Foxc1 (forkhead box C1) - Rat Genome Database

Send us a Message

Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Foxc1 (forkhead box C1) Mus musculus
Symbol: Foxc1
Name: forkhead box C1
RGD ID: 1620902
Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and promoter-specific chromatin binding activity. Involved in several processes, including cell surface receptor signaling pathway; endochondral ossification; and regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including cell surface receptor signaling pathway; circulatory system development; and collagen fibril organization. Located in nucleus. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; heart; and sensory organ. Used to study buphthalmos. Human ortholog(s) of this gene implicated in Axenfeld-Rieger syndrome; Axenfeld-Rieger syndrome type 3; anterior segment dysgenesis 3; and glaucoma. Orthologous to human FOXC1 (forkhead box C1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: ch; congenital hydrocephalus; fkh-1; Fkh1; forkhead box protein C1; forkhead-related protein FKHL7; forkhead-related transcription factor 3; FREA; FREAC-3; FREAC3; frkh; frkhda; mesoderm/mesenchyme forkhead 1; MF-1; Mf1; Mf4; transcription factor FKH-1
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391331,990,629 - 31,994,618 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1331,990,616 - 31,996,459 (+)EnsemblGRCm39 Ensembl
GRCm381331,806,646 - 31,810,635 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1331,806,633 - 31,812,476 (+)EnsemblGRCm38mm10GRCm38
MGSCv371331,898,515 - 31,902,504 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361331,814,111 - 31,818,100 (+)NCBIMGSCv36mm8
Celera1332,016,470 - 32,020,494 (+)NCBICelera
Cytogenetic Map13A3.2NCBI
cM Map1313.52NCBI
JBrowse: View Region in Genome Browser (JBrowse)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-methylcholine  (ISO)
3-chloropropane-1,2-diol  (ISO)
4,4'-sulfonyldiphenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
atrazine  (ISO)
benzalkonium chloride  (EXP)
benzo[a]pyrene  (ISO)
bis(2-chloroethyl) sulfide  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
buta-1,3-diene  (EXP)
cadmium dichloride  (ISO)
calcitriol  (ISO)
carbamazepine  (ISO)
cisplatin  (ISO)
clomiphene  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
coumarin  (ISO)
cyclosporin A  (EXP,ISO)
dexamethasone  (EXP)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
estrone  (ISO)
fenvalerate  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (ISO)
genistein  (EXP,ISO)
hexestrol  (ISO)
hydrogen peroxide  (ISO)
isoflurane  (EXP)
menadione  (ISO)
mercury dibromide  (ISO)
mestranol  (ISO)
methotrexate  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
nickel atom  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
perfluorononanoic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (EXP)
raloxifene  (ISO)
SB 431542  (ISO)
sevoflurane  (EXP)
sodium arsenate  (EXP)
tamoxifen  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
thimerosal  (ISO)
titanium dioxide  (EXP)
toluene  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure morphogenesis  (IBA)
angiogenesis  (IEA)
apoptotic process involved in outflow tract morphogenesis  (IGI)
artery morphogenesis  (IMP)
blood vessel development  (IGI)
blood vessel diameter maintenance  (IGI)
blood vessel remodeling  (IGI)
brain development  (IMP)
camera-type eye development  (IMP)
cardiac muscle cell proliferation  (IGI)
cell differentiation  (IBA)
cell migration  (ISO)
cell population proliferation  (ISO)
cellular response to chemokine  (IMP)
cellular response to epidermal growth factor stimulus  (ISO)
cerebellum development  (IMP)
chemokine-mediated signaling pathway  (IMP)
collagen fibril organization  (IMP)
embryonic heart tube development  (IGI)
endochondral ossification  (IMP)
eye development  (IMP,ISO)
germ cell migration  (IMP)
glomerular epithelium development  (IMP)
glycosaminoglycan metabolic process  (IMP)
heart development  (IGI,IMP,ISO)
heart morphogenesis  (IGI)
in utero embryonic development  (IMP)
kidney development  (IMP)
lacrimal gland development  (IMP)
lymph vessel development  (IGI)
maintenance of lens transparency  (IMP)
mesenchymal cell development  (IDA)
mesenchymal cell differentiation  (IMP)
negative regulation of angiogenesis  (IMP)
negative regulation of apoptotic process involved in outflow tract morphogenesis  (IGI)
negative regulation of lymphangiogenesis  (IMP)
negative regulation of mitotic cell cycle  (ISO)
negative regulation of transcription by RNA polymerase II  (IMP)
neural crest cell development  (IGI)
Notch signaling pathway  (IGI)
odontogenesis of dentin-containing tooth  (ISO)
ossification  (IMP)
ovarian follicle development  (IMP)
paraxial mesoderm formation  (IGI,IMP)
positive regulation of core promoter binding  (IMP)
positive regulation of DNA binding  (ISO)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of epithelial to mesenchymal transition  (ISO)
positive regulation of gene expression  (IDA)
positive regulation of hematopoietic progenitor cell differentiation  (IMP)
positive regulation of hematopoietic stem cell differentiation  (IMP)
positive regulation of keratinocyte differentiation  (ISO)
positive regulation of transcription by RNA polymerase II  (IDA,IMP,ISO)
regulation of DNA-templated transcription  (ISO)
regulation of organ growth  (IGI)
regulation of transcription by RNA polymerase II  (IBA)
skeletal system development  (IMP)
somitogenesis  (IGI)
ureteric bud development  (IMP)
vascular endothelial growth factor receptor signaling pathway  (IGI)
vascular endothelial growth factor signaling pathway  (IMP)
ventricular cardiac muscle tissue morphogenesis  (IGI)

Cellular Component
cytosol  (ISO)
heterochromatin  (ISO)
nucleoplasm  (ISO)
nucleus  (IDA,ISO)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal anterior eye segment morphology  (IAGP)
abnormal aortic valve cusp morphology  (IAGP)
abnormal aortic valve morphology  (IAGP)
abnormal aqueous drainage system morphology  (IAGP)
abnormal arytenoid cartilage morphology  (IEA)
abnormal axial skeleton morphology  (IEA)
abnormal basement membrane morphology  (IAGP)
abnormal bone ossification  (IAGP)
abnormal brain development  (IAGP)
abnormal brain meninges morphology  (IAGP)
abnormal brain ventricular system morphology  (IEA)
abnormal branching involved in ureteric bud morphogenesis  (IAGP)
abnormal canal of Schlemm morphology  (IAGP)
abnormal carpal bone morphology  (IEA)
abnormal cartilage development  (IEA)
abnormal cartilage morphology  (IEA)
abnormal cell migration  (IAGP)
abnormal cerebellum development  (IAGP)
abnormal cerebral aqueduct morphology  (IEA)
abnormal cerebral cortex morphology  (IAGP)
abnormal cervical atlas morphology  (IAGP)
abnormal cervical vertebrae morphology  (IEA)
abnormal choroid plexus morphology  (IEA)
abnormal ciliary body morphology  (IAGP)
abnormal ciliary process morphology  (IAGP)
abnormal cornea morphology  (IAGP)
abnormal corneal endothelium morphology  (IAGP)
abnormal corneal epithelium morphology  (IAGP)
abnormal cortical marginal zone morphology  (IAGP)
abnormal craniofacial bone morphology  (IAGP)
abnormal craniofacial development  (IEA)
abnormal cricoid cartilage morphology  (IEA)
abnormal deltoid tuberosity morphology  (IAGP)
abnormal dorsal aorta morphology  (IAGP)
abnormal dorsal-ventral polarity of the somites  (IAGP)
abnormal exorbital lacrimal gland morphology  (IAGP)
abnormal eye morphology  (IAGP)
abnormal femur morphology  (IEA)
abnormal fibula morphology  (IEA)
abnormal foramen magnum morphology  (IAGP)
abnormal forebrain development  (IAGP)
abnormal forebrain morphology  (IAGP)
abnormal fourth pharyngeal arch artery morphology  (IAGP)
abnormal fourth ventricle morphology  (IEA)
abnormal frontal bone morphology  (IAGP)
abnormal head development  (IAGP)
abnormal heartbeat  (IAGP)
abnormal hindlimb morphology  (IEA)
abnormal hippocampus morphology  (IAGP)
abnormal humerus morphology  (IAGP)
abnormal hyoid bone morphology  (IEA)
abnormal iridocorneal angle  (IAGP)
abnormal iris morphology  (IAGP)
abnormal iris pigment epithelium  (IAGP)
abnormal kidney arterial blood vessel morphology  (IAGP)
abnormal kidney blood vessel morphology  (IAGP)
abnormal kidney development  (IAGP)
abnormal kidney morphology  (IAGP)
abnormal kidney venous blood vessel morphology  (IAGP)
abnormal lacrimal gland branching morphogenesis  (IAGP)
abnormal lacrimal gland morphology  (IAGP)
abnormal lacrimal gland physiology  (IAGP)
abnormal laryngeal cartilage morphology  (IEA)
abnormal lateral ventricle morphology  (IEA)
abnormal lens morphology  (IAGP)
abnormal limb bone morphology  (IEA)
abnormal line of Schwalbe morphology  (IAGP)
abnormal maxillary zygomatic process morphology  (IAGP)
abnormal meninges morphology  (IAGP)
abnormal mesonephros morphology  (IAGP)
abnormal metacarpal bone morphology  (IEA)
abnormal metanephros morphology  (IAGP)
abnormal metatarsal bone morphology  (IEA)
abnormal nasal capsule morphology  (IEA)
abnormal nasolacrimal duct morphology  (IAGP)
abnormal neocortex morphology  (IAGP)
abnormal nervous system development  (IAGP)
abnormal neurocranium morphology  (IEA)
abnormal neuron differentiation  (IAGP)
abnormal neuron proliferation  (IAGP)
abnormal notochord morphology  (IEA)
abnormal occipital bone morphology  (IEA)
abnormal ovarian bursa morphology  (IAGP)
abnormal ovarian cortex morphology  (IAGP)
abnormal ovarian follicle morphology  (IAGP)
abnormal ovarian medulla morphology  (IAGP)
abnormal ovary morphology  (IAGP)
abnormal oviduct morphology  (IAGP)
abnormal patella morphology  (IEA)
abnormal phalanx morphology  (IEA)
abnormal pharyngeal arch artery morphology  (IAGP)
abnormal pharyngeal pouch morphology  (IAGP)
abnormal pituitary diverticulum morphology  (IAGP)
abnormal pituitary gland development  (IEA)
abnormal placement of pupils  (IAGP)
abnormal primordial germ cell migration  (IAGP)
abnormal pulmonary valve cusp morphology  (IAGP)
abnormal pulmonary valve morphology  (IAGP)
abnormal radial glial cell morphology  (IAGP)
abnormal Reichert's cartilage morphology  (IEA)
abnormal renal/urinary system morphology  (IAGP)
abnormal reproductive system morphology  (IAGP)
abnormal rib development  (IEA)
abnormal rib morphology  (IEA)
abnormal right renal artery morphology  (IAGP)
abnormal roof plate morphology  (IAGP)
abnormal scapula morphology  (IEA)
abnormal semilunar valve morphology  (IAGP)
abnormal skeleton development  (IEA)
abnormal skeleton morphology  (IAGP)
abnormal somite development  (IAGP)
abnormal somite shape  (IAGP)
abnormal sphenoid bone morphology  (IEA)
abnormal spinal cord morphology  (IAGP)
abnormal sternebra morphology  (IEA)
abnormal sternocostal joint morphology  (IAGP)
abnormal sternum morphology  (IAGP)
abnormal sternum ossification  (IAGP)
abnormal stratification in cerebral cortex  (IAGP)
abnormal striatum morphology  (IEA)
abnormal superior vena cava morphology  (IAGP)
abnormal tarsal bone morphology  (IAGP)
abnormal testis tunica albuginea morphology  (IAGP)
abnormal third ventricle morphology  (IEA)
abnormal thyroid cartilage morphology  (IAGP)
abnormal tibia morphology  (IEA)
abnormal trabecular meshwork morphology  (IAGP)
abnormal tracheal cartilage morphology  (IEA)
abnormal trigeminal ganglion morphology  (IEA)
abnormal triquetrum morphology  (IEA)
abnormal ureter development  (IAGP)
abnormal urogenital fold morphology  (IAGP)
abnormal vascular development  (IAGP)
abnormal vertebrae development  (IAGP)
abnormal vertebral arch morphology  (IAGP)
abnormal vertebral transverse process morphology  (IEA)
abnormal vibrissa number  (IEA)
abnormal vitelline vascular remodeling  (IAGP)
abnormal Wolffian duct morphology  (IAGP)
abnormal xiphoid process morphology  (IAGP)
absent corpus callosum  (IAGP)
absent epiglottis  (IEA)
absent eye anterior chamber  (IAGP)
absent frontal bone  (IEA)
absent intraorbital lacrimal gland  (IAGP)
absent kidney  (IAGP)
absent neurocranium  (IAGP)
absent paraxial mesoderm  (IAGP)
absent Schlemm's canal  (IAGP)
absent second pharyngeal arch  (IAGP)
absent sesamoid bone of gastrocnemius  (IEA)
absent somites  (IAGP)
absent sternum  (IAGP)
absent sternum body  (IEA)
anterior iris synechia  (IAGP)
aortic arch coarctation  (IAGP)
bifid ureter  (IAGP)
blind ureter  (IAGP)
cataract  (IAGP)
ciliary body hypoplasia  (IAGP)
cornea ulcer  (IAGP)
corneal vascularization  (IAGP)
decreased angiogenesis  (IAGP)
decreased embryo size  (IAGP)
decreased fetal size  (IAGP)
decreased oocyte number  (IAGP)
decreased somite size  (IAGP)
delayed bone ossification  (IEA)
delayed endochondral bone ossification  (IAGP)
dilated dorsal aorta  (IAGP)
dilated lateral ventricle  (IEA)
disorganized myocardium  (IAGP)
disorganized testis cords  (IAGP)
double ureter  (IAGP)
duplex kidney  (IAGP)
ectopic neuron  (IAGP)
ectopic ovary  (IAGP)
ectopic testis  (IAGP)
ectopic ureter  (IAGP)
ectopic ureteric bud  (IAGP)
embryonic lethality during organogenesis, complete penetrance  (IAGP)
enlarged kidney  (IAGP)
enlarged liver  (IAGP)
enlarged maxillary zygomatic process  (IAGP)
enlarged pericardium  (IAGP)
enlarged third pharyngeal arch artery  (IAGP)
eyelids open at birth  (IAGP)
failure of endochondral bone ossification  (IEA)
failure of intramembranous bone ossification  (IEA)
failure of sternum ossification  (IAGP)
fused carpal bones  (IEA)
fused tarsal bones  (IEA)
head mesenchyme hypoplasia  (IAGP)
hydrocephaly  (IAGP)
hydronephrosis  (IAGP)
hydrops fetalis  (IAGP)
hydroureter  (IAGP)
hypoplastic trabecular meshwork  (IAGP)
impaired ovarian folliculogenesis  (IAGP)
incomplete rostral neuropore closure  (IAGP)
increased cornea thickness  (IAGP)
increased corneal epithelium thickness  (IAGP)
increased width of hypertrophic chondrocyte zone  (IAGP)
interrupted aortic arch  (IAGP)
intracranial hemorrhage  (IAGP)
iris hypoplasia  (IAGP)
iris stroma hypoplasia  (IAGP)
iris synechia  (IAGP)
irregularly shaped pupil  (IAGP)
lethality throughout fetal growth and development, incomplete penetrance  (IAGP)
microphthalmia  (IAGP)
mydriasis  (IAGP)
neonatal lethality, complete penetrance  (IAGP)
no abnormal phenotype detected  (IAGP)
non-obstructive hydrocephaly  (IEA)
oocyte degeneration  (IAGP)
ovary cyst  (IAGP)
ovary hemorrhage  (IAGP)
patent ductus arteriosus  (IAGP)
perimembraneous ventricular septal defect  (IAGP)
polyovular ovarian follicle  (IAGP)
radial glial endfoot detachment  (IAGP)
renal hypoplasia  (IAGP)
respiratory failure  (IEA)
short basicranium  (IEA)
short humerus  (IEA)
short limbs  (IAGP)
short mandible  (IEA)
short oviduct  (IAGP)
short radius  (IEA)
short snout  (IEA)
short ulna  (IEA)
small basisphenoid bone  (IAGP)
small first pharyngeal arch  (IAGP)
small gonad  (IAGP)
small heart  (IAGP)
small lens  (IAGP)
small Meckel's cartilage  (IEA)
small ovary  (IAGP)
small testis  (IAGP)
small vertebral body  (IAGP)
thick aortic valve cusps  (IAGP)
thick pulmonary valve cusps  (IAGP)
thin ribs  (IAGP)
trabecula carnea hypoplasia  (IAGP)
ventricle myocardium hypoplasia  (IAGP)
ventricular septal defect  (IAGP)

References - curated
# Reference Title Reference Citation
1. DNA methylation profiling in doxorubicin treated primary locally advanced breast tumours identifies novel genes associated with survival and treatment response. Dejeux E, etal., Mol Cancer. 2010 Mar 25;9:68. doi: 10.1186/1476-4598-9-68.
2. Novel mutations in the FOXC1 gene in Japanese patients with Axenfeld-Rieger syndrome. Fuse N, etal., Mol Vis. 2007 Jun 27;13:1005-9.
3. Primary cellular meningeal defects cause neocortical dysplasia and dyslamination. Hecht JH, etal., Ann Neurol. 2010 Oct;68(4):454-64. doi: 10.1002/ana.22103.
4. A family with Axenfeld-Rieger syndrome and Peters Anomaly caused by a point mutation (Phe112Ser) in the FOXC1 gene. Honkanen RA, etal., Am J Ophthalmol. 2003 Mar;135(3):368-75.
5. The forkhead/winged helix gene Mf1 is disrupted in the pleiotropic mouse mutation congenital hydrocephalus. Kume T, etal., Cell. 1998 Jun 12;93(6):985-96.
6. Axenfeld-Rieger anomaly: a novel mutation in the forkhead box C1 (FOXC1) gene in a 4-generation family. Mortemousque B, etal., Arch Ophthalmol. 2004 Oct;122(10):1527-33.
7. Frequent aberrant DNA methylation of ABCB1, FOXC1, PPP2R2B and PTEN in ductal carcinoma in situ and early invasive breast cancer. Muggerud AA, etal., Breast Cancer Res. 2010;12(1):R3. doi: 10.1186/bcr2466. Epub 2010 Jan 7.
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. Basal-like breast cancer defined by FOXC1 expression offers superior prognostic value: a retrospective immunohistochemical study. Ray PS, etal., Ann Surg Oncol. 2011 Dec;18(13):3839-47. doi: 10.1245/s10434-011-1657-8. Epub 2011 Mar 18.
10. Mouse MP Annotation Import Pipeline RGD automated import pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Haploinsufficiency of the transcription factors FOXC1 and FOXC2 results in aberrant ocular development. Smith RS, etal., Hum Mol Genet. 2000 Apr 12;9(7):1021-32.
14. A novel mutation in the FOXC1 gene in a family with Axenfeld-Rieger syndrome and Peters' anomaly. Weisschuh N, etal., Clin Genet. 2008 Nov;74(5):476-80. doi: 10.1111/j.1399-0004.2008.01025.x. Epub 2008 May 21.
Additional References at PubMed
PMID:4269479   PMID:4784576   PMID:4819561   PMID:5088022   PMID:5500588   PMID:7683413   PMID:7689224   PMID:7957066   PMID:8325367   PMID:8375339   PMID:8661058   PMID:8798505  
PMID:9096120   PMID:9106663   PMID:9126297   PMID:9321480   PMID:9545561   PMID:9767123   PMID:9792859   PMID:10072431   PMID:10208738   PMID:10349636   PMID:10364424   PMID:10367888  
PMID:10395790   PMID:10474162   PMID:10479458   PMID:10660670   PMID:10704385   PMID:11042159   PMID:11076861   PMID:11165495   PMID:11179011   PMID:11217851   PMID:11237714   PMID:11562355  
PMID:11641716   PMID:11688556   PMID:11782474   PMID:12015277   PMID:12015278   PMID:12413905   PMID:12466851   PMID:12477932   PMID:12533514   PMID:12624268   PMID:14512019   PMID:14648841  
PMID:15196959   PMID:15239958   PMID:15314648   PMID:15342473   PMID:15465483   PMID:15618518   PMID:15906377   PMID:16141072   PMID:16141073   PMID:16207763   PMID:16412416   PMID:16459152  
PMID:16470615   PMID:16678147   PMID:16759280   PMID:16839542   PMID:17715063   PMID:17804598   PMID:18187037   PMID:18233958   PMID:18287559   PMID:18296617   PMID:18332127   PMID:18367164  
PMID:18422524   PMID:18424556   PMID:18448648   PMID:18545664   PMID:18579532   PMID:19270025   PMID:19273610   PMID:19369394   PMID:19411759   PMID:19509472   PMID:19668217   PMID:19879845  
PMID:20059953   PMID:20059958   PMID:20960542   PMID:21245162   PMID:21267068   PMID:21539829   PMID:21731673   PMID:21779340   PMID:21873635   PMID:22022403   PMID:22171010   PMID:22248045  
PMID:22365545   PMID:22511595   PMID:22522965   PMID:22639370   PMID:22736606   PMID:22745308   PMID:22921202   PMID:23145080   PMID:23344708   PMID:23472160   PMID:23595735   PMID:23677979  
PMID:23838094   PMID:23862012   PMID:24055172   PMID:24370450   PMID:24385915   PMID:24417671   PMID:24472616   PMID:24586192   PMID:24590069   PMID:24705356   PMID:24803591   PMID:24891614  
PMID:24952961   PMID:25513817   PMID:25733312   PMID:25808752   PMID:26071365   PMID:26120030   PMID:26321200   PMID:26666591   PMID:26718006   PMID:26824887   PMID:26839363   PMID:26912458  
PMID:26912704   PMID:26968737   PMID:27193493   PMID:27214551   PMID:27592801   PMID:27671872   PMID:27820600   PMID:28092268   PMID:28223138   PMID:28253399   PMID:28506991   PMID:28754980  
PMID:29028795   PMID:29070831   PMID:29322554   PMID:29511313   PMID:29959321   PMID:30021842   PMID:30352686   PMID:30615824   PMID:30635555   PMID:30796970   PMID:30943405   PMID:31089719  
PMID:31422096   PMID:31517441   PMID:31588228   PMID:31845891   PMID:31916318   PMID:32015493   PMID:32034090   PMID:32259372   PMID:32510325   PMID:33483579   PMID:33667029   PMID:33681192  
PMID:33898467   PMID:34331943   PMID:34383890   PMID:35831953   PMID:36575170  


Comparative Map Data
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391331,990,629 - 31,994,618 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1331,990,616 - 31,996,459 (+)EnsemblGRCm39 Ensembl
GRCm381331,806,646 - 31,810,635 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1331,806,633 - 31,812,476 (+)EnsemblGRCm38mm10GRCm38
MGSCv371331,898,515 - 31,902,504 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361331,814,111 - 31,818,100 (+)NCBIMGSCv36mm8
Celera1332,016,470 - 32,020,494 (+)NCBICelera
Cytogenetic Map13A3.2NCBI
cM Map1313.52NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh3861,609,915 - 1,613,897 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl61,609,915 - 1,613,897 (+)EnsemblGRCh38hg38GRCh38
GRCh3761,610,150 - 1,614,132 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3661,555,680 - 1,559,131 (+)NCBINCBI36Build 36hg18NCBI36
Build 3461,555,679 - 1,557,341NCBI
Celera62,838,909 - 2,842,360 (+)NCBICelera
Cytogenetic Map6p25.3NCBI
HuRef61,480,597 - 1,483,685 (+)NCBIHuRef
CHM1_161,612,575 - 1,616,026 (+)NCBICHM1_1
T2T-CHM13v2.061,472,916 - 1,476,901 (+)NCBIT2T-CHM13v2.0
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.21732,631,379 - 32,635,361 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1732,633,142 - 32,634,803 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1732,479,163 - 32,483,145 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01734,082,977 - 34,086,959 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01732,474,984 - 32,478,967 (-)NCBIRnor_WKY
Rnor_6.01733,947,501 - 33,951,484 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1733,947,506 - 33,951,484 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01735,833,707 - 35,837,690 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41739,026,186 - 39,030,163 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1732,190,633 - 32,194,475 (-)NCBICelera
Cytogenetic Map17p12NCBI
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
Mhudiblu_PPA_v061,429,051 - 1,433,180 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
Dog10K_Boxer_Tasha352,065,990 - 2,069,716 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0352,012,278 - 2,015,999 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1351,987,281 - 1,991,006 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0352,008,542 - 2,012,243 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0353,344,191 - 3,347,919 (+)NCBIUU_Cfam_GSD_1.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl7837,171 - 838,805 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17837,088 - 840,593 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.271,037,165 - 1,039,040 (+)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.11770,533,048 - 70,536,555 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1770,534,821 - 70,536,476 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660441,552,589 - 1,556,578 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_00462475623,060,751 - 23,062,343 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475623,060,065 - 23,062,407 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID

Predicted Target Of
Summary Value
Count of predictions:557
Count of miRNA genes:353
Interacting mature miRNAs:435
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 (
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301255Cd4ts6_mCD4 T cell subset 6 (mouse)Not determined1316854534168684Mouse
10449140Eosn2_meosinophil differential 2 (mouse)1322131134221311Mouse
15039338Nmrs34_mNAFLD-associated magnetic resonance shift 34 (mouse)1322131134221311Mouse
1301455Bmd3_mbone mineral density 3 (mouse)Not determined13347761237477820Mouse
10045624Heal24_mwound healing/regeneration (mouse)Not determined13347761237477820Mouse
10045625Heal23_mwound healing/regeneration 23 (mouse)Not determined13347761237477820Mouse
1301367Twq1_mtestis weight QTL 1 (mouse)Not determined13361551237615672Mouse
1301733Heal3_mwound healing/regeneration 3 (mouse)Not determined13368020037680343Mouse
26884393Humsd7_mhumerus midshaft diameter 7, 16 week (mouse)13395000076048119Mouse
1558898Hpi1_mhapatic PMN infiltration 1 (mouse)Not determined13441402553101640Mouse
10402494Igmsc1_mimmunoglobulin M secreting cells 1 (mouse)Not determined131716854544918560Mouse
1301984Pbd2_mpeak bone density 2 (mouse)Not determined131718950838947406Mouse
1301880Hypt_mhypertension (mouse)Not determined131815679252156924Mouse
13463469Gssq1_mglomerulosclerosis severity QTL 1 (mouse)131906090853061050Mouse
12880423V25Dq7_mvitamin D inactive form serum level QTL 7 (mouse)131958398353583983Mouse
1301015Sysbp2_msystolic blood pressure 2 (mouse)Not determined132047761259821605Mouse
4142147Mvwf4_mmodifier of von Willebrand factor 4 (mouse)Not determined20477612112898424Mouse
1357591Tesq1_mtestis weight QTL 1 (mouse)Not determined132061551255720517Mouse
4142009Pregq3_mpregnancy QTL 3 (mouse)Not determined132061551272385189Mouse
10045618Heal17_mwound healing/regeneration 17 (mouse)Not determined132074693954747056Mouse
4142489Ath25_matherosclerosis 25 (mouse)Not determined2583652959836529Mouse
10401111Pgia40_mproteoglycan induced arthritis 40 (mouse)Not determined132791846961918560Mouse
1300710Pcd4ts2_mp-glycoprotein positive CD4 T cell subset 2 (mouse)Not determined132821044262210544Mouse
1357802Vtbt15_mvertebral trabecular bone trait 15 (mouse)Not determined132821737962217515Mouse
10045621Heal21_mwound healing/regeneration 21 (mouse)Not determined132821737962217515Mouse
10755533Chol18_mcholesterol 18 (mouse)133096946764969467Mouse
10755517Chol15_mcholesterol 15 (mouse)133096946764969467Mouse
12738439Twq4_mtestis weight QTL 4 (mouse)133112911065129110Mouse
14696729Kidlq2_mkidney weight, left QTL 2 (mouse)133134473665344736Mouse

Markers in Region
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381331,809,617 - 31,809,840UniSTSGRCm38
MGSCv371331,901,486 - 31,901,709UniSTSGRCm37
Celera1332,019,476 - 32,019,699UniSTS
Cytogenetic Map13A3.2UniSTS
cM Map13 UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381331,809,197 - 31,809,931UniSTSGRCm38
MGSCv371331,901,066 - 31,901,800UniSTSGRCm37
Celera1332,019,056 - 32,019,790UniSTS
Cytogenetic Map13A3.2UniSTS
cM Map1320.0UniSTS
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381331,809,731 - 31,809,952UniSTSGRCm38
MGSCv371331,901,600 - 31,901,821UniSTSGRCm37
Celera1332,019,590 - 32,019,811UniSTS
Cytogenetic Map13A3.2UniSTS
cM Map1320.0UniSTS



Reference Sequences
RefSeq Acc Id: ENSMUST00000062292   ⟹   ENSMUSP00000052196
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1331,990,616 - 31,996,459 (+)Ensembl
GRCm38.p6 Ensembl1331,806,633 - 31,812,476 (+)Ensembl
RefSeq Acc Id: NM_008592   ⟹   NP_032618
RefSeq Status: VALIDATED
Mouse AssemblyChrPosition (strand)Source
GRCm391331,990,629 - 31,994,618 (+)NCBI
GRCm381331,806,646 - 31,810,635 (+)ENTREZGENE
MGSCv371331,898,515 - 31,902,504 (+)RGD
Celera1332,016,470 - 32,020,494 (+)RGD
Reference Sequences
RefSeq Acc Id: NP_032618   ⟸   NM_008592
- UniProtKB: Q9QWR9 (UniProtKB/Swiss-Prot),   Q61572 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000052196   ⟸   ENSMUST00000062292

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q61572-F1-model_v2 AlphaFold Q61572 1-553 view protein structure

RGD ID:8680044
Promoter ID:EPDNEW_M18036
Type:initiation region
Description:Mus musculus forkhead box C1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Alternative Promoters:null; see alsoEPDNEW_M18037  
Experiment Methods:Single-end sequencing.
Mouse AssemblyChrPosition (strand)Source
GRCm381331,806,633 - 31,806,693EPDNEW
RGD ID:8680012
Promoter ID:EPDNEW_M18037
Type:initiation region
Description:Mus musculus forkhead box C1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Alternative Promoters:null; see alsoEPDNEW_M18036  
Experiment Methods:Single-end sequencing.
Mouse AssemblyChrPosition (strand)Source
GRCm381331,806,868 - 31,806,928EPDNEW
RGD ID:6823911
Promoter ID:MM_KWN:13718
SO ACC ID:SO:0000170
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   Brain,   Kidney,   Lung,   MEF_B4,   MEF_B6
Mouse AssemblyChrPosition (strand)Source
MGSCv361331,897,841 - 31,900,457 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1347466 AgrOrtholog
Ensembl Genes ENSMUSG00000050295 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000052196 ENTREZGENE
  ENSMUSP00000052196.3 UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000062292 ENTREZGENE
  ENSMUST00000062292.5 UniProtKB/Swiss-Prot
Gene3D-CATH UniProtKB/Swiss-Prot
InterPro Fork_head_dom UniProtKB/Swiss-Prot
  TF_fork_head_CS_1 UniProtKB/Swiss-Prot
  TF_fork_head_CS_2 UniProtKB/Swiss-Prot
  WH-like_DNA-bd_sf UniProtKB/Swiss-Prot
  WH_DNA-bd_sf UniProtKB/Swiss-Prot
KEGG Report mmu:17300 UniProtKB/Swiss-Prot
  PTHR11829:SF68 UniProtKB/Swiss-Prot
Pfam Forkhead UniProtKB/Swiss-Prot
PhenoGen Foxc1 PhenoGen
  FORK_HEAD_2 UniProtKB/Swiss-Prot
  FORK_HEAD_3 UniProtKB/Swiss-Prot
SMART SM00339 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46785 UniProtKB/Swiss-Prot
UniProt Secondary O88409 UniProtKB/Swiss-Prot
  Q61582 UniProtKB/Swiss-Prot
  Q9QWR9 UniProtKB/Swiss-Prot