Hoxc11 (homeobox C11) - 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: Hoxc11 (homeobox C11) Rattus norvegicus
Analyze
Symbol: Hoxc11
Name: homeobox C11
RGD ID: 6489991
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. Predicted to be involved in embryonic skeletal joint morphogenesis and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including embryonic digit morphogenesis; organ induction; and regionalization. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human HOXC11 (homeobox C11); INTERACTS WITH (+)-catechin (ortholog); 17beta-estradiol (ortholog); 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homeobox protein Hox-C11; homeobox protein Hox-C11-like; LOC100911859; RGD1305450
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
GRCr87135,969,707 - 135,973,222 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7135,969,989 - 135,973,222 (+)EnsemblGRCr8
mRatBN7.27134,091,224 - 134,094,738 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,091,552 - 134,094,738 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7135,846,891 - 135,850,122 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,076,265 - 138,079,496 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,062,254 - 138,065,485 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd7138,044,650 - 138,047,881 (+)NCBIDahl_SR_JrHsd
Lyon_Normotensive7138,996,980 - 139,000,212 (+)NCBILyon_Normotensive
Lyon_Hypertensive7139,129,186 - 139,132,418 (+)NCBILyon_Hypertensive
F344_StmMcwi7137,591,604 - 137,594,835 (+)NCBIF344_StmMcwi
Rnor_6.07144,565,392 - 144,568,580 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,565,392 - 144,567,580 (+)Ensemblrn6Rnor6.0
Rnor_5.07142,356,703 - 142,358,942 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera7130,517,972 - 130,520,959 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9582375   PMID:12050119   PMID:12869760   PMID:20978074  


Genomics

Comparative Map Data
Hoxc11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87135,969,707 - 135,973,222 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7135,969,989 - 135,973,222 (+)EnsemblGRCr8
mRatBN7.27134,091,224 - 134,094,738 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,091,552 - 134,094,738 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7135,846,891 - 135,850,122 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,076,265 - 138,079,496 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,062,254 - 138,065,485 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd7138,044,650 - 138,047,881 (+)NCBIDahl_SR_JrHsd
Lyon_Normotensive7138,996,980 - 139,000,212 (+)NCBILyon_Normotensive
Lyon_Hypertensive7139,129,186 - 139,132,418 (+)NCBILyon_Hypertensive
F344_StmMcwi7137,591,604 - 137,594,835 (+)NCBIF344_StmMcwi
Rnor_6.07144,565,392 - 144,568,580 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,565,392 - 144,567,580 (+)Ensemblrn6Rnor6.0
Rnor_5.07142,356,703 - 142,358,942 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera7130,517,972 - 130,520,959 (+)NCBICelera
Cytogenetic Map7q36NCBI
HOXC11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381253,973,126 - 53,977,643 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1253,973,126 - 53,977,643 (+)Ensemblhg38GRCh38
GRCh371254,366,910 - 54,371,427 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,653,177 - 52,656,470 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341252,653,195 - 52,656,468NCBI
Celera1254,016,511 - 54,019,822 (+)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1251,404,138 - 51,407,449 (+)NCBIHuRef
CHM1_11254,333,599 - 54,336,910 (+)NCBICHM1_1
T2T-CHM13v2.01253,938,618 - 53,943,153 (+)NCBIT2T-CHM13v2.0
Hoxc11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,862,961 - 102,865,136 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,862,862 - 102,866,143 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm3815102,954,526 - 102,956,701 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,954,427 - 102,957,708 (+)Ensemblmm10GRCm38
MGSCv3715102,784,957 - 102,787,132 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3615102,782,560 - 102,784,735 (+)NCBIMGSCv36mm8
Celera15105,115,456 - 105,117,632 (+)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1558.02NCBI
Hoxc11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554581,231,445 - 1,234,798 (+)Ensembl
ChiLan1.0NW_0049554581,231,625 - 1,234,785 (+)NCBIChiLan1.0ChiLan1.0
HOXC11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21040,209,471 - 40,213,236 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11240,201,196 - 40,209,548 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01234,777,790 - 34,782,104 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11235,567,093 - 35,570,396 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1235,567,093 - 35,570,396 (-)EnsemblpanPan2panpan1.1
HOXC11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,287,326 - 1,289,577 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,287,380 - 1,289,372 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2744,960,239 - 44,962,245 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0271,291,036 - 1,293,043 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,291,044 - 1,293,036 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,308,728 - 1,310,736 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,290,305 - 1,292,309 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02745,363,845 - 45,365,853 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Hoxc11
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494561,967,514 - 61,970,059 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651211,194,876 - 11,197,316 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493651211,194,876 - 11,197,316 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXC11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl519,178,619 - 19,189,013 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1519,181,580 - 19,189,031 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2519,685,024 - 19,687,605 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXC11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11150,076,648 - 50,087,084 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1150,083,893 - 50,086,060 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666037195,964,311 - 195,965,531 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxc11
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249042,027,993 - 2,030,148 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249042,027,792 - 2,030,148 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Hoxc11
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11260,125,287 - 260,128,474 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:14
Count of miRNA genes:12
Interacting mature miRNAs:14
Transcripts:ENSRNOT00000021589
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 (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
Hoxc11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27134,093,510 - 134,093,848 (+)MAPPERmRatBN7.2
Rnor_6.07144,567,353 - 144,567,690NCBIRnor6.0
Rnor_5.07142,358,710 - 142,359,047UniSTSRnor5.0
Celera7130,519,732 - 130,520,069UniSTS
Hoxc11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27134,091,833 - 134,091,901 (+)MAPPERmRatBN7.2
Rnor_6.07144,565,674 - 144,565,741NCBIRnor6.0
Rnor_5.07142,357,031 - 142,357,098UniSTSRnor5.0
Celera7130,518,254 - 130,518,321UniSTS


Expression

RNA-SEQ Expression

appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
12 1 33 2 1 1 1 5 109 20 10 25 80 61 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000021589   ⟹   ENSRNOP00000021589
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7135,969,989 - 135,973,222 (+)Ensembl
mRatBN7.2 Ensembl7134,091,552 - 134,094,738 (+)Ensembl
Rnor_6.0 Ensembl7144,565,392 - 144,567,580 (+)Ensembl
RefSeq Acc Id: NM_001308639   ⟹   NP_001295568
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87135,969,989 - 135,973,222 (+)NCBI
mRatBN7.27134,091,505 - 134,094,738 (+)NCBI
Dahl_SR_JrHsd7138,044,650 - 138,047,881 (+)NCBI
Lyon_Normotensive7138,996,980 - 139,000,212 (+)NCBI
Lyon_Hypertensive7139,129,186 - 139,132,418 (+)NCBI
F344_StmMcwi7137,591,604 - 137,594,835 (+)NCBI
Rnor_6.07144,565,392 - 144,568,580 (+)NCBI
Celera7130,517,972 - 130,520,959 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078238   ⟹   XP_038934166
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87135,969,707 - 135,973,220 (+)NCBI
mRatBN7.27134,091,224 - 134,094,736 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001295568 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934166 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000021589
  ENSRNOP00000021589.4
RefSeq Acc Id: NP_001295568   ⟸   NM_001308639
- UniProtKB: D4ACL0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000021589   ⟸   ENSRNOT00000021589
RefSeq Acc Id: XP_038934166   ⟸   XM_039078238
- Peptide Label: isoform X1
- UniProtKB: A6KCY4 (UniProtKB/TrEMBL)
Protein Domains
DUF3528   Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACL0-F1-model_v2 AlphaFold D4ACL0 1-304 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:6489991 AgrOrtholog
BioCyc Gene G2FUF-31920 BioCyc
Ensembl Genes ENSRNOG00000016141 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021589 ENTREZGENE
  ENSRNOT00000021589.6 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro DUF3528 UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
  Homeodomain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
KEGG Report rno:100911859 UniProtKB/TrEMBL
NCBI Gene LOC100911859 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-A11-RELATED UniProtKB/TrEMBL
  HOMEOBOX PROTEIN HOX-C11 UniProtKB/TrEMBL
Pfam DUF3528 UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
PhenoGen Hoxc11 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016141 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6KCY4 ENTREZGENE, UniProtKB/TrEMBL
  D4ACL0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-05-18 Hoxc11  homeobox C11  Hoxc11  homeobox C11  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-05-18 Hoxc11  homeobox C11  LOC100911859  homeobox protein Hox-C11-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911859  homeobox protein Hox-C11-like      Symbol and Name status set to provisional 70820 PROVISIONAL