Msx3 (msh homeobox 3) - Rat Genome Database

Name: Msx3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Msx3 (msh homeobox 3) Rattus norvegicus

Analyze

Symbol:

Msx3

Name:

msh homeobox 3

RGD ID:

620932

Description:

Predicted to enable several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; histone acetyltransferase binding activity; and histone acetyltransferase regulator activity. Predicted to be involved in embryonic morphogenesis and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus; INTERACTS WITH bisphenol A; C60 fullerene; Cuprizon.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

homeo box, msh-like 3

RGD Orthologs

Mouse

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Mus musculus (house mouse):	Msx3 (msh homeobox 3)	RGD	RGD
Alliance orthologs ³
Mus musculus (house mouse):	Msx3 (msh homeobox 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	msx1b (muscle segment homeobox 1b)	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|PANTHER\|SonicParanoid)
Danio rerio (zebrafish):	msx3 (muscle segment homeobox 3)	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Dr	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	vab-15	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

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	204,268,688 - 204,271,881 (-)	NCBI		GRCr8
mRatBN7.2	1	194,839,041 - 194,842,209 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	194,839,041 - 194,841,969 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	203,199,915 - 203,202,849 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	210,335,080 - 210,338,014 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	203,008,913 - 203,011,847 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	212,514,223 - 212,517,151 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	212,514,223 - 212,517,151 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	219,428,377 - 219,431,305 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	199,846,341 - 199,848,436 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	199,997,410 - 199,997,525 (-)	NCBI
Celera	1	192,516,231 - 192,519,165 (-)	NCBI		Celera
Cytogenetic Map	1	q41	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

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

4,4'-sulfonyldiphenol (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

C60 fullerene (EXP)

choline (ISO)

Cuprizon (EXP)

folic acid (ISO)

L-methionine (ISO)

lidocaine (EXP)

sodium arsenite (ISO)

trichloroethene (EXP)

XL147 (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

embryonic morphogenesis (IBA)

negative regulation of transcription by RNA polymerase II (ISO)

regulation of transcription by RNA polymerase II (IBA,ISO)

Cellular Component

nucleus (IBA,ISO)

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

histone acetyltransferase binding (ISO)

histone acetyltransferase regulator activity (ISO)

protein binding (ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (IBA)

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.	Distinct activities of Msx1 and Msx3 in dorsal neural tube development.	Liu Y, etal., Development 2004 Mar;131(5):1017-28.
3.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
4.	Delayed seizure activity following enflurane anesthesia.	Ohm WW, etal., Anesthesiology 1975 Mar;42(3):367-8.
5.	GOA pipeline	RGD automated data pipeline
6.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
7.	Comprehensive gene review and curation	RGD comprehensive gene curation

Additional References at PubMed

PMID:11115394	PMID:15663180

Genomics

Comparative Map Data

Msx3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	204,268,688 - 204,271,881 (-)	NCBI		GRCr8
mRatBN7.2	1	194,839,041 - 194,842,209 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	194,839,041 - 194,841,969 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	203,199,915 - 203,202,849 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	210,335,080 - 210,338,014 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	203,008,913 - 203,011,847 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	212,514,223 - 212,517,151 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	212,514,223 - 212,517,151 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	219,428,377 - 219,431,305 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	199,846,341 - 199,848,436 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	199,997,410 - 199,997,525 (-)	NCBI
Celera	1	192,516,231 - 192,519,165 (-)	NCBI		Celera
Cytogenetic Map	1	q41	NCBI

Msx3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	139,626,070 - 139,629,001 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	7	139,626,070 - 139,629,002 (-)	Ensembl		GRCm39 Ensembl
GRCm38	7	140,046,157 - 140,049,088 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	140,046,157 - 140,049,089 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	147,232,056 - 147,234,987 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	7	139,897,582 - 139,900,409 (-)	NCBI		MGSCv36	mm8
Celera	7	139,844,251 - 139,847,182 (-)	NCBI		Celera
Cytogenetic Map	7	F4	NCBI
cM Map	7	85.04	NCBI

Variants

Variants in Msx3
6 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	165
Count of miRNA genes:	131
Interacting mature miRNAs:	138
Transcripts:	ENSRNOT00000074875
Prediction methods:	Miranda
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
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
631670	Iddm10	Insulin dependent diabetes mellitus QTL 10	1.9		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	1	174133260	196383668	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
4889428	Stresp24	Stress response QTL 24		0.05	heart pumping trait (VT:2000009)	absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)	1	155866514	200866514	Rat
6480780	Insul18	Insulin level QTL 18	4.11		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	1	189607473	200611765	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
731168	Bp154	Blood pressure QTL 154	3.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	94642644	214537671	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
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
738032	Hcas5	Hepatocarcinoma susceptibility QTL 5	3.12		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	176426412	257976495	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
634312	Bp143	Blood pressure QTL 143	3	0.0002	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	182623426	219932796	Rat
634321	Hc1	Hypercalciuria QTL 1	2.91		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	1	178810256	240830002	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
7771612	Cm80	Cardiac mass QTL 80	8.4		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	1	149448574	221264292	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
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
1300145	Rf7	Renal function QTL 7	2.96		urine creatinine amount (VT:0010540)	urine creatinine level (CMO:0000125)	1	185145134	221264292	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
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
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	32737458	199368955	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
1354580	Scort1	Serum corticosterone level QTL 1	3.4		blood corticosterone amount (VT:0005345)	blood corticosterone level (CMO:0001172)	1	156677124	256448636	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
1354591	Cm36	Cardiac mass QTL 36	4.1		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	102813953	201278233	Rat
1354606	Bp246	Blood pressure QTL 246	3.6		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	1	102813953	218753816	Rat
1354615	Cm32	Cardiac mass QTL 32	5.2		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	1	102813953	201278233	Rat
1354618	Kidm15	Kidney mass QTL 15	5		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	1	156677124	201278233	Rat
1354620	Kidm19	Kidney mass QTL 19	4		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	151162512	201278233	Rat
1354624	Cm35	Cardiac mass QTL35	5.7		heart left ventricle mass (VT:0007031)	calculated heart weight (CMO:0000073)	1	177227632	256448636	Rat
1354634	Kidm12	Kidney mass QTL 12	3.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	1	151162512	201278233	Rat
1354636	Lmblg1	Limb length QTL 1	6.4		tibia length (VT:0004357)	tibia length (CMO:0000450)	1	151162512	201278233	Rat
1354646	Kidm18	Kidney mass QTL 18	5.7		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	151162512	256448636	Rat
1354652	Kidm20	Kidney mass QTL 20	4.3		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	1	177227632	256448636	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
1359018	Hrtrt20	Heart rate QTL 20	3.08		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	185356336	202902618	Rat
1549837	Hcar15	Hepatocarcinoma resistance QTL 15		0.05	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	153136852	260522016	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
1358886	Bp260	Blood pressure QTL 260	3.67		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	151162766	225824951	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
1549830	Bss1	Bone structure and strength QTL 1	4.8		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	1	172609619	217609619	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
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
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
61343	Bp28	Blood pressure QTL 28			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	151646613	196646613	Rat
61347	Bp197	Blood pressure QTL 197	4.2		arterial blood pressure trait (VT:2000000)	blood pressure measurement (CMO:0000003)	1	158633083	203633083	Rat
61348	Bp30	Blood pressure QTL 30	2.4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	144017057	197814409	Rat
70209	Niddm23	Non-insulin dependent diabetes mellitus QTL 23	2.82		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	94494440	198324465	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
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
2293083	Iddm25	Insulin dependent diabetes mellitus QTL 25	4.18		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	181829673	224569684	Rat
631205	Bp196	Blood pressure QTL 196	4	0.0001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	118944897	199050459	Rat
631214	Bw61	Body weight QTL61	3.4	0.0001	intramuscular adipose amount (VT:0010044)	intramuscular fat area (CMO:0001162)	1	173108781	218108781	Rat
631260	Tcas2	Tongue tumor susceptibility QTL 2	4.93		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	1	192485903	199050587	Rat
724531	Uae5	Urinary albumin excretion QTL 5	4		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	1	150700142	252085212	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
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
2303622	Vencon6	Ventilatory control QTL 6		0.001	respiration trait (VT:0001943)	respiration rate (CMO:0000289)	1	154561505	199561505	Rat
1354661	Bw33	Body weight QTL 33	5.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	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
1578763	Kidm29	Kidney mass QTL 29	3.3	0.0001	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	1	179567751	260522016	Rat
61378	Bp43	Blood pressure QTL 43	22.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	181746937	196383668	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
1354610	Bw34	Body weight QTL 34	4.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	256448636	Rat
2302378	Insul11	Insulin level QTL 11	3.25		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	1	144267353	251128347	Rat
1358294	Bw37	Body weight QTL 37	5	0.000011	body mass (VT:0001259)	body weight (CMO:0000012)	1	171310381	216310381	Rat
1354602	Bw35	Body weight QTL 35	12.2		body mass (VT:0001259)	body weight (CMO:0000012)	1	151162512	201278233	Rat
1558658	Bw59	Body weight QTL 59	3.5	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	1	178784622	223784622	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49393289	199050459	Rat
61341	Bp26	Blood pressure QTL 26			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	169537671	214537671	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
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	81591954	219808434	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
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
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
1331749	Hrtrt11	Heart rate QTL 11	2.973		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	94494440	198211706	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
619614	Bp78	Blood pressure QTL 78		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	169112897	197261052	Rat
619614	Bp78	Blood pressure QTL 78		0.001	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	169112897	197261052	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
631549	Bp89	Blood pressure QTL 89	5.7		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	123350581	201284552	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
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
70163	Bw20	Body weight QTL 20	5.1		body mass (VT:0001259)	body weight (CMO:0000012)	1	174133260	219133260	Rat
70160	Bw18	Body weight QTL 18	5.7		body mass (VT:0001259)	body weight (CMO:0000012)	1	144267353	196383668	Rat
619613	Bp77	Blood pressure QTL 77		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	164747424	209747424	Rat
619613	Bp77	Blood pressure QTL 77		0.01	arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	164747424	209747424	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
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

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

	endocrine system	hemolymphoid system	integumental system	musculoskeletal system	nervous system	reproductive system	respiratory system	appendage
High
Medium
Low			3	5	35	7	9	3
Below cutoff	6	1	4	5	32	10	2	4

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053712	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039107708	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB197924	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF390078	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000074875 ⟹ ENSRNOP00000067831

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	194,839,041 - 194,841,969 (-)	Ensembl
Rnor_6.0 Ensembl	1	212,514,223 - 212,517,151 (-)	Ensembl

RefSeq Acc Id:

NM_053712 ⟹ NP_446164

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	204,268,688 - 204,271,616 (-)	NCBI
mRatBN7.2	1	194,839,041 - 194,841,969 (-)	NCBI
Rnor_6.0	1	212,514,223 - 212,517,151 (-)	NCBI
Rnor_5.0	1	219,428,377 - 219,431,305 (-)	NCBI
Celera	1	192,516,231 - 192,519,165 (-)	NCBI

Sequence:

show sequence

CACGGAACCCAGGGACCTGGCAAAATAAACCGCCGTTGGGTTTTACGCGTCTCAGTCAGGCGGC
TAGCCCGCACCCGCTATCCCATGCATGGCCCGGGCAACACTCGACATGAACGCGGCGGGGCTCG
AAGCTCGCGGCGGGGGCCACATAGAGCAGGGACCACTCCCCTTCAGCGTCGAGTCACTGCTGGA
GGCTGAGCGCGTAAGGGGCTCCGAGTCTGGGGAGCTGGGGGAGGAGAGGCCGCCCGGCGCCTCG
AAGCCTGGAGCCTGGCCCCCACCGGTCGCGCACTCATGCCCCCCACGTGCCCCCAGCCCTCCAC
CCTGCACCCTTCGCAAACACAAAACCAATCGCAAACCACGAACACCCTTCACCACCGCGCAGCT
GCTGGCTCTGGAGCGCAAGTTTCACCAGAAGCAATACTTGTCCATTGCCGAGCGCGCCGAGTTC
TCCAGCAGCTTGAGCCTCACTGAAACTCAGGTCAAGATCTGGTTTCAGAATCGCCGAGCCAAGG
CCAAGCGGCTGCAGGAGGCCGAGCTGGAGAAGCTGAAGCTGACTGCCAAGCCACTACTGCCGGC
GGCATTTGCCCTTCCCTTCCCACTGGGCACCCAGCTGCACAGCTCCGCCGCCACTTTCGGCGGC
AACGCTGTTCCTGGGATCCTCGCTGGGCCGGTCGCGGCTTATGGCATGTACTACTTGTCTTAGA
GCATGGAACCAAGTCTTAACCTCTTGGTTAGGCTCAGGGCTGCGCCGCAGTTCCGCCCGCCGCT
GATGCTCCTGGTAACTTCTTGACCTTTCATTTTAGAGTTTTGGGGTTTTTTTTTCCTCCCTGTT
ATACGATATACTTGATGACTGGAGCCTATTTATAGATATAACAGATATTTTAAACCTTCCTAAA
ACCATGTCCATGTCTGAAGGAAAACACAACTTCATACAGTCCTTGGAACGGACAAAAGCAGATC
TTCCTATTTCGTACAAAGCAGTCGAGAAAGTACTTCTGGGGTGGGTGTGCTCCTTGTATTCACT
CTGCCCCTACACTGAGGACTTCAGAGAGGCTCGATTGAACTGGCATAAGCAAACAAATTCCATA
AGATGAAGTTAAAATACTGATGAGATAATCGGACTGTTAGAAAGACACTTAGAAATTACCACTT
CAACTAAATGTGCGTTGTGACCAAACGGAAACTTCTACGCGATTTAGGTTTTACCCCATTATTA
TTTATTTAGAGTATACGTCGTTCAAGGAGCTAGAGGCAAAATGCTGACTGTGCATGAGAGTAGG
GGAGGTGATGAACGCTGGCACCATGCCTCAAAGGAAGGGTGGCTGCCAGGCAGCACCTTCTGAG
CTTTGAAAGGAGCCTGCTGGGGAGACAGAAGGCTGGTGGCAGCAGGCAGCAGGGACCAAAGCCT
CGCCTCCTGCCAGCAGGTGTCCAACCAATAAAGAGAAGAAACTGAGGGTTGAGTGCCTCAAACC
TCCGTTGTGGGTGCAGTAGGAGGCGAGGCCTGCAAAGGTCCCAAAAGAATTACTCTGAGTGCCA
GCTGCCCCTGTAATCCTGATGTGCCTTAGAAAAATGGTGGACTTGTTTAGGAATCTGGACTTGT
ACATTTATTCTACCTTTATCTGAGGAAAGAAAGCAGATCATCTGAGCTGTTCTGTCCCACTGCC
CCTAATGGAGTCTCAACCCTATCACGCAAGATCGAGGCTCTTCGGGTACCTGACAACCAGCACT
GATAAAACCTGTGGCTGTTTCCATAGCAAGCTTTGGCCACAGTCTGGAGACTTTAGTGGAGTGT
GGAAGGCTCACAAAGGTCCCCTGGAGTCACGCCTAGTACCACTGACAAGGCCCGTCCTTCCAGC
CTTCAAGCTGGAGAGGAAGAACCTGGCTGCAGGGGTCTGGGGTTGTGTGTTCGTGAAGGGAGGA
CCAGGAATTTTACAGTGATGGATGGCCCTGGGTTAGGATGTTCTGCTTGGGAGGAGGGGAAGGA
CTGGGCTATGCTCAGCAGTCCCAGTCAACTCCAGGAAAACTGCTGTCCTTGGACCTTCACTGGT
CCATCTGCTCCAAATAAAGCAAAAAAGATGATATTGCATGGGACTGCCTATTGATACCTATTGA
CATTCCTCTGCCCTGTGTCTCCTGGGAAAATGGATACCAGAAAGGTTTTGTTTTGTTTTGTTTT
GAGACAAAACCATCACTAGGTAGTCCCAACAGACCTAATAGAAAATAGACTTGCTATTCTCCAA
GGATGGCCTTAGACTCACAAAGGTCCACTTTAATCCCAAGTGCTGGGATTAAAGACATACAGCA
CAATGC

hide sequence

RefSeq Acc Id:

XM_039107708 ⟹ XP_038963636

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	204,270,537 - 204,271,881 (-)	NCBI
mRatBN7.2	1	194,840,890 - 194,842,209 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_446164	(Get FASTA)	NCBI Sequence Viewer
	XP_038963636	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAK70505	(Get FASTA)	NCBI Sequence Viewer
	BAE92723	(Get FASTA)	NCBI Sequence Viewer
	EDM11881	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000067831
	ENSRNOP00000067831.1

RefSeq Acc Id:

NP_446164 ⟸ NM_053712

- UniProtKB:

G3V8C7 (UniProtKB/TrEMBL), A6HXE9 (UniProtKB/TrEMBL), A6HXF0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MARATLDMNAAGLEARGGGHIEQGPLPFSVESLLEAERVRGSESGELGEERPPGASKPGAWPPP
VAHSCPPRAPSPPPCTLRKHKTNRKPRTPFTTAQLLALERKFHQKQYLSIAERAEFSSSLSLTE
TQVKIWFQNRRAKAKRLQEAELEKLKLTAKPLLPAAFALPFPLGTQLHSSAATFGGNAVPGILA
GPVAAYGMYYLS

hide sequence

RefSeq Acc Id:

ENSRNOP00000067831 ⟸ ENSRNOT00000074875

RefSeq Acc Id:	XP_038963636 ⟸ XM_039107708
- Peptide Label:	isoform X1

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-G3V8C7-F1-model_v2	AlphaFold	G3V8C7	1-204	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620932	AgrOrtholog
BioCyc Gene	G2FUF-57065	BioCyc
Ensembl Genes	ENSRNOG00000046776	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000074875	ENTREZGENE
	ENSRNOT00000074875.2	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/TrEMBL
	Homeodomain	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	HTH_motif	UniProtKB/TrEMBL
KEGG Report	rno:114504	UniProtKB/TrEMBL
NCBI Gene	114504	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN MSX	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN MSX-3	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
PhenoGen	Msx3	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
	HTHREPRESSR	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000046776	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	A6HXE9	ENTREZGENE, UniProtKB/TrEMBL
	A6HXF0	ENTREZGENE, UniProtKB/TrEMBL
	G3V8C7	ENTREZGENE, UniProtKB/TrEMBL
	Q1XIC9_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-08-14	Msx3	msh homeobox 3	Msx3	homeo box, msh-like 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Msx3	homeo box, msh-like 3			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Msx3	homeo box, msh-like 3			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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