HOXA4 (homeobox A4) - Rat Genome Database

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Gene: HOXA4 (homeobox A4) Canis lupus familiaris
Analyze
Symbol: HOXA4
Name: homeobox A4
RGD ID: 12212962
Description: ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription factor activity (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); INVOLVED IN anterior/posterior pattern specification (ortholog); embryonic skeletal system morphogenesis (ortholog); ASSOCIATED WITH genetic disease (ortholog); pleomorphic xanthoastrocytoma (ortholog); FOUND IN nuclear body (inferred); nucleoplasm (inferred); nucleus (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: homeo box A4; homeobox protein Hox-A4; Hoxa
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
CanFam3.11440,302,106 - 40,304,437 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1440,302,816 - 40,304,321 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1439,733,161 - 39,735,443 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01440,240,879 - 40,243,161 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1440,241,589 - 40,243,094 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11440,354,968 - 40,357,250 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01440,040,052 - 40,042,332 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01440,398,629 - 40,400,911 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:10331940   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
HOXA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11440,302,106 - 40,304,437 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1440,302,816 - 40,304,321 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1439,733,161 - 39,735,443 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01440,240,879 - 40,243,161 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1440,241,589 - 40,243,094 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11440,354,968 - 40,357,250 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01440,040,052 - 40,042,332 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01440,398,629 - 40,400,911 (-)NCBIUU_Cfam_GSD_1.0
HOXA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38727,128,525 - 27,130,757 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl727,128,507 - 27,130,780 (-)EnsemblGRCh38hg38GRCh38
GRCh37727,168,144 - 27,170,376 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36727,134,651 - 27,136,924 (-)NCBINCBI36Build 36hg18NCBI36
Build 34726,941,249 - 26,943,639NCBI
Celera727,157,064 - 27,159,337 (-)NCBICelera
Cytogenetic Map7p15.2NCBI
HuRef727,048,696 - 27,050,969 (-)NCBIHuRef
CHM1_1727,167,837 - 27,170,110 (-)NCBICHM1_1
T2T-CHM13v2.0727,264,506 - 27,266,738 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2727,219,281 - 27,221,554 (-)NCBI
Hoxa4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39652,166,662 - 52,168,683 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl652,166,651 - 52,168,733 (-)EnsemblGRCm39 Ensembl
GRCm38652,189,682 - 52,191,703 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl652,189,671 - 52,191,753 (-)EnsemblGRCm38mm10GRCm38
MGSCv37652,139,686 - 52,141,702 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36652,119,270 - 52,121,286 (-)NCBIMGSCv36mm8
Celera652,711,346 - 52,713,362 (-)NCBICelera
Cytogenetic Map6B3NCBI
cM Map625.4NCBI
Hoxa4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8482,620,294 - 82,622,302 (-)NCBIGRCr8
mRatBN7.2481,289,677 - 81,291,685 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl481,289,682 - 81,291,685 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx486,511,488 - 86,513,496 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0482,286,880 - 82,288,888 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0480,714,011 - 80,716,019 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0482,158,234 - 82,160,317 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl482,158,892 - 82,160,240 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04146,825,065 - 146,827,156 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4480,489,558 - 80,491,562 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Cytogenetic Map4q24NCBI
Hoxa4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541028,823,500 - 28,825,020 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541028,822,814 - 28,827,294 (-)NCBIChiLan1.0ChiLan1.0
HOXA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2631,957,687 - 31,959,927 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1780,282,420 - 80,284,653 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0727,773,001 - 27,775,284 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1727,372,664 - 27,374,961 (-)NCBIpanpan1.1PanPan1.1panPan2
Hoxa4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511884,544,554 - 84,546,285 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049364783,756,289 - 3,758,020 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11845,443,268 - 45,445,662 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21850,076,492 - 50,080,299 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12131,238,087 - 31,240,406 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2131,238,182 - 31,240,384 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604273,481,035 - 73,495,699 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxa4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247393,474,990 - 3,476,486 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247393,474,868 - 3,477,190 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in HOXA4
19 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 1 4 5 6
Low 4 12 6 6 6 6 6 2 3 5
Below cutoff 4 6 7 5

Sequence


RefSeq Acc Id: ENSCAFT00000004722   ⟹   ENSCAFP00000004370
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1440,302,816 - 40,304,321 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845020100   ⟹   ENSCAFP00845015752
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1440,241,589 - 40,243,094 (-)Ensembl
RefSeq Acc Id: XM_038494906   ⟹   XP_038350834
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.11440,354,968 - 40,357,250 (-)NCBI
RefSeq Acc Id: XM_038557180   ⟹   XP_038413108
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01440,398,629 - 40,400,911 (-)NCBI
RefSeq Acc Id: XM_038621120   ⟹   XP_038477048
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01440,040,052 - 40,042,332 (-)NCBI
RefSeq Acc Id: XM_038686797   ⟹   XP_038542725
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01440,240,879 - 40,243,161 (-)NCBI
RefSeq Acc Id: XM_539486   ⟹   XP_539486
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11440,302,106 - 40,304,437 (-)NCBI
Dog10K_Boxer_Tasha1439,733,161 - 39,735,443 (-)NCBI
Sequence:
RefSeq Acc Id: XP_539486   ⟸   XM_539486
- UniProtKB: A0A8C0S465 (UniProtKB/TrEMBL),   A0A8C0JSA1 (UniProtKB/TrEMBL),   A0A8I3N8X5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000004370   ⟸   ENSCAFT00000004722
RefSeq Acc Id: XP_038350834   ⟸   XM_038494906
RefSeq Acc Id: XP_038477048   ⟸   XM_038621120
RefSeq Acc Id: XP_038542725   ⟸   XM_038686797
- UniProtKB: A0A8C0S465 (UniProtKB/TrEMBL),   A0A8C0JSA1 (UniProtKB/TrEMBL),   A0A8I3N8X5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038413108   ⟸   XM_038557180
- UniProtKB: A0A8C0JSA1 (UniProtKB/TrEMBL),   A0A8C0S465 (UniProtKB/TrEMBL),   A0A8I3N8X5 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845015752   ⟸   ENSCAFT00845020100
Protein Domains
Homeobox

Promoters
RGD ID:13685790
Promoter ID:EPDNEW_C3860
Type:single initiation site
Name:HOXA4_1
Description:homeobox A4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11440,304,257 - 40,304,317EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000002948 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030005605 UniProtKB/TrEMBL
  ENSCAFG00040009707 UniProtKB/TrEMBL
  ENSCAFG00845011344 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000004722.4 UniProtKB/TrEMBL
  ENSCAFT00030010253.1 UniProtKB/TrEMBL
  ENSCAFT00040017989.1 UniProtKB/TrEMBL
  ENSCAFT00845020100 ENTREZGENE
  ENSCAFT00845020100.1 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:482369 UniProtKB/TrEMBL
NCBI Gene HOXA4 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-A4 UniProtKB/TrEMBL
  HOMEOTIC PROTEIN DEFORMED 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 A0A8C0JSA1 ENTREZGENE
  A0A8C0S465 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3N8X5 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:41748 ENTREZGENE