Msx2 (msh homeobox 2) - Rat Genome Database

Name: Msx2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Msx2 (msh homeobox 2) Rattus norvegicus

Analyze

Symbol:

Msx2

Name:

msh homeobox 2

RGD ID:

3116

Description:

Enables DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including cartilage development; osteoblast development; and transcription by RNA polymerase II. Predicted to be located in cytosol and nuclear speck. Predicted to be part of transcription regulator complex. Biomarker of hypertension. Human ortholog(s) of this gene implicated in craniosynostosis and parietal foramina. Orthologous to human MSX2 (msh homeobox 2); INTERACTS WITH 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 2,6-dinitrotoluene; 3,7-dihydropurine-6-thione.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

homeobox protein Hox-8-1; homeobox protein MSX-2; hox-8.1; Msh (Drosophila) homeo box homolog; msh homeo box homolog 2; msh homeo box homolog 2 (Drosophila)

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	MSX2 (msh homeobox 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Msx2 (msh homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Msx2 (msh homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	MSX2 (msh homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	MSX2 (msh homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Msx2 (msh homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	MSX2 (msh homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	MSX2 (msh homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Msx2 (msh homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Mus musculus (house mouse):	Msx2 (msh homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|SonicParanoid)
Homo sapiens (human):	MSX2 (msh homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|SonicParanoid)
Danio rerio (zebrafish):	msx2b (muscle segment homeobox 2b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PhylomeDB)
Danio rerio (zebrafish):	msx2a (muscle segment homeobox 2a)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector)
Xenopus tropicalis (tropical clawed frog):	msx2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|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
mRatBN7.2	17	11,097,214 - 11,102,879 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	17	11,097,103 - 11,102,879 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	17	11,105,528 - 11,111,192 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	17	12,641,862 - 12,647,525 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	17	11,104,006 - 11,109,669 (+)	NCBI	Rnor_WKY
Rnor_6.0	17	11,683,862 - 11,689,527 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	17	11,683,862 - 11,689,527 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	17	13,785,024 - 13,790,689 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	17,243,262 - 17,248,927 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	17	17,247,335 - 17,247,755 (+)	NCBI
Celera	17	11,158,359 - 11,164,024 (+)	NCBI		Celera
RH 3.4 Map	17	109.2	RGD
Cytogenetic Map	17	p14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Craniofacial Abnormalities (ISO)

craniosynostosis (ISO,ISS)

Craniosynostosis 2 (ISO)

Craniosynostosis Syndrome, Autosomal Recessive (ISO)

Female Urogenital Diseases (ISO)

Femoral Fractures (IEP)

genetic disease (ISO)

hypertension (IEP)

parietal foramina (ISO)

Parietal Foramina 1 (ISO)

Parietal Foramina with Cleidocranial Dysplasia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine (EXP)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

2,6-dinitrotoluene (EXP)

2-ethylhexan-1-ol (ISO)

3,7-dihydropurine-6-thione (EXP)

4,4'-sulfonyldiphenol (ISO)

5-fluorouracil (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

arsenite(3-) (ISO)

arsenous acid (ISO)

belinostat (ISO)

benzalkonium chloride (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (EXP)

cadmium sulfate (ISO)

calcitriol (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

cobalt dichloride (ISO)

copper atom (EXP)

copper(0) (EXP)

coumestrol (ISO)

Cuprizon (EXP)

deoxynivalenol (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

diethylstilbestrol (ISO)

dioxygen (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

entinostat (ISO)

folic acid (ISO)

furan (EXP)

genistein (ISO)

glycerol 2-phosphate (ISO)

hexaconazole (ISO)

L-ascorbic acid (ISO)

lead diacetate (ISO)

lipopolysaccharide (ISO)

manganese(II) chloride (EXP)

mercaptopurine (EXP)

mercury dibromide (ISO)

methapyrilene (ISO)

methylmercury chloride (ISO)

Muraglitazar (EXP)

N-methyl-4-phenylpyridinium (EXP)

N-nitrosodiethylamine (EXP)

p-chloromercuribenzoic acid (ISO)

panobinostat (ISO)

phenethyl caffeate (EXP)

phenylmercury acetate (ISO)

progesterone (ISO)

purine-6-thiol (EXP)

retinyl acetate (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sunitinib (ISO)

tebuconazole (ISO)

Tesaglitazar (EXP)

triadimefon (EXP)

trichostatin A (ISO)

tripotassium phosphate (EXP)

troglitazone (EXP)

valproic acid (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of meiosis (IEA,ISO)

anterior/posterior pattern specification (IEA,ISO)

BMP signaling pathway (ISO)

BMP signaling pathway involved in heart development (IEA,ISO)

bone morphogenesis (ISO)

bone trabecula formation (IEA,ISO)

branching involved in mammary gland duct morphogenesis (IEA,ISO)

cartilage development (IMP,ISO)

cellular response to estradiol stimulus (IEA,ISO)

cellular response to growth factor stimulus (ISO)

chondrocyte development (IEA,ISO)

embryonic digit morphogenesis (ISO)

embryonic forelimb morphogenesis (IEA,ISO)

embryonic hindlimb morphogenesis (IEA,ISO)

embryonic limb morphogenesis (ISO)

embryonic nail plate morphogenesis (IEA,ISO)

enamel mineralization (IEA,ISO)

endochondral bone growth (IEA,ISO)

epithelial to mesenchymal transition involved in endocardial cushion formation (IEA,ISO)

frontal suture morphogenesis (IEA,ISO)

mammary gland epithelium development (ISO)

mesenchymal cell apoptotic process (IEA,ISO)

negative regulation of apoptotic process (IEA,ISO)

negative regulation of cell population proliferation (IEA,ISO)

negative regulation of CREB transcription factor activity (IEA,ISO)

negative regulation of DNA-templated transcription (ISO,ISS)

negative regulation of fat cell differentiation (IEA,ISO)

negative regulation of keratinocyte differentiation (IEA,ISO)

negative regulation of transcription by RNA polymerase II (IEA,ISO,ISS)

negative regulation of transcription regulatory region DNA binding (IEA,ISO)

odontogenesis (ISO)

ossification (ISO)

osteoblast development (IEA,IEP,ISO)

osteoblast differentiation (ISO,ISS)

outflow tract morphogenesis (ISO)

outflow tract septum morphogenesis (IEA,ISO)

positive regulation of apoptotic process (IMP)

positive regulation of BMP signaling pathway (IEA,ISO)

positive regulation of mesenchymal cell apoptotic process (IEA,ISO)

positive regulation of osteoblast differentiation (IEA,ISO)

positive regulation of response to biotic stimulus (IMP)

positive regulation of timing of catagen (IEA,ISO)

regulation of apoptotic process (ISO)

signal transduction involved in regulation of gene expression (IEA,ISO)

stem cell differentiation (IEA,ISO)

transcription by RNA polymerase II (IDA)

wound healing (ISO)

wound healing, spreading of epidermal cells (IEA,ISO)

Cellular Component

cytosol (ISO)

nuclear speck (ISO)

nucleus (IEA)

transcription regulator complex (IEA,ISO)

Molecular Function

DNA binding (ISO)

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

DNA-binding transcription repressor activity, RNA polymerase II-specific (IEA,ISO)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IDA)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (IEA,ISO)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (ISO)

transcription cis-regulatory region binding (ISO,ISS)

References

References - curated

#	Reference Title	Reference Citation
1.	Individual osteoblasts in the developing calvaria express different gene repertoires.	Candeliere GA, etal., Bone. 2001 Apr;28(4):351-61.
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 GOA human gene data--August 2006	GOA data from the GO Consortium
4.	Msx-2 and p21 mediate the pro-apoptotic but not the anti-proliferative effects of BMP4 on cultured sympathetic neuroblasts.	Gomes WA and Kessler JA, Dev Biol. 2001 Sep 1;237(1):212-21.
5.	[Molecular cloning, expression of rat Msx-1 and Msx-2 during early embryo genesis and roles for mandibular chondrogenesis]	Ishiguro S Kokubyo Gakkai Zasshi. 1999 Mar;66(1):33-45.
6.	Msx2 and p21(CIP1/WAF1) mediate the proapoptotic effects of bone morphogenetic protein-4 on ventricular zone progenitor cells.	Israsena N and Kessler JA, J Neurosci Res 2002 Sep 15;69(6):803-9.
7.	Regulation of MT melatonin receptor expression in the foetal rat pituitary.	Johnston JD, etal., J Neuroendocrinol. 2006 Jan;18(1):50-6.
8.	Calcification of aortic smooth muscle cells isolated from spontaneously hypertensive rats.	Kanemaru K, etal., J Pharmacol Sci. 2008 Feb;106(2):280-6. Epub 2008 Feb 9.
9.	High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence.	Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
10.	The molecular basis of Boston-type craniosynostosis: the Pro148-->His mutation in the N-terminal arm of the MSX2 homeodomain stabilizes DNA binding without altering nucleotide sequence preferences.	Ma L, etal., Hum Mol Genet. 1996 Dec;5(12):1915-20.
11.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
12.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
13.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
14.	GOA pipeline	RGD automated data pipeline
15.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
17.	Comprehensive gene review and curation	RGD comprehensive gene curation
18.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
19.	Msx-2/Hox 8.1: a transcriptional regulator of the rat osteocalcin promoter.	Towler DA, etal., Mol Endocrinol. 1994 Nov;8(11):1484-93.
20.	Functional haploinsufficiency of the human homeobox gene MSX2 causes defects in skull ossification.	Wilkie AO, etal., Nat Genet. 2000 Apr;24(4):387-90.

Additional References at PubMed

PMID:7848824	PMID:8787747	PMID:8861098	PMID:8889548	PMID:9073066	PMID:9265625	PMID:10742104	PMID:11668602	PMID:11744114	PMID:14671321	PMID:15175325	PMID:15383550
PMID:15456894	PMID:15930102	PMID:16115867	PMID:17030628	PMID:17601530	PMID:17693062	PMID:18285513	PMID:18590716	PMID:18667074	PMID:18729207	PMID:19422820	PMID:19769717
PMID:20843790	PMID:21465616	PMID:21503878	PMID:21512281	PMID:22071108	PMID:33691558

Genomics

Comparative Map Data

Msx2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	17	11,097,214 - 11,102,879 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	17	11,097,103 - 11,102,879 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	17	11,105,528 - 11,111,192 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	17	12,641,862 - 12,647,525 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	17	11,104,006 - 11,109,669 (+)	NCBI	Rnor_WKY
Rnor_6.0	17	11,683,862 - 11,689,527 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	17	11,683,862 - 11,689,527 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	17	13,785,024 - 13,790,689 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	17	17,243,262 - 17,248,927 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	17	17,247,335 - 17,247,755 (+)	NCBI
Celera	17	11,158,359 - 11,164,024 (+)	NCBI		Celera
RH 3.4 Map	17	109.2	RGD
Cytogenetic Map	17	p14	NCBI

MSX2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	174,724,582 - 174,730,896 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	5	174,724,582 - 174,730,896 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	5	174,151,585 - 174,157,899 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	174,084,181 - 174,090,508 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	5	174,084,207 - 174,090,507	NCBI
Celera	5	170,185,579 - 170,191,910 (+)	NCBI		Celera
Cytogenetic Map	5	q35.2	NCBI
HuRef	5	169,246,978 - 169,253,303 (+)	NCBI		HuRef
CHM1_1	5	173,583,988 - 173,590,298 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	5	175,263,949 - 175,271,855 (+)	NCBI		T2T-CHM13v2.0

Msx2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	53,620,917 - 53,626,816 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	13	53,620,920 - 53,627,110 (-)	Ensembl		GRCm39 Ensembl
GRCm38	13	53,466,881 - 53,472,780 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	53,466,884 - 53,473,074 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	13	53,562,250 - 53,568,149 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	13	53,475,420 - 53,480,608 (-)	NCBI		MGSCv36	mm8
Celera	13	54,545,172 - 54,551,024 (-)	NCBI		Celera
Cytogenetic Map	13	B1	NCBI
cM Map	13	27.84	NCBI

Msx2
(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_004955408	27,323,360 - 27,329,755 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955408	27,323,405 - 27,329,484 (+)	NCBI	ChiLan1.0	ChiLan1.0

MSX2
(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	5	167,985,531 - 167,992,667 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	5	170,063,137 - 170,070,226 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	5	176,968,315 - 176,974,679 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	5	176,967,902 - 176,976,609 (+)	Ensembl	panpan1.1		panPan2

MSX2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	4	38,002,724 - 38,007,407 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	4	38,002,428 - 38,007,407 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	4	37,948,799 - 37,953,445 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	4	38,376,184 - 38,380,830 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	4	38,375,888 - 38,381,225 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	4	38,192,821 - 38,197,476 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	4	38,380,991 - 38,385,645 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	4	38,891,167 - 38,895,822 (-)	NCBI		UU_Cfam_GSD_1.0

Msx2
(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_024407213	92,492,782 - 92,498,921 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936609	1,216,436 - 1,221,561 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936609	1,216,436 - 1,221,528 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

MSX2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	16	49,765,910 - 49,771,789 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	16	49,765,587 - 49,771,745 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

MSX2
(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	23	76,873,499 - 76,879,935 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	23	76,873,669 - 76,879,553 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666034	1,717,428 - 1,723,746 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Msx2
(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_004624733	15,288,326 - 15,294,568 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624733	15,288,417 - 15,294,481 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Msx2
5 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	143
Count of miRNA genes:	99
Interacting mature miRNAs:	123
Transcripts:	ENSRNOT00000024766
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
9590316	Scort21	Serum corticosterone level QTL 21	4.75	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	17	1	22871563	Rat
10401807	Kidm52	Kidney mass QTL 52			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	17	1	31701463	Rat
70184	BpQTLcluster14	Blood pressure QTL cluster 14	3.38		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	17	1	31990913	Rat
631207	Niddm41	Non-insulin dependent diabetes mellitus QTL 41			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	17	1	37830672	Rat
1354658	Spl8	Serum phospholipid level QTL 8	3.8		blood VLDL phospholipid amount (VT:0010507)	blood very low density lipoprotein phospholipid level (CMO:0001571)	17	1	60781592	Rat
1354581	Bp247	Blood pressure QTL 247	4.5		arterial blood pressure trait (VT:2000000)	pulse pressure (CMO:0000292)	17	1	69599340	Rat
1354662	Rf49	Renal function QTL 49	2.9		blood creatinine amount (VT:0005328)	plasma creatinine level (CMO:0000537)	17	1	69599340	Rat
1641902	Colcr7	Colorectal carcinoma resistance QTL 7	3.35	0.0044	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	17	2115149	21881669	Rat
1300123	Bp194	Blood pressure QTL 194	2.82		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	17	2115149	34551001	Rat
631499	Stl1	Serum triglyceride level QTL 1	3.6		blood triglyceride amount (VT:0002644)	blood triglyceride level (CMO:0000118)	17	3271398	27389946	Rat
2324619	Coatc4	Coat color QTL 4		0.001	coat/hair pigmentation trait (VT:0010463)	pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)	17	4299130	21293263	Rat
2324619	Coatc4	Coat color QTL 4		0.001	coat/hair pigmentation trait (VT:0010463)	pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)	17	4299130	21293263	Rat
1354613	Kidm14	Kidney mass QTL 14	6.2		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	17	4299130	35837242	Rat
1354596	Bw32	Body weight QTL 32	4.5		body mass (VT:0001259)	body weight (CMO:0000012)	17	4299130	60781592	Rat
1354630	Cm34	Cardiac mass QTL 34	8.7		heart left ventricle mass (VT:0007031)	heart left ventricle wet weight (CMO:0000071)	17	4299130	69599340	Rat
1354638	Insul1	Insulin level QTL 1	4.8		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	17	4299130	69599340	Rat
1354651	Lmblg2	Limb length QTL 2	6		tibia length (VT:0004357)	tibia length (CMO:0000450)	17	4299130	69599340	Rat
2293648	Bmd31	Bone mineral density QTL 31	4.5	0.0001	femur size trait (VT:1000369)	femoral neck cortical cross-sectional area (CMO:0001702)	17	4354487	27028127	Rat
2293664	Bmd28	Bone mineral density QTL 28	5.1	0.0001	femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	17	4354487	27028127	Rat
2303627	Vencon8	Ventilatory control QTL 8		0.001	respiration trait (VT:0001943)	tidal volume (CMO:0000222)	17	4528038	49528038	Rat
10054088	Scort28	Serum corticosterone level QTL 28	2.04	0.0102	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	17	4528038	49528038	Rat
1581553	Pur14	Proteinuria QTL 14	5.3	0.0001	urine total protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	17	7979968	16317111	Rat
2303561	Bw91	Body weight QTL 91	2		body mass (VT:0001259)	body weight (CMO:0000012)	17	8868462	53868462	Rat
1582199	Insul5	Insulin level QTL 5	3.4	0.0119	blood insulin amount (VT:0001560)	calculated serum insulin level (CMO:0000359)	17	9201365	23653323	Rat
1582208	Kidm32	Kidney mass QTL 32	3.9	0.0018	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	17	9201365	23653323	Rat
1582224	Epfw4	Epididymal fat weight QTL 4	3.5	0.0058	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	17	9201365	23653323	Rat
1582225	Bw67	Body weight QTL 67	6.2	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
1582226	Bw64	Body weight QTL 64	4.2	0.0017	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
1582241	Bw70	Body weight QTL 70	4.6	0.0003	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
1582245	Bw73	Body weight QTL 73	4.6	0.0004	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
1582258	Bw76	Body weight QTL 76	4.6	0.0005	body mass (VT:0001259)	body weight (CMO:0000012)	17	9201365	23653323	Rat
2300002	Iddm36	Insulin dependent diabetes mellitus QTL 36	1.98		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	17	9991286	40540197	Rat

Markers in Region

RH132753

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	11,101,730 - 11,101,950 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	11,688,379 - 11,688,598	NCBI	Rnor6.0
Rnor_5.0	17	13,789,541 - 13,789,760	UniSTS	Rnor5.0
RGSC_v3.4	17	17,247,779 - 17,247,998	UniSTS	RGSC3.4
Celera	17	11,162,876 - 11,163,095	UniSTS
RH 3.4 Map	17	110.7	UniSTS
Cytogenetic Map	17	p14	UniSTS

RH142308

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	11,101,436 - 11,101,623 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	11,688,085 - 11,688,271	NCBI	Rnor6.0
Rnor_5.0	17	13,789,247 - 13,789,433	UniSTS	Rnor5.0
RGSC_v3.4	17	17,247,485 - 17,247,671	UniSTS	RGSC3.4
Celera	17	11,162,582 - 11,162,768	UniSTS
RH 3.4 Map	17	109.2	UniSTS
Cytogenetic Map	17	p14	UniSTS

BI284209

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	11,102,483 - 11,102,686 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	11,689,132 - 11,689,334	NCBI	Rnor6.0
Rnor_5.0	17	13,790,294 - 13,790,496	UniSTS	Rnor5.0
RGSC_v3.4	17	17,248,532 - 17,248,734	UniSTS	RGSC3.4
Celera	17	11,163,629 - 11,163,831	UniSTS
RH 3.4 Map	17	107.8	UniSTS
Cytogenetic Map	17	p14	UniSTS

BE103912

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	17	11,102,640 - 11,102,799 (+)	MAPPER	mRatBN7.2
Rnor_6.0	17	11,689,289 - 11,689,447	NCBI	Rnor6.0
Rnor_5.0	17	13,790,451 - 13,790,609	UniSTS	Rnor5.0
RGSC_v3.4	17	17,248,689 - 17,248,847	UniSTS	RGSC3.4
Celera	17	11,163,786 - 11,163,944	UniSTS
RH 3.4 Map	17	110.2	UniSTS
Cytogenetic Map	17	p14	UniSTS

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

	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	8							14		7
Low	35	6	6		6	1	1	56	24	23		1
Below cutoff		11	2	9	2	7	9	4	11	9	11	7

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_012982	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BF414483	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474032	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000284	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U12514	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000024766 ⟹ ENSRNOP00000024765

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	17	11,097,103 - 11,102,879 (+)	Ensembl
Rnor_6.0 Ensembl	17	11,683,862 - 11,689,527 (+)	Ensembl

RefSeq Acc Id:

NM_012982 ⟹ NP_037114

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	17	11,097,214 - 11,102,879 (+)	NCBI
Rnor_6.0	17	11,683,862 - 11,689,527 (+)	NCBI
Rnor_5.0	17	13,785,024 - 13,790,689 (+)	NCBI
RGSC_v3.4	17	17,243,262 - 17,248,927 (+)	RGD
Celera	17	11,158,359 - 11,164,024 (+)	RGD

Sequence:

show sequence

ATGGCTTCTCCGTCCAAAGGCGGTGACTTGTTTTCGTCTGATGAGGAGGGCCCCGCGGTGCTGG
CCGGCCCGGGCCCCGGGCCTGGAGGAGCCGAGGGCGGCGCGGAGGAGCGCAGGGTCAAGGTCTC
CAGCCTGCCCTTCAGCGTGGAGGCGCTCATGTCCGACAAGAAGCCGCCCAAGGAATCGCCCGCG
GTGCCACCCGACTGCGCCTCGGCTGGCGCTGTCCTGCGGCCGCTGTTGCTGCCGGGACACGGCG
TCCGGGACGCTCACAGTCCCGGGCCTCTCGTCAAGCCCTTCGAGACCGCCTCGGTCAAGTCGGA
AAATTCCGAAGACGGAGCGCCGTGGATACAGGAGCCCGGCAGATACTCCCCGCCGCCCAGACAC
ATGAGCCCCACCACCTGCACCCTGAGGAAACACAAGACCAACCGGAAGCCACGCACACCGTTCA
CCACGTCCCAGCTTCTAGCCTTGGAGCGCAAGTTCCGCCAGAAACAGTACCTCTCCATCGCAGA
GCGGGCCGAGTTCTCCAGCTCTCTGAACCTTACAGAAACCCAGGTCAAAATCTGGTTCCAGAAC
CGAAGGGCTAAGGCAAAAAGACTGCAGGAGGCGGAACTGGAAAAGCTGAAAATGGCTGCCAAAC
CTATGCTGCCCTCGGGCTTCAGTCTGCCCTTCCCTATCAACTCCCCCTTGCAAGCGGCATCCAT
ATACAGCGCCTCCTACCCCTTCCATAGACCTGTGCTTCCCATCCCGCCTGTGGGACTCTATGCC
ACGCCGGTGGGATATGGCATGTACCATCTATCCTAAAGAAGACCAGATGGACACACTCTAGGAT
GGATGTTTGTGGAAAGCATTCCCCTCCCTCTCCAGGAAGGCGGTGCCAATTTTGCTCCTGAACG
CAAACCCTGCGTTGTCGCCCTAAGCAACAGGCCTGTGGGGGGGCCACTTGATACAGAGTGAATT
TGTTATTTACGTGAGAGGCACTAAGACCGATTTTGTTTTCATAATTTCCCAAATGTCCCCTTTT
CCTCTCACAGTTATTGGCTCTGCTAGTTTTTATGTATAAATATATAATAAAATATAAGACTTTT
TATATGCCAGATGTAAAAATTCAAGTTATTTTGGAAGGCAAAATTTATATATACGCTTATCCAT
TTTTCTAGATAGCATTTTCTTAAGATATTGTGTTTAGTCCATTTGCTACCTTTTCTTAAAGGGA
AAGAGATTTGTTTGCAGAACTTTCAAGGAGGATGGACTTGCTTATGGAGGACATGCCAGGAGTA
GACATAGTGCATACAAGATACAGTTTCAGATATATTCTTGCAAGGGAAGGGGGATGTGTAACAT
GTTCTTATGCATTTTAGGTGCGTAAGAAACAAAACCTCTTGAGATGCACATTTGATCTTATTTT
TCTCTCTTCTCCATTCCATGTTGTCAAATCTGAGGATAACTCTGAGAATTACTCAGGGTAAAAG
TGGGATTCCATTTCAGGGCCCTGGCGTGCGAGGGTTTAGAAGATAAAACTTGTGTAGGAATTGG
TTTCTGTGAAATGCTAACTACATCAGTCCTCACAGGGCACAGAGGAGATTGCAAGAGGGCGTAG
TTAAATATCTGCTTAGAAATGAGTGTCTTGTAACTGTTGCCTATATTTGAAAGATTCTTCAACA
GTCCATAGAATCAGGAAGGGGAAAAAATGCTTTCTCTCTGTGTGTGTGTACTTACTGTATGTGC
TAAATGTATTAGGGACTCGAACGTGTTTGGGGTAGACAATGAAGCCATGTGTTGGGCTTGGTGG
AAACAAACGGTGTTGTCAGACAACACAGTCAGCTAGCCCCTTGGTCTTTCACCTGCCTGTCCAC
CTCTTCCCAATATATTTTTATCCCGTTGAAAGGGTATCTTGTATAATTTTATATATTTTATTGA
AGAGTTATTTCTTATCTCATACTCTGAATTAAATTAAAATGTTTTATTGCAGTAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_037114	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA20669	(Get FASTA)	NCBI Sequence Viewer
	EDL94072	(Get FASTA)	NCBI Sequence Viewer
	P52953	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_037114 ⟸ NM_012982

- UniProtKB:

G3V8D1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MASPSKGGDLFSSDEEGPAVLAGPGPGPGGAEGGAEERRVKVSSLPFSVEALMSDKKPPKESPA
VPPDCASAGAVLRPLLLPGHGVRDAHSPGPLVKPFETASVKSENSEDGAPWIQEPGRYSPPPRH
MSPTTCTLRKHKTNRKPRTPFTTSQLLALERKFRQKQYLSIAERAEFSSSLNLTETQVKIWFQN
RRAKAKRLQEAELEKLKMAAKPMLPSGFSLPFPINSPLQAASIYSASYPFHRPVLPIPPVGLYA
TPVGYGMYHLS

hide sequence

RefSeq Acc Id:

ENSRNOP00000024765 ⟸ ENSRNOT00000024766

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P52953-F1-model_v2	AlphaFold	P52953	1-139	view protein structure

Transcriptome

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

Promoters

RGD ID:

13700329

Promoter ID:

EPDNEW_R10853

Type:

initiation region

Name:

Msx2_1

Description:

msh homeobox 2

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	17	11,683,799 - 11,683,859	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3116	AgrOrtholog
BioCyc Gene	G2FUF-10135	BioCyc
Ensembl Genes	ENSRNOG00000018355	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000024765	ENTREZGENE
	ENSRNOP00000024765.2	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000024766	ENTREZGENE
	ENSRNOT00000024766.4	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HTH_motif	UniProtKB/Swiss-Prot
KEGG Report	rno:25483	UniProtKB/TrEMBL
NCBI Gene	25483	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN MSX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX PROTEIN MSX-2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Msx2	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HTHREPRESSR	UniProtKB/Swiss-Prot
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	HOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR	TC232949
UniProt	G3V8D1	ENTREZGENE, UniProtKB/TrEMBL
	MSX2_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-02-15	Msx2	msh homeobox 2	Msx2	msh homeo box homolog 2 (Drosophila)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-11-06	Msx2	msh homeo box homolog 2 (Drosophila)		Msh (Drosophila) homeo box homolog	Name updated	625702	APPROVED
2002-06-10	Msx2	Msh (Drosophila) homeo box homolog			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_process	mediates the proapoptotic effects of BMP4 on VZ progenitor cells	727419

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 - MGI

Imported Disease Annotations - OMIM

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Imported Disease Annotations - ClinVar

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