Hoxc10 (homeobox C10) - Rat Genome Database

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Gene: Hoxc10 (homeobox C10) Mus musculus
Analyze
Symbol: Hoxc10
Name: homeobox C10
RGD ID: 1316333
MGI Page MGI
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including embryonic limb morphogenesis; regionalization; and spinal cord motor neuron cell fate specification. Predicted to be located in nuclear body. Predicted to be active in nucleus. Is expressed in several structures, including embryo mesenchyme; genitourinary system; intestine; limb; and spinal cord. Orthologous to human HOXC10 (homeobox C10).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AI506621; homeo box C10; homeobox protein Hox-3.6; homeobox protein Hox-C10; Hox-3.; Hox-3.6
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,875,231 - 102,880,333 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,875,231 - 102,880,328 (+)EnsemblGRCm39 Ensembl
GRCm3815102,966,796 - 102,971,898 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,966,796 - 102,971,893 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715102,797,296 - 102,802,152 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,794,899 - 102,799,755 (+)NCBIMGSCv36mm8
Celera15105,127,796 - 105,132,646 (+)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1558.03NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nuclear body  (ISO)
nucleoplasm  (ISO)
nucleus  (IBA)

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, etal., Science 2004 Dec 24;306(5705):2255-7.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. Mouse MP Annotation Import Pipeline RGD automated import pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Abnormalities of vertebral formation and Hox expression in congenital kyphoscoliotic rats. Seki T, etal., Mol Cell Biochem. 2008 May;312(1-2):193-9. doi: 10.1007/s11010-008-9734-4. Epub 2008 Mar 9.
Additional References at PubMed
PMID:1353983   PMID:1358459   PMID:1683707   PMID:1720547   PMID:7848872   PMID:7959778   PMID:8099712   PMID:9242489   PMID:9510030   PMID:10349636   PMID:10391213   PMID:11042159  
PMID:11076861   PMID:11150241   PMID:11217851   PMID:11493536   PMID:12441290   PMID:12466851   PMID:12477932   PMID:12869760   PMID:14681479   PMID:15042701   PMID:15489334   PMID:16141072  
PMID:16141073   PMID:16495162   PMID:16602821   PMID:16790475   PMID:16845371   PMID:16989801   PMID:17481601   PMID:17520166   PMID:17626057   PMID:18065432   PMID:18077221   PMID:18287559  
PMID:18519639   PMID:18667151   PMID:19204410   PMID:19591821   PMID:19623272   PMID:20059953   PMID:20412779   PMID:20417598   PMID:20932939   PMID:21256124   PMID:21529712   PMID:21670281  
PMID:21677750   PMID:21858105   PMID:21873635   PMID:22174793   PMID:22438573   PMID:22701719   PMID:22819676   PMID:22972626   PMID:22988430   PMID:23763947   PMID:24075995   PMID:24146773  
PMID:24155669   PMID:24651482   PMID:24952961   PMID:25152336   PMID:25848055   PMID:26018586   PMID:27453501   PMID:28186086   PMID:28188179   PMID:28605223   PMID:29688375   PMID:30262816  
PMID:30959515   PMID:31747609   PMID:32098917   PMID:32156750   PMID:32479258   PMID:32597756   PMID:33028607   PMID:33257809   PMID:33990396   PMID:34544261   PMID:34994686   PMID:35315772  
PMID:37167859  


Genomics

Comparative Map Data
Hoxc10
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,875,231 - 102,880,333 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,875,231 - 102,880,328 (+)EnsemblGRCm39 Ensembl
GRCm3815102,966,796 - 102,971,898 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,966,796 - 102,971,893 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715102,797,296 - 102,802,152 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,794,899 - 102,799,755 (+)NCBIMGSCv36mm8
Celera15105,127,796 - 105,132,646 (+)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1558.03NCBI
HOXC10
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381253,985,146 - 53,990,279 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1253,985,065 - 53,990,279 (+)EnsemblGRCh38hg38GRCh38
GRCh371254,378,930 - 54,384,063 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,665,213 - 52,670,330 (+)NCBINCBI36Build 36hg18NCBI36
Build 341252,665,220 - 52,670,327NCBI
Celera1254,028,565 - 54,033,680 (+)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1251,416,659 - 51,421,773 (+)NCBIHuRef
CHM1_11254,345,653 - 54,350,768 (+)NCBICHM1_1
T2T-CHM13v2.01253,950,654 - 53,955,785 (+)NCBIT2T-CHM13v2.0
Hoxc10
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87135,982,222 - 135,987,442 (+)NCBIGRCr8
mRatBN7.27134,103,741 - 134,108,966 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,103,643 - 134,108,966 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,859,132 - 135,864,346 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,088,515 - 138,093,726 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,074,491 - 138,079,716 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07144,577,578 - 144,582,802 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,577,465 - 144,582,622 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,368,850 - 142,374,159 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,717,910 - 141,734,613 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17141,808,802 - 141,813,297 (+)NCBI
Celera7130,529,927 - 130,535,151 (+)NCBICelera
Cytogenetic Map7q36NCBI
Hoxc10
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554581,243,529 - 1,248,661 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554581,243,529 - 1,248,653 (+)NCBIChiLan1.0ChiLan1.0
HOXC10
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21040,195,618 - 40,201,937 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11240,192,386 - 40,198,918 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01234,764,956 - 34,770,088 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11235,553,262 - 35,558,393 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1235,553,262 - 35,558,393 (-)Ensemblpanpan1.1panPan2
HOXC10
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,272,272 - 1,277,411 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,273,131 - 1,323,370 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2744,972,213 - 44,976,533 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,276,751 - 1,281,074 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,275,931 - 1,280,977 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,294,448 - 1,298,772 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,275,967 - 1,280,296 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02745,375,816 - 45,380,136 (+)NCBIUU_Cfam_GSD_1.0
Hoxc10
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494561,952,465 - 61,957,657 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651211,207,173 - 11,212,365 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651211,207,173 - 11,212,365 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXC10
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl519,197,807 - 19,202,970 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1519,197,810 - 19,202,975 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2519,670,823 - 19,675,191 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXC10
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11150,092,230 - 50,100,934 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1150,095,810 - 50,100,940 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037195,941,257 - 195,946,422 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxc10
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249042,039,754 - 2,045,096 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249042,040,018 - 2,044,881 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hoxc10
172 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:298
Count of miRNA genes:198
Interacting mature miRNAs:223
Transcripts:ENSMUST00000001699
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357526Hyplip2_mhyperlipidemia 2 (mouse)Not determined1512402203102896555Mouse
1558985Eae32_mexperimental allergic encephalomyelitis susceptibility 32 (mouse)Not determined1532578416103425899Mouse
1302074Bmd4_mbone mineral density 4 (mouse)Not determined1556186708103425899Mouse
1302197Bhr2_mbronchial hyperresponsiveness 2 (mouse)Not determined1564306334103425899Mouse
1300627Sluc26_msusceptibility to lung cancer 26 (mouse)Not determined1570345653104073951Mouse
1300648Dbsty4_mdiabesity 4 (mouse)Not determined1570349271104073951Mouse
1300726Pitm4_mprion incubation time 4 (mouse)Not determined1570349271104073951Mouse
14747011Mancz13_mmandible centroid size 13 (mouse)1572382669104073951Mouse
12791003Aath8_maortic arch atherosclerosis 8 (mouse)1573430144104073951Mouse
1300851Heal4_mwound healing/regeneration 4 (mouse)Not determined1577527592104073951Mouse
4142060W3q6_mweight 3 weeks QTL 6 (mouse)Not determined78601103102901704Mouse
1357894Epfpq3_mepididymal fat percentage QTL 3 (mouse)Not determined1578601103102901704Mouse
14928306Manh79_mmandible shape 79 (mouse)1578847557104073951Mouse
12880411V125Dq11_mvitamin D active form serum level QTL 11 (mouse)1578897881104073951Mouse
10402490Dipa5_mdrug induced psychomotor activation 5 (mouse)Not determined1579163411104073951Mouse
4141897Imrfq2_mimmune response to Factor IX QTL 2 (mouse)Not determined79908940104073951Mouse
1301284Cosz3_mcocaine seizure 3 (mouse)Not determined1580313634104073951Mouse
4141902Cia37_mcollagen induced arthritis 37 (mouse)Not determined1580884933104073951Mouse
1300974Pgia9_mproteoglycan induced arthritis 9 (mouse)Not determined1580884933104073951Mouse
4141511Gdcr1_mglycerolphosphate dehydrogenase regulator 1 (mouse)Not determined82615474104073951Mouse
11530037Sluc34a_msusceptibility to lung cancer 34a (mouse)1585896437104073951Mouse
11530038Sluc34b_msusceptibility to lung cancer 34b (mouse)1585896437104073951Mouse
1357614Bmca_mbile mucin accumulation (mouse)Not determined1585896437104073951Mouse
1301918Skull22_mskull morphology 22 (mouse)Not determined1585901546104073951Mouse
4141581Dshv1_mdorsal hippocampal volume 1 (mouse)Not determined92788640103425899Mouse
14700689Carg5_mCandida albicans resistance gene 5 (mouse)1597697881103008427Mouse
11528547Sluc34_msusceptibility to lung cancer 34 (mouse)1597884933102896555Mouse

Markers in Region
AI506621  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3815102,971,650 - 102,971,788UniSTSGRCm38
MGSCv3715102,802,081 - 102,802,219UniSTSGRCm37
Celera15105,132,575 - 105,132,713UniSTS
Cytogenetic Map15F3UniSTS
cM Map1557.4UniSTS
Whitehead/MRC_RH15909.19UniSTS
Hoxc10  
Mouse AssemblyChrPosition (strand)SourceJBrowse
MGSCv3715102,801,249 - 102,801,441UniSTSGRCm37
Celera15105,131,743 - 105,131,935UniSTS
Cytogenetic Map15F3UniSTS
cM Map1557.4UniSTS
cM Map1557.4UniSTS
Hoxc10  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3815102,970,818 - 102,971,010UniSTSGRCm38
MGSCv3715102,801,249 - 102,801,441UniSTSGRCm37
Celera15105,131,743 - 105,131,935UniSTS
Cytogenetic Map15F3UniSTS
cM Map1557.4UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000001699   ⟹   ENSMUSP00000001699
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl15102,875,231 - 102,880,328 (+)Ensembl
GRCm38.p6 Ensembl15102,966,796 - 102,971,893 (+)Ensembl
RefSeq Acc Id: NM_010462   ⟹   NP_034592
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3915102,875,231 - 102,880,333 (+)NCBI
GRCm3815102,966,796 - 102,971,898 (+)ENTREZGENE
MGSCv3715102,797,296 - 102,802,152 (+)RGD
Celera15105,127,727 - 105,132,823 (+)ENTREZGENE
cM Map15 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_034592 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA63310 (Get FASTA)   NCBI Sequence Viewer  
  AAH53405 (Get FASTA)   NCBI Sequence Viewer  
  BAC28189 (Get FASTA)   NCBI Sequence Viewer  
  EDL03948 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000001699
  ENSMUSP00000001699.8
GenBank Protein P31257 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_034592   ⟸   NM_010462
- UniProtKB: P31312 (UniProtKB/Swiss-Prot),   Q7TMT7 (UniProtKB/Swiss-Prot),   P31257 (UniProtKB/Swiss-Prot),   Q8BZY5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000001699   ⟸   ENSMUST00000001699
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P31257-F1-model_v2 AlphaFold P31257 1-342 view protein structure

Promoters
RGD ID:6826095
Promoter ID:MM_KWN:19874
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney
Transcripts:ENSMUST00000001699
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3615102,797,291 - 102,797,791 (+)MPROMDB
RGD ID:8685238
Promoter ID:EPDNEW_M20649
Type:multiple initiation site
Name:Hoxc10_1
Description:Mus musculus homeobox C10 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3815102,966,865 - 102,966,925EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:96192 AgrOrtholog
Ensembl Genes ENSMUSG00000022484 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000001699 ENTREZGENE
  ENSMUST00000001699.8 UniProtKB/Swiss-Prot
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
  HXA10/ABDB-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:209448 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:96192 ENTREZGENE
NCBI Gene 209448 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-C10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR45874 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hoxc10 PhenoGen
PRINTS HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
UniProt HXC10_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  P31312 ENTREZGENE
  Q7TMT7 ENTREZGENE
  Q8BZY5 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary P31312 UniProtKB/Swiss-Prot
  Q7TMT7 UniProtKB/Swiss-Prot