Hoxc13 (homeobox C13) - Rat Genome Database

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Gene: Hoxc13 (homeobox C13) Rattus norvegicus
Analyze
Symbol: Hoxc13
Name: homeobox C13
RGD ID: 1563984
Description: Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Predicted to be involved in positive regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including hair follicle development; nail development; and tongue morphogenesis. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in ectodermal dysplasia 9. Orthologous to human HOXC13 (homeobox C13); INTERACTS WITH alpha-Zearalanol; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: homeobox protein Hox-C13; LOC315337; RGD1563984; similar to homeodomain protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87135,937,126 - 135,943,962 (+)NCBIGRCr8
mRatBN7.27134,058,640 - 134,065,479 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,058,640 - 134,064,800 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.07144,531,814 - 144,538,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,531,814 - 144,537,966 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,323,171 - 142,329,323 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,685,004 - 141,691,159 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7130,489,719 - 130,491,373 (+)NCBICelera
Cytogenetic Map7q36NCBI
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
nucleus  (ISO)

References

References - curated
# Reference Title Reference Citation
1. 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.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9420327   PMID:21191399  


Genomics

Comparative Map Data
Hoxc13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87135,937,126 - 135,943,962 (+)NCBIGRCr8
mRatBN7.27134,058,640 - 134,065,479 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,058,640 - 134,064,800 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.07144,531,814 - 144,538,298 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,531,814 - 144,537,966 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,323,171 - 142,329,323 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,685,004 - 141,691,159 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7130,489,719 - 130,491,373 (+)NCBICelera
Cytogenetic Map7q36NCBI
HOXC13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381253,938,831 - 53,946,544 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1253,938,831 - 53,946,544 (+)EnsemblGRCh38hg38GRCh38
GRCh371254,332,615 - 54,340,328 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,618,843 - 52,626,595 (+)NCBINCBI36Build 36hg18NCBI36
Build 341252,618,842 - 52,626,594NCBI
Celera1253,982,194 - 53,989,933 (+)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1251,370,279 - 51,377,685 (+)NCBIHuRef
CHM1_11254,299,300 - 54,307,033 (+)NCBICHM1_1
T2T-CHM13v2.01253,904,353 - 53,912,048 (+)NCBIT2T-CHM13v2.0
Hoxc13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,829,566 - 102,837,249 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,829,538 - 102,837,249 (+)EnsemblGRCm39 Ensembl
GRCm3815102,921,131 - 102,928,814 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,921,103 - 102,928,814 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715102,751,562 - 102,759,245 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,749,165 - 102,756,848 (+)NCBIMGSCv36mm8
Celera15105,078,954 - 105,086,637 (+)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1557.99NCBI
Hoxc13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554581,197,295 - 1,205,127 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554581,197,295 - 1,205,098 (+)NCBIChiLan1.0ChiLan1.0
HOXC13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21040,239,252 - 40,246,959 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11240,236,020 - 40,243,727 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01234,808,575 - 34,816,324 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11235,596,821 - 35,604,560 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1235,596,821 - 35,604,560 (-)Ensemblpanpan1.1panPan2
HOXC13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,315,532 - 1,323,470 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,273,131 - 1,323,370 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2744,926,178 - 44,934,051 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,319,256 - 1,327,126 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,319,221 - 1,327,051 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,336,900 - 1,344,764 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,318,461 - 1,326,337 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02745,329,789 - 45,337,670 (+)NCBIUU_Cfam_GSD_1.0
Hoxc13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494561,997,436 - 62,004,487 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493651211,160,343 - 11,166,616 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXC13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl519,151,084 - 19,158,646 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1519,151,096 - 19,159,008 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2519,624,272 - 19,632,185 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXC13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11150,039,034 - 50,057,178 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1150,049,509 - 50,055,895 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037195,985,021 - 195,992,836 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxc13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249041,993,854 - 2,000,500 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249041,993,854 - 2,001,623 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:85
Count of miRNA genes:68
Interacting mature miRNAs:72
Transcripts:ENSRNOT00000033300
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
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7121393075137014596Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)7132099939137014596Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7115313999136544683Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7135371291137014596Rat

Markers in Region
Hoxc13  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27134,064,551 - 134,064,780 (+)MAPPERmRatBN7.2
Rnor_6.07144,537,718 - 144,537,946NCBIRnor6.0
Rnor_5.07142,329,075 - 142,329,303UniSTSRnor5.0
Celera7130,490,793 - 130,491,021UniSTS
Cytogenetic Map7q36UniSTS
Hoxc13  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27134,058,981 - 134,059,061 (+)MAPPERmRatBN7.2
Rnor_6.07144,532,156 - 144,532,235NCBIRnor6.0
Rnor_5.07142,323,513 - 142,323,592UniSTSRnor5.0
Cytogenetic Map7q36UniSTS


Expression

RNA-SEQ Expression

appendage
ectoderm
endocrine system
endoderm
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
2 18 2 1 6 5 2 11 2 19 1

Sequence


Ensembl Acc Id: ENSRNOT00000033300   ⟹   ENSRNOP00000034124
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7134,058,640 - 134,064,800 (+)Ensembl
Rnor_6.0 Ensembl7144,531,814 - 144,537,966 (+)Ensembl
RefSeq Acc Id: XM_235695   ⟹   XP_235695
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87135,937,126 - 135,943,962 (+)NCBI
mRatBN7.27134,058,640 - 134,065,479 (+)NCBI
Rnor_6.07144,531,814 - 144,538,298 (+)NCBI
Rnor_5.07142,323,171 - 142,329,323 (+)NCBI
RGSC_v3.47141,685,004 - 141,691,159 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_235695 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000034124.4
RefSeq Acc Id: XP_235695   ⟸   XM_235695
- UniProtKB: D3ZKV8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000034124   ⟸   ENSRNOT00000033300
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKV8-F1-model_v2 AlphaFold D3ZKV8 1-328 view protein structure

Transcriptome

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

Promoters
RGD ID:13695712
Promoter ID:EPDNEW_R6234
Type:multiple initiation site
Name:Hoxc13_1
Description:homeobox C13
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07144,531,887 - 144,531,947EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563984 AgrOrtholog
BioCyc Gene G2FUF-31922 BioCyc
Ensembl Genes ENSRNOG00000028679 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000033300.5 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro AP_axis_regulatory_Homeobox UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  HoxA13_N UniProtKB/TrEMBL
KEGG Report rno:315337 UniProtKB/TrEMBL
NCBI Gene 315337 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-C13 UniProtKB/TrEMBL
  SEGMENTATION PROTEIN FUSHI TARAZU-LIKE PROTEIN UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
  HoxA13_N UniProtKB/TrEMBL
PhenoGen Hoxc13 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028679 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt D3ZKV8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Hoxc13  homeobox C13  RGD1563984_predicted  similar to homeodomain protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563984_predicted  similar to homeodomain protein (predicted)  LOC315337  similar to homeodomain protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC315337  similar to homeodomain protein      Symbol and Name status set to provisional 70820 PROVISIONAL