Msx1 (msh homeobox 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Msx1 (msh homeobox 1) Rattus norvegicus
Analyze
Symbol: Msx1
Name: msh homeobox 1
RGD ID: 620929
Description: Biomarker of cryptorchidism. Human ortholog(s) of this gene implicated in cleft lip; cleft palate; orofacial cleft 5; tooth and nail syndrome; and tooth disease (multiple). Orthologous to human MSX1 (msh homeobox 1); INTERACTS WITH (S)-nicotine; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homeo box, msh-like 1; homeobox protein MSX-1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81477,185,802 - 77,189,735 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1477,185,802 - 77,189,735 (+)EnsemblGRCr8
mRatBN7.21472,961,036 - 72,964,970 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1472,961,148 - 72,964,966 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1477,415,192 - 77,419,125 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01478,656,060 - 78,659,993 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01475,096,617 - 75,100,553 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01477,712,262 - 77,716,061 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1477,712,240 - 77,716,059 (+)Ensemblrn6Rnor6.0
Rnor_5.01477,690,990 - 77,694,789 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41478,257,345 - 78,261,144 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1471,923,586 - 71,927,385 (+)NCBICelera
RGSC_v3.11478,259,735 - 78,263,533 (+)NCBI
Cytogenetic Map14q21NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (EXP)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP,ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
choline  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cyproconazole  (ISO)
cytarabine  (ISO)
DDT  (EXP)
diiodine  (ISO)
dimethylarsinous acid  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
glycidol  (EXP)
hexaconazole  (ISO)
L-methionine  (ISO)
Licochalcone B  (ISO)
mercury dibromide  (ISO)
nicotine  (EXP)
okadaic acid  (ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
quercetin  (EXP,ISO)
retinyl acetate  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sulindac sulfide  (ISO)
temozolomide  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

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)
cartilage development  (IMP)
cartilage morphogenesis  (ISO)
cell morphogenesis  (ISO)
cellular response to nicotine  (IEP)
embryonic digit morphogenesis  (ISO)
embryonic forelimb morphogenesis  (ISO)
embryonic hindlimb morphogenesis  (ISO)
embryonic limb morphogenesis  (ISO)
embryonic nail plate morphogenesis  (ISO)
epithelial to mesenchymal transition  (ISO)
epithelial to mesenchymal transition involved in endocardial cushion formation  (ISO)
face morphogenesis  (ISO)
forebrain development  (ISO)
heart development  (ISO)
heart morphogenesis  (ISO)
in utero embryonic development  (ISO)
inner ear development  (ISO)
mammary gland epithelium development  (ISO)
mesenchymal cell proliferation  (ISO)
midbrain development  (ISO)
middle ear morphogenesis  (ISO)
muscle organ development  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cell growth  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of DNA-templated transcription  (ISO)
negative regulation of gene expression  (ISO)
negative regulation of odontoblast differentiation  (ISO)
negative regulation of striated muscle cell differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (ISO)
nose development  (ISO)
odontogenesis  (ISO)
odontogenesis of dentin-containing tooth  (ISO)
pituitary gland development  (IEP)
positive regulation of BMP signaling pathway  (ISO)
positive regulation of cell cycle  (ISO)
positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator  (ISO)
positive regulation of mesenchymal cell apoptotic process  (ISO)
positive regulation of odontogenesis  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
protein localization to nucleus  (ISO)
protein stabilization  (ISO)
regulation of DNA-templated transcription  (IEA)
regulation of odontogenesis  (ISO)
roof of mouth development  (ISO)
signal transduction involved in regulation of gene expression  (ISO)
stem cell differentiation  (ISO)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Altered expression of muscle- and cytoskeleton-related genes in a rat strain with inherited cryptorchidism. Barthold JS, etal., J Androl. 2008 May-Jun;29(3):352-66. Epub 2008 Jan 24.
2. Endogenous Msx1 antisense transcript: in vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals. Blin-Wakkach C, etal., Proc Natl Acad Sci U S A 2001 Jun 19;98(13):7336-41.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
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. Complete sequencing shows a role for MSX1 in non-syndromic cleft lip and palate. Jezewski PA, etal., J Med Genet. 2003 Jun;40(6):399-407.
7. Regulation of MT melatonin receptor expression in the foetal rat pituitary. Johnston JD, etal., J Neuroendocrinol. 2006 Jan;18(1):50-6.
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Comprehensive gene review and curation RGD comprehensive gene curation
15. A human MSX1 homeodomain missense mutation causes selective tooth agenesis. Vastardis H, etal., Nat Genet. 1996 Aug;13(4):417-21.
16. Nicotine promotes cardiomyocyte apoptosis via oxidative stress and altered apoptosis-related gene expression. Zhou X, etal., Cardiology. 2010;115(4):243-50. Epub 2010 Mar 26.
Additional References at PubMed
PMID:7916326   PMID:8858134   PMID:8861098   PMID:8898217   PMID:9369446   PMID:9697309   PMID:10340755   PMID:10742093   PMID:10742104   PMID:11023873   PMID:11332647   PMID:11369996  
PMID:12489152   PMID:12651933   PMID:15188430   PMID:15192231   PMID:15217086   PMID:15705871   PMID:15930102   PMID:16002402   PMID:16330189   PMID:17030628   PMID:17601530   PMID:17693062  
PMID:18285513   PMID:18590716   PMID:18667074   PMID:19422820   PMID:20004191   PMID:20123092   PMID:21465616   PMID:22071108   PMID:27741242  


Genomics

Comparative Map Data
Msx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81477,185,802 - 77,189,735 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1477,185,802 - 77,189,735 (+)EnsemblGRCr8
mRatBN7.21472,961,036 - 72,964,970 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1472,961,148 - 72,964,966 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1477,415,192 - 77,419,125 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01478,656,060 - 78,659,993 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01475,096,617 - 75,100,553 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01477,712,262 - 77,716,061 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1477,712,240 - 77,716,059 (+)Ensemblrn6Rnor6.0
Rnor_5.01477,690,990 - 77,694,789 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41478,257,345 - 78,261,144 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1471,923,586 - 71,927,385 (+)NCBICelera
RGSC_v3.11478,259,735 - 78,263,533 (+)NCBI
Cytogenetic Map14q21NCBI
MSX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3844,859,665 - 4,863,936 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl44,859,665 - 4,863,936 (+)Ensemblhg38GRCh38
GRCh3744,861,392 - 4,865,663 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3644,912,293 - 4,916,564 (+)NCBIBuild 36Build 36hg18NCBI36
Build 3444,979,477 - 4,983,530NCBI
Celera44,758,413 - 4,762,671 (+)NCBICelera
Cytogenetic Map4p16.2NCBI
HuRef44,797,648 - 4,801,917 (+)NCBIHuRef
CHM1_144,859,330 - 4,863,591 (+)NCBICHM1_1
T2T-CHM13v2.044,829,290 - 4,833,545 (+)NCBIT2T-CHM13v2.0
Msx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39537,977,835 - 37,981,929 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl537,977,829 - 37,981,927 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38537,820,491 - 37,824,585 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl537,820,485 - 37,824,583 (-)Ensemblmm10GRCm38
MGSCv37538,211,730 - 38,215,824 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36538,108,742 - 38,112,705 (-)NCBIMGSCv36mm8
Celera535,276,257 - 35,280,351 (-)NCBICelera
Cytogenetic Map5B3NCBI
cM Map520.21NCBI
Msx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555144,923,552 - 4,927,471 (-)Ensembl
ChiLan1.0NW_0049555144,923,552 - 4,927,471 (-)NCBIChiLan1.0ChiLan1.0
MSX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v235,122,740 - 5,127,000 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan145,055,790 - 5,060,071 (+)NCBINHGRI_mPanPan1
PanPan1.144,935,603 - 4,939,117 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl44,935,600 - 4,939,079 (+)EnsemblpanPan2panpan1.1
MSX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1370,232,790 - 70,236,295 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl370,232,052 - 70,236,447 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha372,783,942 - 72,787,987 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0370,991,546 - 70,995,590 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl370,991,361 - 70,995,465 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1370,263,330 - 70,267,578 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0370,426,128 - 70,430,168 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0370,808,811 - 70,812,856 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Msx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528563,704,859 - 63,711,968 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647717,409,191 - 17,412,919 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647717,406,551 - 17,413,615 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl85,628,380 - 5,632,607 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.185,628,381 - 5,632,375 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.285,246,698 - 5,250,692 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MSX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12741,028,763 - 41,032,676 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2741,028,919 - 41,033,006 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604787,832,093 - 87,836,013 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Msx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475521,857,461 - 21,861,337 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475521,857,360 - 21,861,235 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Msx1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11167,352,539 - 67,356,449 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Msx1
9 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:384
Count of miRNA genes:212
Interacting mature miRNAs:248
Transcripts:ENSRNOT00000009101
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143802371083023710Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1459848686104848686Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143900944484009444Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)147297021087582095Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143067446985041098Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1474255551109089856Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143802371083023710Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1462398852107398852Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1460854936105854936Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1474255551109089856Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1459848686104848686Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144261625899224555Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143802371083023710Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)146592028399224555Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143941117087582095Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143802371083023710Rat

Markers in Region
RH130342  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21472,964,607 - 72,964,791 (+)MAPPERmRatBN7.2
Rnor_6.01477,715,700 - 77,715,883NCBIRnor6.0
Rnor_5.01477,694,428 - 77,694,611UniSTSRnor5.0
RGSC_v3.41478,260,783 - 78,260,966UniSTSRGSC3.4
Celera1471,927,024 - 71,927,207UniSTS
Cytogenetic Map14q21UniSTS
AI324650  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21472,964,681 - 72,964,798 (+)MAPPERmRatBN7.2
Rnor_6.01477,715,774 - 77,715,890NCBIRnor6.0
Rnor_5.01477,694,502 - 77,694,618UniSTSRnor5.0
RGSC_v3.41478,260,857 - 78,260,973UniSTSRGSC3.4
Celera1471,927,098 - 71,927,214UniSTS
Cytogenetic Map14q21UniSTS
Msx1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21472,961,262 - 72,961,723 (+)MAPPERmRatBN7.2
Rnor_6.01477,712,356 - 77,712,815NCBIRnor6.0
Rnor_5.01477,691,084 - 77,691,543UniSTSRnor5.0
Celera1471,923,680 - 71,924,139UniSTS
Cytogenetic Map14q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 155 74 73 42 27 42 6 266 127 11 131 73 92 31 11 11

Sequence


Ensembl Acc Id: ENSRNOT00000009101   ⟹   ENSRNOP00000009101
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1477,712,240 - 77,716,059 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000109302
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1472,961,148 - 72,964,966 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000155041   ⟹   ENSRNOP00000103599
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1477,185,802 - 77,189,735 (+)Ensembl
RefSeq Acc Id: NM_031059   ⟹   NP_112321
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81477,185,802 - 77,189,735 (+)NCBI
mRatBN7.21472,961,036 - 72,964,970 (+)NCBI
Rnor_6.01477,712,262 - 77,716,061 (+)NCBI
Rnor_5.01477,690,990 - 77,694,789 (+)NCBI
RGSC_v3.41478,257,345 - 78,261,144 (+)RGD
Celera1471,923,586 - 71,927,385 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_112321 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK70504 (Get FASTA)   NCBI Sequence Viewer  
  BAA11750 (Get FASTA)   NCBI Sequence Viewer  
  EDM00020 (Get FASTA)   NCBI Sequence Viewer  
  EDM00021 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000103599
  ENSRNOP00000103599.1
RefSeq Acc Id: NP_112321   ⟸   NM_031059
- UniProtKB: A6IJV7 (UniProtKB/TrEMBL),   Q9QUG0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000009101   ⟸   ENSRNOT00000009101
Ensembl Acc Id: ENSRNOP00000103599   ⟸   ENSRNOT00000155041
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6U7-F1-model_v2 AlphaFold G3V6U7 1-297 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620929 AgrOrtholog
BioCyc Gene G2FUF-15370 BioCyc
Ensembl Genes ENSRNOG00000006876 Ensembl
  ENSRNOG00000068566 Ensembl
  ENSRNOG00000078426 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000155041 ENTREZGENE
  ENSRNOT00000155041.1 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Msh_Homeobox_Regulators UniProtKB/TrEMBL
KEGG Report rno:81710 UniProtKB/TrEMBL
NCBI Gene 81710 ENTREZGENE
PANTHER HOMEOBOX PROTEIN MSX UniProtKB/TrEMBL
  HOMEOBOX PROTEIN MSX-1 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Msx1 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006876 RatGTEx
  ENSRNOG00000068566 RatGTEx
  ENSRNOG00000078426 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0ABK0LJN7_RAT UniProtKB/TrEMBL
  A6IJV6_RAT UniProtKB/TrEMBL
  A6IJV7 ENTREZGENE, UniProtKB/TrEMBL
  Q9QUG0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Msx1  msh homeobox 1  Msx1  homeo box, msh-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Msx1  homeo box, msh-like 1      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Msx1  homeo box, msh-like 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in dental and craniofacial tissues 724434