LOC100909593 (class II histocompatibility antigen, M alpha chain-like)

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Gene: LOC100909593 (class II histocompatibility antigen, M alpha chain-like) Rattus norvegicus

Analyze

Symbol:

LOC100909593

Name:

class II histocompatibility antigen, M alpha chain-like

RGD ID:

6502526

Description:

Predicted to be involved in positive regulation of germinal center formation and positive regulation of humoral immune response. Predicted to act upstream of or within several processes, including antigen processing and presentation of exogenous peptide antigen via MHC class II; chaperone cofactor-dependent protein refolding; and positive thymic T cell selection. Predicted to be located in endosome membrane; lysosomal membrane; and multivesicular body. Orthologous to human HLA-DMA (major histocompatibility complex, class II, DM alpha); INTERACTS WITH 1,2-dimethylhydrazine (ortholog); 17alpha-ethynylestradiol (ortholog); 2,2',4,4',5,5'-hexachlorobiphenyl (ortholog).

Type:

protein-coding

RefSeq Status:

WITHDRAWN

RGD Orthologs

Mouse

Alliance Genes

More Info

more info ...

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
Rnor_6.0	20	3,935,501 - 3,938,915 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	6,015,055 - 6,018,463 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Cytogenetic Map	20		NCBI

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

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

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

2-butoxyethanol (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

benzo[a]pyrene (ISO)

carbon nanotube (ISO)

chloroprene (ISO)

clobetasol (ISO)

dexamethasone (ISO)

dextran sulfate (ISO)

diethylstilbestrol (ISO)

doxorubicin (ISO)

genistein (ISO)

isoprenaline (ISO)

ozone (ISO)

pirinixic acid (ISO)

quercetin (ISO)

titanium dioxide (ISO)

Triptolide (ISO)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

antigen processing and presentation (ISO)

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

chaperone cofactor-dependent protein refolding (ISO)

immunoglobulin mediated immune response (ISO)

inner ear development (ISO)

positive regulation of germinal center formation (ISO)

positive regulation of humoral immune response (ISO)

positive regulation of immune response (ISO)

positive regulation of T cell differentiation (ISO)

positive thymic T cell selection (ISO)

protein transport (ISO)

protein-containing complex assembly (ISO)

Cellular Component

endosome membrane (ISO)

late endosome (ISO)

lysosomal membrane (ISO)

lysosome (ISO)

multivesicular body (ISO)

Molecular Function

protein binding (ISO)

References

References - curated


1.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:7584146	PMID:7985028	PMID:8598040	PMID:8598041	PMID:8638109	PMID:8890155	PMID:9432982	PMID:9492004	PMID:11027433	PMID:11148202	PMID:11714799	PMID:11854359
PMID:21795542

Genomics

Comparative Map Data

LOC100909593
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	20	3,935,501 - 3,938,915 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	20	6,015,055 - 6,018,463 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Cytogenetic Map	20		NCBI

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		mm39
GRCm39 Ensembl	17	34,338,515 - 34,358,075 (+)	Ensembl
GRCm38	17	34,119,693 - 34,139,101 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	34,119,541 - 34,139,101 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	34,272,616 - 34,275,480 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	17	33,746,082 - 33,749,555 (+)	NCBI			mm8
Celera	17	36,887,536 - 36,890,397 (+)	NCBI		Celera
Cytogenetic Map	17	B1	NCBI
cM Map	17	17.98	NCBI

Position Markers

D20Yum76

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	4,709,029 - 4,709,134 (-)	MAPPER	mRatBN7.2
mRatBN7.2	20	4,709,029 - 4,709,134 (+)	MAPPER	mRatBN7.2
Rnor_6.0	20	3,936,810 - 3,936,914	NCBI	Rnor6.0
Rnor_6.0	20	5,242,976 - 5,243,080	NCBI	Rnor6.0
Rnor_5.0	20	7,304,037 - 7,304,141	UniSTS	Rnor5.0
Rnor_5.0	20	6,016,358 - 6,016,462	UniSTS	Rnor5.0
RGSC_v3.4	20	4,845,459 - 4,845,563	UniSTS	RGSC3.4
Celera	20	6,309,689 - 6,309,793	UniSTS
Cytogenetic Map	20	p12	UniSTS

RH136915

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	20	4,707,045 - 4,707,261 (-)	MAPPER	mRatBN7.2
mRatBN7.2	20	4,707,045 - 4,707,261 (+)	MAPPER	mRatBN7.2
Rnor_6.0	20	5,240,993 - 5,241,208	NCBI	Rnor6.0
Rnor_6.0	20	3,938,682 - 3,938,897	NCBI	Rnor6.0
Rnor_5.0	20	6,018,230 - 6,018,445	UniSTS	Rnor5.0
Rnor_5.0	20	7,302,054 - 7,302,269	UniSTS	Rnor5.0
RGSC_v3.4	20	4,843,476 - 4,843,691	UniSTS	RGSC3.4
Celera	20	6,307,706 - 6,307,921	UniSTS
RH 3.4 Map	20	69.2	UniSTS
Cytogenetic Map	20	p12	UniSTS

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_003751924	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006256035	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC098547	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

XM_006256035 ⟹ XP_006256097

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	20	3,935,501 - 3,938,915 (+)	NCBI
Rnor_5.0	20	6,015,055 - 6,018,463 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_006256097	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

XP_006256097 ⟸ XM_006256035

Additional Information

External Database Links

Database	Acc Id	Source(s)
NCBI Gene	LOC100909593	ENTREZGENE
PhenoGen	LOC100909593	PhenoGen

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2012-07-05	LOC100909593	class II histocompatibility antigen, M alpha chain-like			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)

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