiLan1.0

LOC100968989
(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	47,423,704 - 47,428,283 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	43,295,262 - 43,299,831 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	32,518,060 - 32,537,989 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	33,633,497 - 33,639,091 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	33,634,123 - 33,637,988 (-)	Ensembl			panPan2	panpan1.1

LOC101963772
(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	38,120,076 - 38,124,109 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936476	25,836,142 - 25,840,197 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936476	25,836,163 - 25,840,191 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SLA-DMA
(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	25,133,497 - 25,137,966 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	7	25,133,494 - 25,137,928 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	29,500,103 - 29,504,572 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3
Pig Cytomap	7	q1.1	NCBI

MHC-DMA
(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	39,142,340 - 39,151,804 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	17	39,142,395 - 39,146,252 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666044	32,737,022 - 32,757,552 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

LOC101700274
(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	23,762,051 - 23,765,593 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624754	23,752,352 - 23,765,319 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Variants

Variants in RT1-DMa
73 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	236
Count of miRNA genes:	123
Interacting mature miRNAs:	139
Transcripts:	ENSRNOT00000070886, ENSRNOT00000072458
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
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
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
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
7387283	Uae44	Urinary albumin excretion QTL 44		0.1712	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	20	1	26123605	Rat
7411668	Foco32	Food consumption QTL 32	8	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	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
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
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
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
8694189	Bw153	Body weight QTL 153	3.13	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	20	1	29191651	Rat
1300152	Bp195	Blood pressure QTL 195	3.46		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	20	3621649	9243559	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
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
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
9589155	Insul32	Insulin level QTL 32	6.38	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	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
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
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
61432	Cia1	Collagen induced arthritis QTL 1			joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	20	3621656	14101050	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
6893685	Bw111	Body weight QTL 111	2.7	0.004	body mass (VT:0001259)	body weight (CMO:0000012)	20	1	32578807	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

Related Rat Strains

The following Strains have been annotated to RT1-DMa

DA.E3-(RT1-DMa-Ggnbp1) DA.KHW-(RT1-DMa-Mln)

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	hemolymphoid system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
12	2	18	57	2	6	76	157	106	11	55	39	33	6	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_198741	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC098547	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC091107	(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
	CV106229	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ233863	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000020	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222882	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222883	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222884	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222885	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KC222886	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U31598	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	Z49761	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000070886 ⟹ ENSRNOP00000066343

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	20	4,708,933 - 4,712,335 (-)	Ensembl
mRatBN7.2 Ensembl	20	4,707,029 - 4,710,432 (-)	Ensembl
Rnor_6.0 Ensembl	20	5,240,975 - 5,244,386 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000072458 ⟹ ENSRNOP00000067364

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	20	4,708,933 - 4,712,195 (-)	Ensembl
mRatBN7.2 Ensembl	20	4,707,029 - 4,710,292 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000078036 ⟹ ENSRNOP00000093448

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	4,707,028 - 4,710,432 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000078382

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	20	5,242,322 - 5,244,330 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000080583

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	4,707,028 - 4,710,017 (-)	Ensembl
Rnor_6.0 Ensembl	20	5,240,975 - 5,241,496 (-)	Ensembl

RefSeq Acc Id:

NM_198741 ⟹ NP_942036

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	20	4,708,932 - 4,712,335 (-)	NCBI
mRatBN7.2	20	4,707,028 - 4,710,432 (-)	NCBI
Rnor_6.0	20	3,935,512 - 3,938,915 (+)	NCBI
Rnor_5.0	20	7,302,036 - 7,305,439 (-)	NCBI
RGSC_v3.4	20	4,843,458 - 4,846,861 (-)	RGD
Celera	20	6,307,688 - 6,311,091 (-)	RGD

Sequence:

show sequence

GAAGGGAGCTGGGCACCCGGGAGTGAAAGCGCTCACTCGCTGAGGGTGTTAAGGTATGGAGCAT
GAGCAGAAGTCAGGAGGGCTGCTGAGGCTGCTGCGGCTTCTGTGGCTGCTGCCTCACTCCTGGG
CGGTGCTTGAAGCTTCTCCCCAGGCGTGGTGGGATGAGTCGCAGAACCACACATTCCGTCACAC
TCTGTTCTGCCAGGATGGGTTTCCCAACATAGGGCTCTCCGAGACCTACGACGAGGACGCACTC
TTCTCCTTCGACTTCTCCCAGAACACCAGAGTGCCCCGGCTGCCTGAGTTTGCTGAGTGGGCTC
AGGAACAGGGAGATGCCTCTGCCATTGCGTTTGACAAAGGCTTCTGCGACATGTTGATGCAGAA
TGTGAGCCCGCGGCTTGAAGGTCAAATCCCAGTGTCCAGAGGTTTGCCTTCGGCTGAGGTGTTC
ACCCTGAAGCCCCTGGAGTTTGGCAAGCCCAACACGCTGGTCTGTTTCATCAGCAACCTCTTTC
CACCGACTTTGACGGTGACCTGGCAGCATCATTTCGTCCCCGTGGAGGGAGCCAGCCCCACATC
CGTTTCAGCCATCGATGGGCTCACCTTCCAGGCCTTCTCTTATTTAAACTTCACACCGGAACCC
TTCGACCTTTACTCCTGCACTGTGACGCACGAGATTGACCGCTACACGGCGATTGCCTATTGGG
TACCCCAGAACGCCCTGCCTTCAGATCTCCTGGAGAATGTACTGTGCGGTGTGGCCTTCGGCCT
CGGTGTGCTGGGCCTCGTCGTGGGCATTGTCTTCTTCATCCGCTCCCAGAGACCTTGCTCAGGG
GACTGATTCTTCCCAAGGAGGGCTTGGAACTGCACCAGCCAGGCCGGCAGCGATGTCCAGGCAT
CTCGCGCTTACCAGGGTCTTTCCTCAGAGCCGAAGTCCCCGGGATCCCTTGGGGTGCGTGCCGG
CATGCTAAGGGGTTCCGCTGTCCCTGGACTTACATCCAGAAAAGCCGGAGTCAGGAGCCCCGGG
CCCCACCAGACCACTACCTTATACCTTCCCTCTTCCAGGAAATAAAGTTTATTTCTTAACATCA
AAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_942036	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA87845	(Get FASTA)	NCBI Sequence Viewer
	AAH91107	(Get FASTA)	NCBI Sequence Viewer
	AGV38979	(Get FASTA)	NCBI Sequence Viewer
	AGV38980	(Get FASTA)	NCBI Sequence Viewer
	AGV38981	(Get FASTA)	NCBI Sequence Viewer
	AGV38982	(Get FASTA)	NCBI Sequence Viewer
	AGV38983	(Get FASTA)	NCBI Sequence Viewer
	CAA89831	(Get FASTA)	NCBI Sequence Viewer
	CAE83938	(Get FASTA)	NCBI Sequence Viewer
	EDL96814	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000066343
	ENSRNOP00000066343.1
	ENSRNOP00000067364.2
	ENSRNOP00000092677.1
	ENSRNOP00000093448.1

RefSeq Acc Id:	NP_942036 ⟸ NM_198741
- Peptide Label:	precursor
- UniProtKB:	Q95574 (UniProtKB/TrEMBL), A6JJE8 (UniProtKB/TrEMBL), A0A8I6AFU3 (UniProtKB/TrEMBL), A0A023IKC6 (UniProtKB/TrEMBL)
- Sequence:	show sequence MEHEQKSGGLLRLLRLLWLLPHSWAVLEASPQAWWDESQNHTFRHTLFCQDGFPNIGLSETYDE DALFSFDFSQNTRVPRLPEFAEWAQEQGDASAIAFDKGFCDMLMQNVSPRLEGQIPVSRGLPSA EVFTLKPLEFGKPNTLVCFISNLFPPTLTVTWQHHFVPVEGASPTSVSAIDGLTFQAFSYLNFT PEPFDLYSCTVTHEIDRYTAIAYWVPQNALPSDLLENVLCGVAFGLGVLGLVVGIVFFIRSQRP CSGD hide sequence

Ensembl Acc Id:

ENSRNOP00000066343 ⟸ ENSRNOT00000070886

Ensembl Acc Id:

ENSRNOP00000093448 ⟸ ENSRNOT00000078036

Ensembl Acc Id:

ENSRNOP00000067364 ⟸ ENSRNOT00000072458

Protein Domains

Ig-like

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q95574-F1-model_v2	AlphaFold	Q95574	1-260	view protein structure

Transcriptome

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

Promoters

RGD ID:

13701324

Promoter ID:

EPDNEW_R11844

Type:

multiple initiation site

Name:

LOC108348072_1

Description:

class II histocompatibility antigen, M alpha 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	3,935,546 - 3,935,606	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:735053	AgrOrtholog
BioCyc Gene	G2FUF-4550	BioCyc
Ensembl Genes	ENSRNOG00000047864	Ensembl
	ENSRNOG00000066773	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000070886	ENTREZGENE
	ENSRNOT00000070886.3	UniProtKB/TrEMBL
	ENSRNOT00000072458.3	UniProtKB/TrEMBL
	ENSRNOT00000078036.2	UniProtKB/TrEMBL
	ENSRNOT00000080583.2	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.10	UniProtKB/TrEMBL
	Class II Histocompatibility Antigen, M Beta Chain, Chain B, domain 1	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7377707	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/Immunoglobulin	UniProtKB/TrEMBL
	MHC_I/II-like_Ag-recog	UniProtKB/TrEMBL
	MHC_II_a/b_N	UniProtKB/TrEMBL
	MHC_II_a_N	UniProtKB/TrEMBL
KEGG Report	rno:294274	UniProtKB/TrEMBL
MGC_CLONE	MGC:108532	IMAGE-MGC_LOAD
NCBI Gene	294274	ENTREZGENE
PANTHER	HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DM ALPHA CHAIN	UniProtKB/TrEMBL
	MHC CLASS II-RELATED	UniProtKB/TrEMBL
Pfam	C1-set	UniProtKB/TrEMBL
	MHC_II_alpha	UniProtKB/TrEMBL
PhenoGen	RT1-DMa	PhenoGen
PROSITE	IG_LIKE	UniProtKB/TrEMBL
	IG_MHC	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000047864	RatGTEx
	ENSRNOG00000066773	RatGTEx
SMART	IGc1	UniProtKB/TrEMBL
	MHC_II_alpha	UniProtKB/TrEMBL
Superfamily-SCOP	MHC_I/II-like_Ag-recog	UniProtKB/TrEMBL
	SSF48726	UniProtKB/TrEMBL
UniProt	A0A023IKC6	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6AFU3	ENTREZGENE, UniProtKB/TrEMBL
	A0A8I6AIM7_RAT	UniProtKB/TrEMBL
	A6JJE8	ENTREZGENE
	M0RCN9_RAT	UniProtKB/TrEMBL
	Q95574	ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary	A6JJE8	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2021-03-09	RT1-DMa	RT1 class II, locus DMa	LOC108348072	class II histocompatibility antigen, M alpha chain	Data merged from RGD:11505944	737654	PROVISIONAL
2016-08-02	LOC108348072	class II histocompatibility antigen, M alpha chain			Symbol and Name status set to provisional	70820	PROVISIONAL
2009-09-14	RT1-DMa	RT1 class II, locus DMa	Hla-dma	major histocompatibility complex, class II, DM alpha	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Hla-dma	major histocompatibility complex, class II, DM alpha			Symbol and Name status set to approved	1299863	APPROVED
2005-09-30	Hla-dma				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 - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Annotations - KEGG (archival)