Hoxc12 (homeobox C12) - Rat Genome Database

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Gene: Hoxc12 (homeobox C12) Mus musculus
Analyze
Symbol: Hoxc12
Name: homeobox C12
RGD ID: 1321501
MGI Page MGI
Description: Predicted to enable sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. Is expressed in several structures, including genitourinary system; integumental system; jaw; limb; and spinal cord. Orthologous to human HOXC12 (homeobox C12).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homeo box C12; homeobox protein Hox-3.8; homeobox protein Hox-C12; Homeobox protein Hox-C12 (Hox-3F); Hox-3.; Hox-3.8
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,845,261 - 102,847,044 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,845,192 - 102,847,044 (+)EnsemblGRCm39 Ensembl
GRCm3815102,936,826 - 102,938,609 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,936,757 - 102,938,609 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715102,767,284 - 102,768,948 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,764,887 - 102,766,551 (+)NCBIMGSCv36mm8
Celera15105,097,783 - 105,099,447 (+)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1558.01NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. MGDs mouse GO annotations MGD data from the GO Consortium
2. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1354638   PMID:1683707   PMID:7848872   PMID:7959778   PMID:11960714   PMID:12477932   PMID:14610273   PMID:15042701   PMID:15489334   PMID:15618518   PMID:16971476   PMID:17520166  
PMID:19204410   PMID:20059953   PMID:20211142   PMID:20417598   PMID:21267068   PMID:21670281   PMID:21677750   PMID:21873635   PMID:22639370   PMID:22701719   PMID:24155669   PMID:24194600  
PMID:27977683   PMID:28188179   PMID:32479258   PMID:33199643   PMID:33257809   PMID:35017475   PMID:38355793  


Genomics

Comparative Map Data
Hoxc12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,845,261 - 102,847,044 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,845,192 - 102,847,044 (+)EnsemblGRCm39 Ensembl
GRCm3815102,936,826 - 102,938,609 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,936,757 - 102,938,609 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715102,767,284 - 102,768,948 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,764,887 - 102,766,551 (+)NCBIMGSCv36mm8
Celera15105,097,783 - 105,099,447 (+)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1558.01NCBI
HOXC12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381253,954,903 - 53,958,956 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1253,954,903 - 53,958,956 (+)EnsemblGRCh38hg38GRCh38
GRCh371254,348,687 - 54,352,740 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,634,981 - 52,636,617 (+)NCBINCBI36Build 36hg18NCBI36
Build 341252,634,980 - 52,636,617NCBI
Celera1253,998,317 - 53,999,953 (+)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1251,386,483 - 51,387,575 (+)NCBIHuRef
CHM1_11254,315,405 - 54,317,041 (+)NCBICHM1_1
T2T-CHM13v2.01253,920,393 - 53,924,445 (+)NCBIT2T-CHM13v2.0
Hoxc12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87135,952,682 - 135,954,280 (+)NCBIGRCr8
mRatBN7.27134,074,199 - 134,075,797 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,074,199 - 134,075,797 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,829,592 - 135,831,190 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,058,966 - 138,060,564 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,044,913 - 138,046,510 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07144,547,939 - 144,549,537 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,547,939 - 144,549,537 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,339,296 - 142,340,894 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,700,558 - 141,702,156 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17141,779,873 - 141,781,472 (+)NCBI
Celera7130,500,439 - 130,502,037 (+)NCBICelera
Cytogenetic Map7q36NCBI
Hoxc12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554581,213,269 - 1,214,835 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554581,213,269 - 1,214,835 (+)NCBIChiLan1.0ChiLan1.0
HOXC12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21040,226,979 - 40,231,017 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11240,223,747 - 40,227,785 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01234,796,301 - 34,800,333 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11235,586,456 - 35,588,629 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1235,586,456 - 35,588,567 (-)Ensemblpanpan1.1panPan2
HOXC12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,305,219 - 1,307,350 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,305,770 - 1,307,350 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2744,942,269 - 44,944,908 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,308,411 - 1,311,050 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,309,471 - 1,311,050 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,326,051 - 1,328,688 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,307,623 - 1,310,261 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02745,345,889 - 45,348,527 (+)NCBIUU_Cfam_GSD_1.0
Hoxc12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494561,984,247 - 61,988,087 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651211,176,743 - 11,178,360 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651211,176,743 - 11,178,360 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXC12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl519,167,157 - 19,169,795 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1519,167,174 - 19,169,684 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2519,518,428 - 19,520,932 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HOXC12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11150,065,394 - 50,074,796 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1150,065,598 - 50,067,226 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037195,972,601 - 195,976,631 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxc12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249042,010,025 - 2,011,606 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249042,010,025 - 2,011,606 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hoxc12
35 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:259
Count of miRNA genes:239
Interacting mature miRNAs:257
Transcripts:ENSMUST00000055562
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
1300627Sluc26_msusceptibility to lung cancer 26 (mouse)Not determined1570345653104073951Mouse
1357526Hyplip2_mhyperlipidemia 2 (mouse)Not determined1512402203102896555Mouse
11528547Sluc34_msusceptibility to lung cancer 34 (mouse)1597884933102896555Mouse
1301918Skull22_mskull morphology 22 (mouse)Not determined1585901546104073951Mouse
14928306Manh79_mmandible shape 79 (mouse)1578847557104073951Mouse
1357894Epfpq3_mepididymal fat percentage QTL 3 (mouse)Not determined1578601103102901704Mouse
4142060W3q6_mweight 3 weeks QTL 6 (mouse)Not determined78601103102901704Mouse
12791003Aath8_maortic arch atherosclerosis 8 (mouse)1573430144104073951Mouse
11530038Sluc34b_msusceptibility to lung cancer 34b (mouse)1585896437104073951Mouse
11530037Sluc34a_msusceptibility to lung cancer 34a (mouse)1585896437104073951Mouse
1558985Eae32_mexperimental allergic encephalomyelitis susceptibility 32 (mouse)Not determined1532578416103425899Mouse
12880411V125Dq11_mvitamin D active form serum level QTL 11 (mouse)1578897881104073951Mouse
1300851Heal4_mwound healing/regeneration 4 (mouse)Not determined1577527592104073951Mouse
14747011Mancz13_mmandible centroid size 13 (mouse)1572382669104073951Mouse
10402490Dipa5_mdrug induced psychomotor activation 5 (mouse)Not determined1579163411104073951Mouse
1300726Pitm4_mprion incubation time 4 (mouse)Not determined1570349271104073951Mouse
1302197Bhr2_mbronchial hyperresponsiveness 2 (mouse)Not determined1564306334103425899Mouse
1302074Bmd4_mbone mineral density 4 (mouse)Not determined1556186708103425899Mouse
4141902Cia37_mcollagen induced arthritis 37 (mouse)Not determined1580884933104073951Mouse
14700689Carg5_mCandida albicans resistance gene 5 (mouse)1597697881103008427Mouse
4141581Dshv1_mdorsal hippocampal volume 1 (mouse)Not determined92788640103425899Mouse
4141897Imrfq2_mimmune response to Factor IX QTL 2 (mouse)Not determined79908940104073951Mouse
1301284Cosz3_mcocaine seizure 3 (mouse)Not determined1580313634104073951Mouse
4141511Gdcr1_mglycerolphosphate dehydrogenase regulator 1 (mouse)Not determined82615474104073951Mouse
1357614Bmca_mbile mucin accumulation (mouse)Not determined1585896437104073951Mouse
1300648Dbsty4_mdiabesity 4 (mouse)Not determined1570349271104073951Mouse
1300974Pgia9_mproteoglycan induced arthritis 9 (mouse)Not determined1580884933104073951Mouse

Markers in Region
Hoxc12  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map15F3UniSTS
cM Map1558.01UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000055562   ⟹   ENSMUSP00000051003
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl15102,845,192 - 102,847,044 (+)Ensembl
GRCm38.p6 Ensembl15102,936,757 - 102,938,609 (+)Ensembl
RefSeq Acc Id: NM_010463   ⟹   NP_034593
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm3915102,845,261 - 102,847,044 (+)NCBI
GRCm3815102,936,826 - 102,938,609 (+)NCBI
MGSCv3715102,767,284 - 102,768,948 (+)RGD
Celera15105,097,783 - 105,099,447 (+)RGD
cM Map15 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_034593 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA20230 (Get FASTA)   NCBI Sequence Viewer  
  AAI20846 (Get FASTA)   NCBI Sequence Viewer  
  AAI20848 (Get FASTA)   NCBI Sequence Viewer  
  AAM28679 (Get FASTA)   NCBI Sequence Viewer  
  EDL03952 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000051003
  ENSMUSP00000051003.3
GenBank Protein Q8K5B8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_034593   ⟸   NM_010463
- UniProtKB: Q8K5B8 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000051003   ⟸   ENSMUST00000055562

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8K5B8-F1-model_v2 AlphaFold Q8K5B8 1-280 view protein structure

Promoters
RGD ID:6826100
Promoter ID:MM_KWN:19870
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lung
Transcripts:ENSMUST00000055562
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv3615102,767,241 - 102,767,741 (+)MPROMDB
RGD ID:8685234
Promoter ID:EPDNEW_M20648
Type:multiple initiation site
Name:Hoxc12_1
Description:Mus musculus homeobox C12 , 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
GRCm3815102,936,837 - 102,936,897EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:96194 AgrOrtholog
Ensembl Genes ENSMUSG00000050328 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000055562 ENTREZGENE
  ENSMUST00000055562.3 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
KEGG Report mmu:15421 UniProtKB/Swiss-Prot
MGD MGI:96194 ENTREZGENE
NCBI Gene 15421 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-C12 UniProtKB/Swiss-Prot
  HOMEOBOX PROTEIN HOX-D12-RELATED UniProtKB/Swiss-Prot
Pfam Homeodomain UniProtKB/Swiss-Prot
PhenoGen Hoxc12 PhenoGen
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 HXC12_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE