Ms4a1 (membrane spanning 4-domains A1)

Advanced Search (OLGA)

Gene: Ms4a1 (membrane spanning 4-domains A1) Rattus norvegicus

Analyze

Symbol:

Ms4a1

Name:

membrane spanning 4-domains A1

RGD ID:

1311999

Description:

Enables epidermal growth factor receptor binding activity. Predicted to be involved in several processes, including B cell receptor signaling pathway; calcium ion transport; and positive regulation of calcium ion import across plasma membrane. Predicted to act upstream of or within response to bacterium. Predicted to be located in cell surface; nucleoplasm; and plasma membrane raft. Predicted to be active in external side of plasma membrane. Biomarker of glomerulonephritis. Human ortholog(s) of this gene implicated in common variable immunodeficiency 5. Orthologous to human MS4A1 (membrane spanning 4-domains A1); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

B-lymphocyte antigen CD20; Cd20; LOC309217; membrane-spanning 4-domains, subfamily A, member 1

RGD Orthologs

Alliance Orthologs

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
GRCr8	1	217,331,274 - 217,351,934 (-)	NCBI		GRCr8
mRatBN7.2	1	207,906,370 - 207,927,028 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	207,906,374 - 207,918,512 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	216,281,228 - 216,293,400 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	223,345,173 - 223,357,355 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	216,035,633 - 216,047,806 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	227,429,241 - 227,441,492 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	227,429,596 - 227,441,442 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	234,494,128 - 234,506,370 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	213,763,696 - 213,770,756 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	213,921,879 - 213,934,027 (-)	NCBI
Celera	1	205,381,782 - 205,388,842 (-)	NCBI		Celera
Cytogenetic Map	1	q43	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

B-Cell Chronic Lymphocytic Leukemia (ISO)

common variable immunodeficiency (ISO)

common variable immunodeficiency 5 (ISO)

glomerulonephritis (IEP)

intellectual disability (ISO)

leukocyte adhesion deficiency 3 (ISO)

lung adenocarcinoma (ISO)

lung non-small cell carcinoma (ISO)

Mycoplasma pneumoniae pneumonia (ISO)

ovarian cyst (ISO)

squamous cell carcinoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17beta-estradiol (EXP,ISO)

17beta-estradiol 3-benzoate (EXP)

2,3',4,4',5-Pentachlorobiphenyl (ISO)

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

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

4-hydroxyphenyl retinamide (ISO)

aflatoxin B1 (ISO)

aldehydo-D-glucose (ISO)

alpha-Zearalanol (EXP)

arsane (ISO)

arsenic atom (ISO)

asbestos (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bisphenol A (EXP,ISO)

bromobenzene (EXP)

buta-1,3-diene (ISO)

capecitabine (ISO)

carbon nanotube (ISO)

chloroprene (ISO)

chrysene (ISO)

curcumin (ISO)

D-glucose (ISO)

dexamethasone phosphate (EXP)

dextran sulfate (ISO)

dimethylarsinic acid (ISO)

dioxygen (ISO)

diuron (ISO)

formaldehyde (ISO)

fructose (ISO)

genistein (ISO)

gentamycin (EXP)

glucose (ISO)

glyphosate (ISO)

hydrazine (ISO)

hydroxychloroquine (ISO)

lidocaine (EXP)

lipopolysaccharide (EXP)

methotrexate (ISO)

methyl methanesulfonate (ISO)

methylarsonic acid (ISO)

N-nitrosodiethylamine (ISO)

nickel atom (ISO)

oxaliplatin (EXP)

ozone (ISO)

perfluorooctane-1-sulfonic acid (ISO)

pirinixic acid (ISO)

silicon dioxide (EXP)

sodium arsenate (ISO)

sodium arsenite (ISO)

sulfasalazine (ISO)

testosterone (EXP)

tetrachloromethane (EXP)

tetraphene (ISO)

titanium dioxide (ISO)

topotecan (EXP)

trimellitic anhydride (ISO)

triphenyl phosphate (ISO)

valproic acid (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

B cell activation (ISO)

B cell differentiation (ISO)

B cell receptor signaling pathway (ISO)

biological_process (ND)

calcium ion import into cytosol (ISO)

cell surface receptor signaling pathway (IBA)

positive regulation of calcium ion import across plasma membrane (ISO)

protein tetramerization (ISO)

response to bacterium (ISO)

store-operated calcium entry (ISO)

Cellular Component

cell surface (ISO)

external side of plasma membrane (IBA,ISO)

nucleoplasm (IEA,ISO)

plasma membrane (IBA,ISO)

plasma membrane raft (ISO)

Molecular Function

epidermal growth factor receptor binding (IPI)

identical protein binding (ISO)

immunoglobulin binding (ISO)

protein binding (ISO)

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.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	Integrin alpha(5) interacts with EGFR, is necessary for FcvarepsilonRI signaling and is necessary for allergic inflammation in relation with angiogenesis.	Kim Y, etal., Mol Immunol. 2011 Apr;48(8):1035-45. Epub 2011 Feb 23.
4.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
5.	Characterization of the mononuclear cell infiltrate in the glomerulus of rats with glomerulonephritis.	Radounikli A, etal., Nephrol Dial Transplant. 1995;10(2):185-90.
6.	GOA pipeline	RGD automated data pipeline
7.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	Comprehensive gene review and curation	RGD comprehensive gene curation
10.	Current and emerging treatments for chronic lymphocytic leukaemia.	Robak T, etal., Drugs. 2009;69(17):2415-49. doi: 10.2165/11319270-000000000-00000.

Additional References at PubMed

PMID:3925015	PMID:7684739	PMID:12477932	PMID:12920111	PMID:14688067	PMID:18474602	PMID:19723499	PMID:20458337	PMID:22664934	PMID:23012479

Genomics

Comparative Map Data

Ms4a1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	217,331,274 - 217,351,934 (-)	NCBI		GRCr8
mRatBN7.2	1	207,906,370 - 207,927,028 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	207,906,374 - 207,918,512 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	216,281,228 - 216,293,400 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	223,345,173 - 223,357,355 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	216,035,633 - 216,047,806 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	227,429,241 - 227,441,492 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	227,429,596 - 227,441,442 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	234,494,128 - 234,506,370 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	213,763,696 - 213,770,756 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	213,921,879 - 213,934,027 (-)	NCBI
Celera	1	205,381,782 - 205,388,842 (-)	NCBI		Celera
Cytogenetic Map	1	q43	NCBI

MS4A1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	11	60,455,847 - 60,470,752 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	11	60,455,846 - 60,470,752 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	11	60,223,320 - 60,238,225 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	11	59,979,858 - 59,994,801 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	11	59,979,864 - 59,993,129	NCBI
Celera	11	57,587,550 - 57,602,493 (+)	NCBI		Celera
Cytogenetic Map	11	q12.2	NCBI
HuRef	11	56,569,727 - 56,584,670 (+)	NCBI		HuRef
CHM1_1	11	60,089,320 - 60,104,266 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	11	60,406,975 - 60,421,883 (+)	NCBI		T2T-CHM13v2.0

Ms4a1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	11,227,043 - 11,243,513 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	19	11,227,039 - 11,243,605 (-)	Ensembl		GRCm39 Ensembl
GRCm38	19	11,249,679 - 11,266,149 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	11,249,675 - 11,266,241 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	11,325,093 - 11,340,641 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	19	11,316,865 - 11,333,194 (-)	NCBI		MGSCv36	mm8
Celera	19	11,933,232 - 11,941,389 (-)	NCBI		Celera
Cytogenetic Map	19	A	NCBI
cM Map	19	8.19	NCBI

Ms4a1
(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_004955511	5,258,341 - 5,267,113 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955511	5,252,934 - 5,263,961 (+)	NCBI	ChiLan1.0	ChiLan1.0

MS4A1
(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	9	61,597,728 - 61,612,704 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	11	62,641,996 - 62,656,548 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	11	55,691,750 - 55,706,697 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	11	59,134,579 - 59,148,832 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	11	59,134,617 - 59,149,521 (+)	Ensembl	panpan1.1		panPan2

MS4A1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	21	50,722,142 - 50,734,934 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	21	50,722,041 - 50,733,704 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	21	50,162,433 - 50,173,865 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	21	51,895,623 - 51,907,069 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	21	51,895,348 - 51,908,292 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	21	50,941,639 - 50,953,065 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	21	51,040,140 - 51,051,579 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	21	51,664,248 - 51,675,690 (+)	NCBI		UU_Cfam_GSD_1.0

Ms4a1
(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_024404947	12,352,445 - 12,358,299 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936581	2,466,312 - 2,477,530 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936581	2,466,294 - 2,477,530 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

MS4A1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	11,215,901 - 11,222,914 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	11,216,238 - 11,229,060 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	2	10,774,975 - 10,787,878 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

MS4A1
(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	1	13,343,647 - 13,358,639 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	1	13,345,253 - 13,358,547 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666038	110,684,697 - 110,700,399 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants

Variants in Ms4a1
114 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	63
Count of miRNA genes:	49
Interacting mature miRNAs:	58
Transcripts:	ENSRNOT00000028433
Prediction methods:	Miranda, 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
1578778	Pur4	Proteinuria QTL 4	3.3	0.003	urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	1	150700247	252085048	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	151162512	256448636	Rat
1357335	Bw39	Body weight QTL 39	3.3		body mass (VT:0001259)	body weight (CMO:0000012)	1	197814409	242814409	Rat
2302375	Bw83	Body weight QTL 83	4.87	0.0002	body mass (VT:0001259)	body weight (CMO:0000012)	1	197697768	242697768	Rat
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	81591954	219808434	Rat
2293674	Bss39	Bone structure and strength QTL 39	7.1	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	1	201554356	246554356	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	177227632	256448636	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	144267353	251128347	Rat
1354653	Despr9	Despair related QTL 9		0.00019	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	167909849	212909849	Rat
2293673	Bss27	Bone structure and strength QTL 27	18.63	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	1	171629477	216629477	Rat
2293677	Bss41	Bone structure and strength QTL 41	9.38	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra cross-sectional area (CMO:0001689)	1	171629477	216629477	Rat
1302787	Stl25	Serum triglyceride level QTL 25	2.7	0.0073	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	1	180359209	210702199	Rat
1549830	Bss1	Bone structure and strength QTL 1	4.8		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	172609619	217609619	Rat
70163	Bw20	Body weight QTL 20	5.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	174133260	219133260	Rat
7794788	Mcs32	Mammary carcinoma susceptibility QTL 32	2.61		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	1	115540693	238914717	Rat
1600395	Niddm69	Non-insulin dependent diabetes mellitus QTL 69	4.14	0.0002	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	195804352	257091168	Rat
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	179567751	260522016	Rat
1600396	Niddm68	Non-insulin dependent diabetes mellitus QTL 68	4.97	0.0003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	195804352	257091168	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	177227632	256448636	Rat
1600397	Edcs4	Endometrial carcinoma susceptibility QTL 4	2.2		uterus morphology trait (VT:0001120)	percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)	1	206081677	251081677	Rat
1558658	Bw59	Body weight QTL 59	3.5	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	1	178784622	223784622	Rat
631838	Niddm36	Non-insulin dependent diabetes mellitus QTL 36		0.01	insulin secretion trait (VT:0003564)	calculated pancreatic islet insulin release measurement (CMO:0001217)	1	184550676	229550676	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	153136852	260522016	Rat
2293689	Bss47	Bone structure and strength QTL 47	7.25	0.0001	lumbar vertebra size trait (VT:0010518)	lumbar vertebra trabecular cross-sectional area (CMO:0001692)	1	171629477	216629477	Rat
2293694	Bss38	Bone structure and strength QTL 38	7.05	0.0001	femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	1	201554356	246554356	Rat
1600388	Niddm67	Non-insulin dependent diabetes mellitus QTL 67	5.84	0.000004	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	1	195804352	257091168	Rat
152025235	Bw194	Body weight QTL 194	4.86		body mass (VT:0001259)		1	123556856	242907031	Rat
1598853	Memor3	Memory QTL 3	4.5		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	1	143506580	212458660	Rat
61341	Bp26	Blood pressure QTL 26			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	169537671	214537671	Rat
2293693	Bss22	Bone structure and strength QTL 22	33.52	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	1	171629477	216629477	Rat
1578759	Uae30	Urinary albumin excretion QTL 30	3.3	0.003	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	150700247	252085048	Rat
2300161	Bmd43	Bone mineral density QTL 43	8.4	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	171629477	216629477	Rat
1300145	Rf7	Renal function QTL 7	2.96		urine creatinine amount (VT:0010540)	urine creatinine level (CMO:0000125)	1	185145134	221264292	Rat
8655655	Arrd2	Age-related retinal degeneration QTL 2	7.79		retinal layer morphology trait (VT:0003727)	percentage of study population developing retinopathy during a period of time (CMO:0002453)	1	183970203	243914901	Rat
1358898	Bp255	Blood pressure QTL 255	3.6		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	191019702	246062233	Rat
631214	Bw61	Body weight QTL61	3.4	0.0001	intramuscular adipose amount (VT:0010044)	intramuscular fat area (CMO:0001162)	1	173108781	218108781	Rat
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	149448574	221264292	Rat
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	94642644	214537671	Rat
2300175	Bmd40	Bone mineral density QTL 40	15.4	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	1	201554356	246554356	Rat
2300174	Bmd42	Bone mineral density QTL 42	8.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	bone mineral density (CMO:0001226)	1	171629477	216629477	Rat
737828	Hcas3	Hepatocarcinoma susceptibility QTL 3	4.9		liver integrity trait (VT:0010547)	liver tumorous lesion volume to total liver volume ratio (CMO:0001082)	1	144267353	222987745	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	Rat
737977	Bp160	Blood pressure QTL 160		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	181133855	226133855	Rat
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	151162766	225824951	Rat
2293654	Bss30	Bone structure and strength QTL 30	32.65	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	1	171629477	216629477	Rat
2293655	Bss36	Bone structure and strength QTL 36	10.66	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	201554356	246554356	Rat
1298084	Thym4	Thymus enlargement QTL 4	10.68		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	1	197814409	242814409	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	150700142	252085212	Rat
2300187	Bmd41	Bone mineral density QTL 41	8.9	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	171629477	216629477	Rat
8552891	Epfw5	Epididymal fat weight QTL 5	4.4		epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	1	193113876	238113876	Rat
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	156677124	256448636	Rat
634313	Niddm43	Non-insulin dependent diabetes mellitus QTL 43			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	199050459	259647894	Rat
1358292	Cm37	Cardiac mass QTL 37	6.2	8e-07	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	1	196248093	241248093	Rat
61376	Bp42	Blood pressure QTL 42	23.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	197814409	242814409	Rat
634312	Bp143	Blood pressure QTL 143	3	0.0002	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	182623426	219932796	Rat
1358294	Bw37	Body weight QTL 37	5	0.000011	body mass (VT:0001259)	body weight (CMO:0000012)	1	171310381	216310381	Rat
1357399	Bw45	Body weight QTL 45	3.05		body mass (VT:0001259)	body mass index (BMI) (CMO:0000105)	1	206329708	251329708	Rat
724559	Pancm1	Pancreatic morphology QTL 1	7.1		islet of Langerhans morphology trait (VT:0005215)	pancreatic islet damage composite score (CMO:0001156)	1	181759564	214537555	Rat
2312420	Pur17	Proteinuria QTL 17	7.1	0.0001	urine protein amount (VT:0005160)	urine total protein excretion rate (CMO:0000756)	1	156677124	218753816	Rat
1357404	Bw42	Body weight QTL 42	4.49	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	206329708	251329708	Rat
10059600	Bp378	Blood pressure QTL 378	3.08	0.05	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	176869060	221869060	Rat
7421630	Bp362	Blood pressure QTL 362		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	118608292	241799120	Rat
619613	Bp77	Blood pressure QTL 77		0.01	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	164747424	209747424	Rat
2312564	Glom18	Glomerulus QTL 18	2.4	0.003	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	1	185356336	231689108	Rat
2292218	Kidm35	Kidney mass QTL 35			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	199368955	224569684	Rat
634321	Hc1	Hypercalciuria QTL 1	2.91		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	178810256	240830002	Rat
724562	Rends1	Renal damage susceptibility QTL 1		0.05	kidney glomerulus integrity trait (VT:0010546)	index of glomerular damage (CMO:0001135)	1	169537671	214537671	Rat
1331790	Bp201	Blood pressure QTL 201	3.127		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	198211513	225126682	Rat
10059587	Bw173	Body weight QTL 173	3.23	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	1	202069611	247069611	Rat
1300168	Bp170	Blood pressure QTL 170	2.76		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	207702246	228581766	Rat
61403	Niddm4	Non-insulin dependent diabetes mellitus QTL 4			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	206329708	222745518	Rat
2292222	Bp307	Blood pressure QTL 307	3.06	0.0014	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	164310393	213533942	Rat
2292220	Bp306	Blood pressure QTL 306	3.47	0.00087	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	164310393	243914901	Rat
1641926	Teswt2	Testicular weight QTL 2	2.82		testis mass (VT:1000644)	both testes wet weight (CMO:0000175)	1	197697768	238755659	Rat
10059590	Kidm44	Kidney mass QTL 44	3.42	0.025	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	191033875	236033875	Rat
631658	Cm7	Cardiac mass QTL 7	5.32	0.0001	aorta mass (VT:0002845)	aorta weight (CMO:0000076)	1	196248093	241248093	Rat
1600380	Niddm70	Non-insulin dependent diabetes mellitus QTL 70	3.1	0.0008	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	176550523	221550523	Rat
1582206	Kidm33	Kidney mass QTL 33	6.9		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	1	188377360	224054420	Rat
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	Rat
634338	Hcar4	Hepatocarcinoma resistance QTL 4	4.6		liver integrity trait (VT:0010547)	liver tumorous lesion number to liver area ratio (CMO:0001210)	1	193422268	214537671	Rat
8655855	Arrd3	Age-related retinal degeneration QTL 3	3.07		lens clarity trait (VT:0001304)	cataract incidence/prevalence measurement (CMO:0001585)	1	183970203	243914901	Rat
1600374	Mcs17	Mammary carcinoma susceptibility QTL 17	3		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	197670404	242670404	Rat
6903303	Scl34	Serum cholesterol QTL 34	2.5	0.0033	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	180359209	218108781	Rat
1600363	Hc6	Hypercalciuria QTL 6	2.7		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	203995416	244113296	Rat
2293083	Iddm25	Insulin dependent diabetes mellitus QTL 25	4.18		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	181829673	224569684	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	102813953	218753816	Rat
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	176426412	257976495	Rat
1358191	Ept10	Estrogen-induced pituitary tumorigenesis QTL 10	3.8		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	1	192825253	243914732	Rat
7394701	Uae46	Urinary albumin excretion QTL 46	3.6	0.0056	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	1	201554356	246554356	Rat

Markers in Region

Ms4a2

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	207,906,618 - 207,906,722 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	227,429,490 - 227,429,593	NCBI	Rnor6.0
Rnor_5.0	1	234,494,377 - 234,494,480	UniSTS	Rnor5.0
RGSC_v3.4	1	213,763,703 - 213,763,806	UniSTS	RGSC3.4
Celera	1	205,381,789 - 205,381,892	UniSTS
Cytogenetic Map	1	q43	UniSTS

M62541

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	207,906,701 - 207,906,862 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	227,429,573 - 227,429,733	NCBI	Rnor6.0
Rnor_5.0	1	234,494,460 - 234,494,620	UniSTS	Rnor5.0
RGSC_v3.4	1	213,763,786 - 213,763,946	UniSTS	RGSC3.4
Celera	1	205,381,872 - 205,382,032	UniSTS
Cytogenetic Map	1	q43	UniSTS

RH135092

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	207,906,482 - 207,906,688 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	227,429,354 - 227,429,559	NCBI	Rnor6.0
Rnor_5.0	1	234,494,241 - 234,494,446	UniSTS	Rnor5.0
RGSC_v3.4	1	213,763,567 - 213,763,772	UniSTS	RGSC3.4
Celera	1	205,381,653 - 205,381,858	UniSTS
RH 3.4 Map	1	1506.2	UniSTS
Cytogenetic Map	1	q43	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	nervous system	renal system	reproductive system	respiratory system
9	9	29	47	72	71	41	25	41	5	160	74	28	28	38	30

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001399452	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039079860	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC098745	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ225563	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ226425	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ235337	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000028433 ⟹ ENSRNOP00000028433

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	207,906,374 - 207,918,512 (-)	Ensembl
Rnor_6.0 Ensembl	1	227,429,596 - 227,441,442 (-)	Ensembl

RefSeq Acc Id:

NM_001399452 ⟹ NP_001386381

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	217,331,274 - 217,343,447 (-)	NCBI
mRatBN7.2	1	207,906,370 - 207,918,543 (-)	NCBI

RefSeq Acc Id:

XM_039079860 ⟹ XP_038935788

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	217,331,274 - 217,351,934 (-)	NCBI
mRatBN7.2	1	207,906,370 - 207,927,028 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_001386381	(Get FASTA)	NCBI Sequence Viewer
	XP_038935788	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM12866	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000028433.6

Ensembl Acc Id:

ENSRNOP00000028433 ⟸ ENSRNOT00000028433

RefSeq Acc Id:	XP_038935788 ⟸ XM_039079860
- Peptide Label:	isoform X1
- UniProtKB:	D4A4Y3 (UniProtKB/TrEMBL), A6I085 (UniProtKB/TrEMBL)

RefSeq Acc Id:	NP_001386381 ⟸ NM_001399452
- UniProtKB:	D4A4Y3 (UniProtKB/TrEMBL)

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A4Y3-F1-model_v2	AlphaFold	D4A4Y3	1-298	view protein structure

Transcriptome

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

Promoters

RGD ID:

13690786

Promoter ID:

EPDNEW_R1309

Type:

multiple initiation site

Name:

Ms4a1_1

Description:

membrane spanning 4-domains A1

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	1	227,441,415 - 227,441,475	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311999	AgrOrtholog
BioCyc Gene	G2FUF-56382	BioCyc
Ensembl Genes	ENSRNOG00000020945	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000028433.8	UniProtKB/TrEMBL
InterPro	CD20-like	UniProtKB/TrEMBL
	MS4A	UniProtKB/TrEMBL
NCBI Gene	309217	ENTREZGENE
PANTHER	PTHR23320	UniProtKB/TrEMBL
	PTHR23320:SF79	UniProtKB/TrEMBL
Pfam	CD20	UniProtKB/TrEMBL
PharmGKB	MS4A1	RGD
PhenoGen	Ms4a1	PhenoGen
RatGTEx	ENSRNOG00000020945	RatGTEx
UniProt	A6I085	ENTREZGENE, UniProtKB/TrEMBL
	D4A4Y3	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-01-27	Ms4a1	membrane spanning 4-domains A1	Ms4a1	membrane-spanning 4-domains, subfamily A, member 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	Ms4a1	membrane-spanning 4-domains, subfamily A, member 1	Ms4a1_predicted	membrane-spanning 4-domains, subfamily A, member 1 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Ms4a1_predicted	membrane-spanning 4-domains, subfamily A, member 1 (predicted)			Symbol and Name status set to approved	70820	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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Send us a Message

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM