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) Ictidomys tridecemlineatus

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Symbol:

Msx2

Name:

msh homeobox 2

RGD ID:

12661718

Description:

ENCODES a protein that exhibits DNA-binding transcription factor activity, RNA polymerase II-specific (ortholog); RNA polymerase II cis-regulatory region sequence-specific DNA binding (ortholog); INVOLVED IN activation of meiosis (ortholog); anterior/posterior pattern specification (ortholog); BMP signaling pathway (ortholog); ASSOCIATED WITH Craniofacial Abnormalities (ortholog); craniosynostosis (ortholog); Craniosynostosis 2 (ortholog); FOUND IN cytosol (inferred); nuclear speck (inferred); nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

homeobox protein MSX-2

RGD Orthologs

Alliance Orthologs

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)	NCBI	Ortholog
Mus musculus (house mouse):	Msx2 (msh homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	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
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

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

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 Ensembl
SpeTri2.0	NW_004936609	1,216,436 - 1,221,528 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

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)

Craniosynostosis 2 (ISO)

Craniosynostosis Syndrome, Autosomal Recessive (ISO)

Female Urogenital Diseases (ISO)

Femoral Fractures (ISO)

genetic disease (ISO)

hypertension (ISO)

parietal foramina (ISO)

Parietal Foramina 1 (ISO)

Parietal Foramina with Cleidocranial Dysplasia (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 (IEA,ISO)

bone morphogenesis (IEA,ISO)

bone trabecula formation (IEA,ISO)

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

cartilage development (IEA,ISO)

cell surface receptor signaling pathway involved in heart development (IEA,ISO)

cellular response to estradiol stimulus (IEA,ISO)

cellular response to growth factor stimulus (IEA,ISO)

chondrocyte development (IEA,ISO)

embryonic digit morphogenesis (IEA,ISO)

embryonic forelimb morphogenesis (IEA,ISO)

embryonic hindlimb morphogenesis (IEA,ISO)

embryonic limb morphogenesis (IEA,ISO)

embryonic morphogenesis (IEA)

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 (IEA,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 (ISO)

negative regulation of DNA-templated transcription (IEA)

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)

odontogenesis (IEA,ISO)

ossification (IEA,ISO)

osteoblast development (IEA,ISO)

osteoblast differentiation (IEA)

outflow tract morphogenesis (IEA,ISO)

outflow tract septum morphogenesis (IEA,ISO)

positive regulation of apoptotic process (ISO)

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 (ISO)

positive regulation of timing of catagen (IEA,ISO)

regulation of apoptotic process (IEA,ISO)

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IEA)

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

stem cell differentiation (IEA,ISO)

transcription by RNA polymerase II (ISO)

wound healing (IEA,ISO)

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

Cellular Component

cytosol (IEA)

nuclear speck (IEA)

nucleus (IEA)

transcription regulator complex (IEA)

Molecular Function

DNA binding (IEA)

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

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

protein binding (ISO)

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

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

sequence-specific DNA binding (IEA)

sequence-specific double-stranded DNA binding (IEA)

transcription cis-regulatory region binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

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 Ensembl
SpeTri2.0	NW_004936609	1,216,436 - 1,221,528 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

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.p14 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
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	17	11,102,284 - 11,107,949 (+)	NCBI		GRCr8
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_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	17	12,641,862 - 12,647,525 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	17	11,104,006 - 11,109,669 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
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
(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-v2	4	169,845,949 - 169,853,128 (+)	NCBI		NHGRI_mPanPan1-v2
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
(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

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005334106	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010002273	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000000397 ⟹ ENSSTOP00000000359

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936609	1,216,436 - 1,221,561 (-)	Ensembl

RefSeq Acc Id:

XM_005334106 ⟹ XP_005334163

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024407213	92,492,782 - 92,498,921 (-)	NCBI
SpeTri2.0	NW_004936609	1,216,436 - 1,221,528 (-)	NCBI

Sequence:

show sequence

GCCGCGGGGCTGCCAGCGGAGTTGCGCGCGGGGATCTACACAGGGCTGGGAAGTCATGGCTTCT
CCGTCCAAAGGCAACGACTTGTTCTCGTCTGATGAGGAGGGCCCGGCCATGGTGGCTGGGCCGG
GCCCGGGGCCTGGGGGCGCCGAGGGGGTCGCCGAGGAGCGTCGCGTCAAGGTCTCCAGCCTGCC
CTTCAGCGTGGAGGCGCTCATGTCGGACAAGAAGCCGCCCAAGGAGGCGTCCCCGCTGCCGGCC
GAAAGCGCCTCGGCGGGGGCCACCCTGCGGCCGCTGCTGCTGCCGGGTCATGGCTCCCGGGAAG
CGCACAGTCCCGGGCCTTTGGTCAAGCCTTTCGAGACCGCCTCAGTCAAGTCGGAAAATTCGGA
AGACGGAGCGTCGTGGATGCAGGAACCCGGCAGATACTCGCCGCCACCAAGACACATGAGCCCC
ACCACCTGCACCCTGAGGAAACACAAGACCAATCGGAAGCCTCGCACGCCCTTCACCACGTCCC
AGCTCCTGGCGCTGGAGCGCAAGTTCCGCCAGAAACAGTACCTCTCCATCGCGGAGCGCGCGGA
GTTCTCTAGCTCTCTGAACCTCACAGAGACCCAGGTCAAAATCTGGTTCCAGAACCGAAGGGCC
AAGGCCAAAAGACTGCAGGAGGCAGAACTGGAAAAGCTGAAGATGGCAGCTAAACCTATGCTGC
CCTCCGGCTTCAGTCTCCCTTTCCCCATCAACTCGCCCCTGCAAGCAGCGTCCCTGTACGGAGC
CTCCTACCCTTTCCATAGACCTGTGCTTCCCATCCCGCCCGTCGGACTCTATGCCACGCCAGTG
GGATATGGCATGTACCATCTATCCTAAGGCCTTAAGACCGGATCCAGAGACTCCAGGACGGATA
TTCGTTTAAAAGGGTTCCCCTCTCTCAAAGAAGGCGACCAACCCAGTCCTCCTGCAGCGGAAAT
TTCCGGCACCATCTGAAGAAGCCGCTGGGCCCGCAGGGCCCCAAGTCATAGTTTGAATTTCTTC
TTTAGGAGGGAGGCACCAATGTCCTGTTTACACGGTGTCATATCCTAAATGCCCCCTTCTCCTT
TCACGAAAATTGGCTCTGGCAGTTTCTATGTATAAATATATATATATAATAAAATATAAGACAT
TTTTATACAGCAAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_005334163	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000000359.2
GenBank Protein	KAG3265231	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_005334163 ⟸ XM_005334106

- UniProtKB:

I3LWJ7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MASPSKGNDLFSSDEEGPAMVAGPGPGPGGAEGVAEERRVKVSSLPFSVEALMSDKKPPKEASP
LPAESASAGATLRPLLLPGHGSREAHSPGPLVKPFETASVKSENSEDGASWMQEPGRYSPPPRH
MSPTTCTLRKHKTNRKPRTPFTTSQLLALERKFRQKQYLSIAERAEFSSSLNLTETQVKIWFQN
RRAKAKRLQEAELEKLKMAAKPMLPSGFSLPFPINSPLQAASLYGASYPFHRPVLPIPPVGLYA
TPVGYGMYHLS

hide sequence

Ensembl Acc Id:

ENSSTOP00000000359 ⟸ ENSSTOT00000000397

Protein Domains

Homeobox

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000000399	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000000397.3	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/TrEMBL
	Msh_Homeobox_Regulators	UniProtKB/TrEMBL
NCBI Gene	Msx2	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN MSX	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN MSX-2	UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/TrEMBL
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	I3LWJ7	ENTREZGENE, UniProtKB/TrEMBL

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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