Hoxc4 (homeo box C4) - Rat Genome Database

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Gene: Hoxc4 (homeo box C4) Rattus norvegicus
Analyze
Symbol: Hoxc4
Name: homeo box C4
RGD ID: 1586210
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; HMG box domain binding activity; and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in cellular response to glial cell derived neurotrophic factor and positive regulation of male germ-line stem cell asymmetric division. Predicted to be located in nucleoplasm. Orthologous to human HOXC4 (homeobox C4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: homeo box C4 (mapped); Homeobox gene C4; homeobox protein Hox-C4; homeobox protein R3; Hox3r3; Hoxc4_mapped
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87136,049,059 - 136,051,601 (+)NCBIGRCr8
mRatBN7.27134,135,279 - 134,173,133 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,170,591 - 134,173,133 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,926,005 - 135,928,548 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,155,381 - 138,157,924 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,141,262 - 138,143,805 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07144,646,605 - 144,652,589 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,647,587 - 144,650,129 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,378,916 - 142,441,486 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,796,934 - 141,799,476 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7130,596,539 - 130,599,081 (+)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
nucleoplasm  (IEA,ISO)
nucleus  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Expression of homeotic genes Hoxa3, Hoxb3, Hoxd3 and Hoxc4 is decreased in the lungs but not in the hearts of adriamycin-exposed mice. Calonge WM, etal., Pediatr Surg Int. 2007 May;23(5):419-24.
2. Chromosomal assignment of seven rat homeobox genes to rat chromosomes 3, 4, 7, and 10. Chung SY, etal., Mamm Genome 1993 Sep;4(9):537-40.
3. 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.
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Identification of glial cell line-derived neurotrophic factor-regulated genes important for spermatogonial stem cell self-renewal in the rat. Schmidt JA, etal., Biol Reprod. 2009 Jul;81(1):56-66. Epub 2009 Apr 1.
Additional References at PubMed
PMID:2907739   PMID:8626021   PMID:8660891   PMID:15252056   PMID:16582099  


Genomics

Comparative Map Data
Hoxc4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87136,049,059 - 136,051,601 (+)NCBIGRCr8
mRatBN7.27134,135,279 - 134,173,133 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,170,591 - 134,173,133 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,926,005 - 135,928,548 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,155,381 - 138,157,924 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,141,262 - 138,143,805 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07144,646,605 - 144,652,589 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,647,587 - 144,650,129 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,378,916 - 142,441,486 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,796,934 - 141,799,476 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7130,596,539 - 130,599,081 (+)NCBICelera
Cytogenetic Map7q36NCBI
HOXC4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381254,016,888 - 54,056,030 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1254,016,931 - 54,056,030 (+)EnsemblGRCh38hg38GRCh38
GRCh371254,410,672 - 54,449,814 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,696,909 - 52,736,081 (+)NCBINCBI36Build 36hg18NCBI36
Build 341252,733,927 - 52,735,630NCBI
Celera1254,060,259 - 54,098,621 (+)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1251,448,399 - 51,487,572 (+)NCBIHuRef
CHM1_11254,377,346 - 54,416,498 (+)NCBICHM1_1
T2T-CHM13v2.01253,982,461 - 54,021,597 (+)NCBIT2T-CHM13v2.0
Hoxc4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,926,531 - 102,945,281 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,927,366 - 102,945,278 (+)EnsemblGRCm39 Ensembl
GRCm3815103,018,097 - 103,036,856 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15103,018,934 - 103,036,852 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715102,864,826 - 102,867,283 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,862,429 - 102,864,631 (+)NCBIMGSCv36mm8
Celera15105,195,304 - 105,197,761 (+)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1558.08NCBI
Hoxc4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554581,309,119 - 1,313,344 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554581,251,601 - 1,313,291 (+)NCBIChiLan1.0ChiLan1.0
HOXC4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21040,130,013 - 40,169,600 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11240,126,781 - 40,166,801 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01234,699,357 - 34,702,368 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11235,487,619 - 35,489,853 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1235,487,619 - 35,526,627 (-)Ensemblpanpan1.1panPan2
HOXC4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,209,510 - 1,246,873 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,172,229 - 1,226,572 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2744,981,922 - 45,041,680 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,211,609 - 1,271,363 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,211,769 - 1,248,693 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,229,321 - 1,289,063 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,210,851 - 1,270,586 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02745,385,528 - 45,445,321 (+)NCBIUU_Cfam_GSD_1.0
Hoxc4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494561,887,299 - 61,904,863 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651211,274,416 - 11,277,531 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651211,238,905 - 11,277,531 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXC4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl519,265,081 - 19,268,257 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1519,250,411 - 19,268,267 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2520,151,903 - 20,169,649 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXC4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11150,127,573 - 50,167,077 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1150,164,980 - 50,166,267 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037195,875,175 - 195,914,587 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxc4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249042,092,055 - 2,109,979 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249042,104,504 - 2,109,729 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hoxc4
155 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:84
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000022398
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
HOX3A  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27134,171,404 - 134,172,100 (+)MAPPERmRatBN7.2
Rnor_6.07144,648,401 - 144,649,096NCBIRnor6.0
Rnor_5.07142,439,758 - 142,440,453UniSTSRnor5.0
RGSC_v3.47141,797,748 - 141,798,443UniSTSRGSC3.4
Celera7130,597,353 - 130,598,048UniSTS
Cytogenetic Map7q35UniSTS
Hoxc4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27134,171,277 - 134,172,284 (+)MAPPERmRatBN7.2
Rnor_6.07144,648,274 - 144,649,280NCBIRnor6.0
Rnor_5.07142,439,631 - 142,440,637UniSTSRnor5.0
RGSC_v3.47141,797,621 - 141,798,627UniSTSRGSC3.4
Celera7130,597,226 - 130,598,232UniSTS
Cytogenetic Map7q35UniSTS
Hoxc4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27134,171,411 - 134,172,028 (+)MAPPERmRatBN7.2
Rnor_6.07144,648,408 - 144,649,024NCBIRnor6.0
Rnor_5.07142,439,765 - 142,440,381UniSTSRnor5.0
Celera7130,597,360 - 130,597,976UniSTS
Cytogenetic Map7q35UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4 4 4 2 20 24
Low 2 4 11 2 6 2 8 11 16 15 11 2 8
Below cutoff 1 20 19 16 9 16 19 6 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000022398   ⟹   ENSRNOP00000022398
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7134,170,591 - 134,173,133 (+)Ensembl
Rnor_6.0 Ensembl7144,647,587 - 144,650,129 (+)Ensembl
RefSeq Acc Id: NM_001109884   ⟹   NP_001103354
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87136,049,059 - 136,051,601 (+)NCBI
mRatBN7.27134,170,591 - 134,173,133 (+)NCBI
Rnor_6.07144,647,587 - 144,650,129 (+)NCBI
Rnor_5.07142,378,916 - 142,441,486 (+)NCBI
RGSC_v3.47141,796,934 - 141,799,476 (+)RGD
Celera7130,596,539 - 130,599,081 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001103354 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41343 (Get FASTA)   NCBI Sequence Viewer  
  EDL86800 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022398
  ENSRNOP00000022398.3
GenBank Protein P18865 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001103354   ⟸   NM_001109884
- UniProtKB: D3ZK87 (UniProtKB/TrEMBL),   A6KCZ2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000022398   ⟸   ENSRNOT00000022398
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P18865-F1-model_v2 AlphaFold P18865 1-76 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:1586210 AgrOrtholog
BioCyc Gene G2FUF-31911 BioCyc
Ensembl Genes ENSRNOG00000016613 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022398 ENTREZGENE
  ENSRNOT00000022398.5 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_antennapedia UniProtKB/TrEMBL
  Homeobox_Antennapedia_CS UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24459 UniProtKB/TrEMBL
NCBI Gene 24459 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-C4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOTIC PROTEIN DEFORMED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hoxc4 PhenoGen
PRINTS ANTENNAPEDIA UniProtKB/TrEMBL
  HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ANTENNAPEDIA UniProtKB/TrEMBL
  HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016613 RatGTEx
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6KCZ2 ENTREZGENE, UniProtKB/TrEMBL
  D3ZK87 ENTREZGENE, UniProtKB/TrEMBL
  HXC4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-04-13   homeo box C4  Hoxc4  homeo box C4 (mapped)  Name updated 737654 APPROVED
2007-04-11 Hoxc4  homeo box C4 (mapped)  Hoxc4_mapped  homeo box C4 (mapped)  Data merged from RGD:2820 737654 APPROVED
2006-11-19 Hoxc4  homeo box C4 (mapped)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Hoxc4_mapped  homeo box C4 (mapped)      Symbol and Name updated 1556543 APPROVED
2002-06-10 Hoxc4  Homeobox gene C4      Symbol and Name status set to approved 70586 APPROVED