HOXA1 (homeobox A1) - Rat Genome Database

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Gene: HOXA1 (homeobox A1) Sus scrofa
Analyze
Symbol: HOXA1
Name: homeobox A1
RGD ID: 13932952
Description: ENCODES a protein that exhibits DNA-binding transcription activator activity, RNA polymerase II-specific (ortholog); identical protein binding (ortholog); sequence-specific DNA binding (ortholog); INVOLVED IN abducens nerve formation (ortholog); anatomical structure formation involved in morphogenesis (ortholog); anatomical structure morphogenesis (ortholog); ASSOCIATED WITH Microtia-Anotia; Athabaskan brainstem dysgenesis syndrome (ortholog); autistic disorder (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Also known as: homeobox protein Hox-A1; mutant homeobox protein Hox-A1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1845,477,548 - 45,480,413 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11845,477,561 - 45,480,306 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21850,110,695 - 50,113,440 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA)

References
Additional References at PubMed
PMID:26035869  


Genomics

Comparative Map Data
HOXA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1845,477,548 - 45,480,413 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11845,477,561 - 45,480,306 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21850,110,695 - 50,113,440 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl727,092,993 - 27,096,000 (-)EnsemblGRCh38hg38GRCh38
GRCh38727,092,993 - 27,096,000 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37727,132,612 - 27,135,619 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36727,099,137 - 27,102,150 (-)NCBINCBI36hg18NCBI36
Build 34726,905,855 - 26,908,834NCBI
Celera727,121,549 - 27,124,562 (-)NCBI
Cytogenetic Map7p15.2NCBI
HuRef727,013,203 - 27,016,216 (-)NCBIHuRef
CHM1_1727,132,309 - 27,135,322 (-)NCBICHM1_1
CRA_TCAGchr7v2727,183,765 - 27,186,778 (-)NCBI
Hoxa1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39652,132,347 - 52,135,297 (-)NCBIGRCm39mm39
GRCm39 Ensembl652,132,570 - 52,135,297 (-)Ensembl
GRCm38652,155,367 - 52,160,007 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl652,155,590 - 52,158,317 (-)EnsemblGRCm38mm10GRCm38
MGSCv37652,105,366 - 52,108,316 (-)NCBIGRCm37mm9NCBIm37
MGSCv36652,084,950 - 52,087,900 (-)NCBImm8
Celera652,677,008 - 52,679,958 (-)NCBICelera
Cytogenetic Map6B3NCBI
cM Map625.4NCBI
Hoxa1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2481,255,814 - 81,258,504 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl481,255,883 - 81,258,504 (-)Ensembl
Rnor_6.0482,124,358 - 82,127,182 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl482,125,406 - 82,127,066 (-)EnsemblRnor6.0rn6Rnor6.0
Celera476,147,124 - 76,149,948 (-)NCBICelera
Cytogenetic Map4q24NCBI
Hoxa1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541028,787,817 - 28,790,962 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541028,788,245 - 28,790,971 (-)NCBIChiLan1.0ChiLan1.0
HOXA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1727,336,737 - 27,339,747 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl727,335,710 - 27,339,747 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0727,737,432 - 27,740,442 (-)NCBIMhudiblu_PPA_v0panPan3
HOXA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11440,267,033 - 40,272,212 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1440,267,528 - 40,269,681 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1439,698,088 - 39,703,711 (-)NCBI
ROS_Cfam_1.01440,205,795 - 40,211,418 (-)NCBI
UMICH_Zoey_3.11440,319,907 - 40,325,530 (-)NCBI
UNSW_CanFamBas_1.01440,004,976 - 40,010,599 (-)NCBI
UU_Cfam_GSD_1.01440,363,561 - 40,369,177 (-)NCBI
Hoxa1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511884,509,768 - 84,512,994 (-)NCBI
SpeTri2.0NW_0049364783,721,662 - 3,724,471 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12131,272,410 - 31,275,503 (+)NCBI
ChlSab1.1 Ensembl2131,272,889 - 31,275,551 (+)Ensembl
Vero_WHO_p1.0NW_02366604273,458,340 - 73,461,050 (-)NCBI
Hoxa1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247393,509,020 - 3,511,890 (+)NCBI


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 hemolymphoid system nervous system renal system reproductive system respiratory system
High
Medium
Low 2 1 2 3 2 1 1
Below cutoff 1 1 3 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000018188   ⟹   ENSSSCP00000017697
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1845,477,548 - 45,480,413 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000058453   ⟹   ENSSSCP00000037164
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1845,477,548 - 45,480,413 (+)Ensembl
RefSeq Acc Id: XM_003134844   ⟹   XP_003134892
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11845,477,561 - 45,480,306 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005673302   ⟹   XP_005673359
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11845,477,561 - 45,478,928 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003134892 (Get FASTA)   NCBI Sequence Viewer  
  XP_005673359 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AIV00553 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_003134892   ⟸   XM_003134844
- Peptide Label: isoform X1
- UniProtKB: F1SHS9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005673359   ⟸   XM_005673302
- Peptide Label: isoform X2
- UniProtKB: A0A286ZZU6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000037164   ⟸   ENSSSCT00000058453
RefSeq Acc Id: ENSSSCP00000017697   ⟸   ENSSSCT00000018188
Protein Domains
Homeobox


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000016707 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00070011812 UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00000017697 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00000037164 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00070019051 UniProtKB/TrEMBL
  ENSSSCP00070019103 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000018188 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00000058453 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00070023041 UniProtKB/TrEMBL
  ENSSSCT00070023097 UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
KEGG Report ssc:100520162 UniProtKB/TrEMBL
NCBI Gene HOXA1 ENTREZGENE
Pfam Homeodomain UniProtKB/TrEMBL
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt A0A0A0R835_PIG UniProtKB/TrEMBL
  A0A286ZZU6 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1TRV8_PIG UniProtKB/TrEMBL
  A0A4X1TUQ4_PIG UniProtKB/TrEMBL
  F1SHS9 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:88933 ENTREZGENE