MSX2 (msh homeobox 2) - Rat Genome Database

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Gene: MSX2 (msh homeobox 2) Canis lupus familiaris
Analyze
Symbol: MSX2
Name: msh homeobox 2
RGD ID: 12425979
Description: ENCODES a protein that exhibits DNA-binding transcription factor activity, RNA polymerase II-specific (ortholog); DNA-binding transcription repressor 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 transcription regulator complex (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: homeobox protein Hox-8; homeobox protein MSX-2; msh homeo box homolog 2; msh homeobox homolog 2; muscle segmentation homologue (MSX2)
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1438,002,724 - 38,007,407 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl438,002,428 - 38,007,407 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha437,948,799 - 37,953,445 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0438,376,184 - 38,380,830 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl438,375,888 - 38,381,225 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1438,192,821 - 38,197,476 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0438,380,991 - 38,385,645 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0438,891,167 - 38,895,822 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of meiosis  (ISO)
anterior/posterior pattern specification  (ISO)
BMP signaling pathway  (ISO)
bone morphogenesis  (ISO)
bone trabecula formation  (ISO)
branching involved in mammary gland duct morphogenesis  (ISO)
cartilage development  (ISO)
cell surface receptor signaling pathway involved in heart development  (ISO)
cellular response to estradiol stimulus  (ISO)
cellular response to growth factor stimulus  (ISO)
chondrocyte development  (ISO)
embryonic digit morphogenesis  (ISO)
embryonic forelimb morphogenesis  (ISO)
embryonic hindlimb morphogenesis  (ISO)
embryonic limb morphogenesis  (ISO)
embryonic morphogenesis  (IBA)
embryonic nail plate morphogenesis  (ISO)
enamel mineralization  (ISO)
endochondral bone growth  (ISO)
epithelial to mesenchymal transition involved in endocardial cushion formation  (ISO)
frontal suture morphogenesis  (ISO)
heart development  (ISO)
mammary gland epithelium development  (ISO)
mesenchymal cell apoptotic process  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of CREB transcription factor activity  (ISO)
negative regulation of DNA-templated transcription  (ISS)
negative regulation of fat cell differentiation  (ISO)
negative regulation of keratinocyte differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (IEA,ISO,ISS)
odontogenesis  (ISO)
ossification  (IEA,ISO)
osteoblast development  (ISO)
osteoblast differentiation  (ISS)
outflow tract morphogenesis  (ISO)
outflow tract septum morphogenesis  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of BMP signaling pathway  (ISO)
positive regulation of mesenchymal cell apoptotic process  (ISO)
positive regulation of osteoblast differentiation  (ISO)
positive regulation of response to biotic stimulus  (ISO)
positive regulation of timing of catagen  (ISO)
regulation of apoptotic process  (ISO)
regulation of DNA-templated transcription  (IEA)
regulation of transcription by RNA polymerase II  (IBA)
signal transduction involved in regulation of gene expression  (ISO)
stem cell differentiation  (ISO)
transcription by RNA polymerase II  (ISO)
wound healing  (ISO)
wound healing, spreading of epidermal cells  (ISO)

Cellular Component

References
Additional References at PubMed
PMID:11419342   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
MSX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1438,002,724 - 38,007,407 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl438,002,428 - 38,007,407 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha437,948,799 - 37,953,445 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0438,376,184 - 38,380,830 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl438,375,888 - 38,381,225 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1438,192,821 - 38,197,476 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0438,380,991 - 38,385,645 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0438,891,167 - 38,895,822 (-)NCBIUU_Cfam_GSD_1.0
MSX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385174,724,582 - 174,730,896 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5174,724,582 - 174,730,896 (+)EnsemblGRCh38hg38GRCh38
GRCh375174,151,585 - 174,157,899 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365174,084,181 - 174,090,508 (+)NCBINCBI36Build 36hg18NCBI36
Build 345174,084,207 - 174,090,507NCBI
Celera5170,185,579 - 170,191,910 (+)NCBICelera
Cytogenetic Map5q35.2NCBI
HuRef5169,246,978 - 169,253,303 (+)NCBIHuRef
CHM1_15173,583,988 - 173,590,298 (+)NCBICHM1_1
T2T-CHM13v2.05175,263,949 - 175,271,855 (+)NCBIT2T-CHM13v2.0
Msx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391353,620,917 - 53,626,816 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1353,620,920 - 53,627,110 (-)EnsemblGRCm39 Ensembl
GRCm381353,466,881 - 53,472,780 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1353,466,884 - 53,473,074 (-)EnsemblGRCm38mm10GRCm38
MGSCv371353,562,250 - 53,568,149 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361353,475,420 - 53,480,608 (-)NCBIMGSCv36mm8
Celera1354,545,172 - 54,551,024 (-)NCBICelera
Cytogenetic Map13B1NCBI
cM Map1327.84NCBI
Msx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81711,102,284 - 11,107,949 (+)NCBIGRCr8
mRatBN7.21711,097,214 - 11,102,879 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1711,097,103 - 11,102,879 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1711,105,528 - 11,111,192 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01712,641,862 - 12,647,525 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01711,104,006 - 11,109,669 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01711,683,862 - 11,689,527 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1711,683,862 - 11,689,527 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01713,785,024 - 13,790,689 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41717,243,262 - 17,248,927 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11717,247,335 - 17,247,755 (+)NCBI
Celera1711,158,359 - 11,164,024 (+)NCBICelera
RH 3.4 Map17109.2RGD
Cytogenetic Map17p14NCBI
Msx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540827,323,360 - 27,329,755 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540827,323,405 - 27,329,484 (+)NCBIChiLan1.0ChiLan1.0
MSX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24169,845,949 - 169,853,128 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15167,985,531 - 167,992,667 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05170,063,137 - 170,070,226 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15176,968,315 - 176,974,679 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5176,967,902 - 176,976,609 (+)Ensemblpanpan1.1panPan2
Msx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721392,492,782 - 92,498,921 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366091,216,436 - 1,221,561 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366091,216,436 - 1,221,528 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1649,765,910 - 49,771,789 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11649,765,587 - 49,771,745 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
MSX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12376,873,499 - 76,879,935 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2376,873,669 - 76,879,553 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660341,717,428 - 1,723,746 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Msx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473315,288,326 - 15,294,568 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473315,288,417 - 15,294,481 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in MSX2
41 total Variants

Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
integumental system
mesenchyme
mesoderm
nervous system
reproductive system
respiratory system
6 5 5 23 16 10 6 6 24 19 12 14 10

Sequence


Ensembl Acc Id: ENSCAFT00000046226   ⟹   ENSCAFP00000041488
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl438,002,428 - 38,007,407 (-)Ensembl
Ensembl Acc Id: ENSCAFT00845000718   ⟹   ENSCAFP00845000523
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl438,375,888 - 38,381,225 (-)Ensembl
RefSeq Acc Id: NM_001003098   ⟹   NP_001003098
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1438,002,724 - 38,007,407 (-)NCBI
Dog10K_Boxer_Tasha437,948,799 - 37,953,445 (-)NCBI
ROS_Cfam_1.0438,376,184 - 38,380,830 (-)NCBI
UMICH_Zoey_3.1438,192,821 - 38,197,476 (-)NCBI
UNSW_CanFamBas_1.0438,380,991 - 38,385,645 (-)NCBI
UU_Cfam_GSD_1.0438,891,167 - 38,895,822 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001003098 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAC19897 (Get FASTA)   NCBI Sequence Viewer  
  CAC37368 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCAFP00000041488.1
  ENSCAFP00030003362.1
  ENSCAFP00040030240.1
  ENSCAFP00845000523
  ENSCAFP00845000523.1
GenBank Protein Q9GK08 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001003098   ⟸   NM_001003098
- UniProtKB: Q9GK08 (UniProtKB/Swiss-Prot),   A0A8C0KF78 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCAFP00000041488   ⟸   ENSCAFT00000046226
Ensembl Acc Id: ENSCAFP00845000523   ⟸   ENSCAFT00845000718

Promoters
RGD ID:13682972
Promoter ID:EPDNEW_C1041
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:
Dog AssemblyChrPosition (strand)Source
CanFam3.1438,007,471 - 38,007,531EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000016731 Ensembl, UniProtKB/Swiss-Prot
  ENSCAFG00030002082 UniProtKB/Swiss-Prot
  ENSCAFG00040018772 UniProtKB/Swiss-Prot
  ENSCAFG00845000450 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSCAFT00000046226.3 UniProtKB/Swiss-Prot
  ENSCAFT00030003789.1 UniProtKB/Swiss-Prot
  ENSCAFT00040034730.1 UniProtKB/Swiss-Prot
  ENSCAFT00845000718 ENTREZGENE
  ENSCAFT00845000718.1 UniProtKB/Swiss-Prot
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot
  Homeobox_metazoa UniProtKB/Swiss-Prot
  Msh_Homeobox_Regulators UniProtKB/Swiss-Prot
KEGG Report cfa:403663 UniProtKB/Swiss-Prot
NCBI Gene MSX2 ENTREZGENE
PANTHER HOMEOBOX PROTEIN MSX UniProtKB/Swiss-Prot
  HOMEOBOX PROTEIN MSX-2 UniProtKB/Swiss-Prot
Pfam Homeodomain UniProtKB/Swiss-Prot
PRINTS HOMEOBOX UniProtKB/Swiss-Prot
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot
SMART HOX UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot
UniProt A0A8C0KF78 ENTREZGENE
  MSX2_CANLF UniProtKB/Swiss-Prot, ENTREZGENE
VGNC ID VGNC:43455 ENTREZGENE