HOXC5 (homeobox C5) - Rat Genome Database

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Gene: HOXC5 (homeobox C5) Canis lupus familiaris
Analyze
Symbol: HOXC5
Name: homeobox C5
RGD ID: 12111395
Description: ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); RNA polymerase II cis-regulatory region sequence-specific DNA binding (inferred); INVOLVED IN anterior/posterior pattern specification (ortholog); embryonic skeletal system development (ortholog); ASSOCIATED WITH genetic disease (ortholog); Neurodevelopmental Disorders (ortholog); FOUND IN cell junction (inferred); nucleoplasm (inferred); nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: homeobox protein Hox-C5
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,227,739 - 1,232,802 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,229,600 - 1,231,359 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2745,004,585 - 45,021,664 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,231,615 - 1,248,697 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,231,805 - 1,233,191 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,249,332 - 1,266,409 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,230,865 - 1,247,956 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02745,408,207 - 45,425,291 (+)NCBIUU_Cfam_GSD_1.0
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
cell junction  (IEA)
nucleoplasm  (IEA)
nucleus  (IEA)

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
HOXC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,227,739 - 1,232,802 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,229,600 - 1,231,359 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2745,004,585 - 45,021,664 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,231,615 - 1,248,697 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,231,805 - 1,233,191 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,249,332 - 1,266,409 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,230,865 - 1,247,956 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02745,408,207 - 45,425,291 (+)NCBIUU_Cfam_GSD_1.0
HOXC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381254,016,888 - 54,035,361 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1254,033,050 - 54,035,361 (+)EnsemblGRCh38hg38GRCh38
GRCh371254,410,672 - 54,429,145 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,696,909 - 52,715,412 (+)NCBINCBI36Build 36hg18NCBI36
Build 341252,713,098 - 52,715,412NCBI
Celera1254,060,259 - 54,078,762 (+)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1251,448,399 - 51,466,902 (+)NCBIHuRef
CHM1_11254,377,346 - 54,395,833 (+)NCBICHM1_1
T2T-CHM13v2.01253,982,461 - 54,000,926 (+)NCBIT2T-CHM13v2.0
Hoxc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,922,440 - 102,925,861 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,875,878 - 102,925,861 (+)EnsemblGRCm39 Ensembl
GRCm3815103,014,008 - 103,017,429 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,967,443 - 103,017,429 (+)EnsemblGRCm38mm10GRCm38
MGSCv3715102,844,439 - 102,847,860 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,842,042 - 102,845,463 (+)NCBIMGSCv36mm8
Celera15105,174,918 - 105,178,339 (+)NCBICelera
Cytogenetic Map15F3NCBI
cM Map1558.07NCBI
Hoxc5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87136,029,454 - 136,032,876 (+)NCBIGRCr8
mRatBN7.27134,150,988 - 134,154,410 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7134,150,988 - 134,154,410 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,906,383 - 135,909,805 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07138,135,761 - 138,139,183 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07138,121,700 - 138,125,122 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07144,628,120 - 144,631,542 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,628,120 - 144,631,542 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,419,477 - 142,422,899 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,777,331 - 141,780,753 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.17141,856,371 - 141,857,803 (+)NCBI
Celera7130,576,883 - 130,580,305 (+)NCBICelera
Cytogenetic Map7q36NCBI
Hoxc5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554581,288,411 - 1,293,270 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554581,288,411 - 1,293,095 (+)NCBIChiLan1.0ChiLan1.0
HOXC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21040,150,654 - 40,154,631 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11240,147,426 - 40,151,785 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01234,720,006 - 34,722,202 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11235,508,711 - 35,510,388 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1235,508,711 - 35,510,388 (-)Ensemblpanpan1.1panPan2
Hoxc5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494561,907,734 - 61,910,013 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651211,254,942 - 11,258,702 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651211,254,959 - 11,258,702 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXC5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl519,245,851 - 19,248,172 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1519,245,857 - 19,248,183 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2520,146,815 - 20,150,108 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXC5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11150,141,814 - 50,146,089 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1150,143,849 - 50,146,080 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037195,877,415 - 195,900,505 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxc5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249042,086,531 - 2,090,428 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249042,086,437 - 2,091,542 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in HOXC5
67 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 3
Low 9 3 3 5 8 6
Below cutoff 5 5 13 6 3 6 1 12 8 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000049441   ⟹   ENSCAFP00000041898
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl271,229,600 - 1,231,359 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845032091   ⟹   ENSCAFP00845025093
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl271,231,805 - 1,233,191 (-)Ensembl
RefSeq Acc Id: XM_005636751   ⟹   XP_005636808
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1271,227,739 - 1,232,802 (-)NCBI
Dog10K_Boxer_Tasha2745,004,585 - 45,021,664 (+)NCBI
Sequence:
RefSeq Acc Id: XM_038438018   ⟹   XP_038293946
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0271,231,615 - 1,248,697 (-)NCBI
RefSeq Acc Id: XM_038512723   ⟹   XP_038368651
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1271,249,332 - 1,266,409 (-)NCBI
RefSeq Acc Id: XM_038577839   ⟹   XP_038433767
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.02745,408,207 - 45,425,291 (+)NCBI
RefSeq Acc Id: XM_038640476   ⟹   XP_038496404
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0271,230,865 - 1,247,956 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_005636808   ⟸   XM_005636751
- UniProtKB: A0A8C0L8Y2 (UniProtKB/TrEMBL),   A0A8C0NPX4 (UniProtKB/TrEMBL),   A0A8I3PAE7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000041898   ⟸   ENSCAFT00000049441
RefSeq Acc Id: XP_038368651   ⟸   XM_038512723
RefSeq Acc Id: XP_038496404   ⟸   XM_038640476
RefSeq Acc Id: XP_038293946   ⟸   XM_038438018
- UniProtKB: A0A8C0L8Y2 (UniProtKB/TrEMBL),   A0A8C0NPX4 (UniProtKB/TrEMBL),   A0A8I3PAE7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038433767   ⟸   XM_038577839
- UniProtKB: A0A8C0L8Y2 (UniProtKB/TrEMBL),   A0A8C0NPX4 (UniProtKB/TrEMBL),   A0A8I3PAE7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845025093   ⟸   ENSCAFT00845032091
Protein Domains
Homeobox


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000028496 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030019017 UniProtKB/TrEMBL
  ENSCAFG00040020277 UniProtKB/TrEMBL
  ENSCAFG00845018144 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000049441.3 UniProtKB/TrEMBL
  ENSCAFT00030034946.1 UniProtKB/TrEMBL
  ENSCAFT00040037494.1 UniProtKB/TrEMBL
  ENSCAFT00845032091 ENTREZGENE
  ENSCAFT00845032091.1 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_antennapedia UniProtKB/TrEMBL
  Homeobox_Antennapedia_CS UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
KEGG Report cfa:102152615 UniProtKB/TrEMBL
NCBI Gene HOXC5 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX UniProtKB/TrEMBL
  HOMEOBOX PROTEIN HOX-C5 UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/TrEMBL
PRINTS ANTENNAPEDIA UniProtKB/TrEMBL
  HOMEOBOX UniProtKB/TrEMBL
PROSITE ANTENNAPEDIA UniProtKB/TrEMBL
  HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt A0A8C0L8Y2 ENTREZGENE
  A0A8C0NPX4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PAE7 ENTREZGENE, UniProtKB/TrEMBL