Free for academic non-profit institutions. Other users need a Commercial license

Aliases for HOXA1 Gene

Aliases for HOXA1 Gene

  • Homeobox A1 2 3 5
  • Homeobox Protein Hox-1F 3 4
  • Homeo Box A1 2 3
  • HOX1F 3 4
  • HOX A1 Homeodomain Protein 3
  • Homeobox Protein Hox-A1 3
  • Hox 1.6-Like Protein 3
  • Lab-Like Protein 3
  • Homeobox 1F 3
  • BSAS 3
  • HOX1 3

External Ids for HOXA1 Gene

Previous HGNC Symbols for HOXA1 Gene

  • HOX1F
  • HOX1

Previous GeneCards Identifiers for HOXA1 Gene

  • GC07M026776
  • GC07M026874
  • GC07M026905
  • GC07M027099
  • GC07M027013

Summaries for HOXA1 Gene

Entrez Gene Summary for HOXA1 Gene

  • In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. The encoded protein may be involved in the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. Two transcript variants encoding two different isoforms have been found for this gene, with only one of the isoforms containing the homeodomain region. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXA1 Gene

HOXA1 (Homeobox A1) is a Protein Coding gene. Diseases associated with HOXA1 include Athabaskan Brainstem Dysgenesis Syndrome and Hoxa1-Related Disorders. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Mesodermal Commitment Pathway. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXB1.

UniProtKB/Swiss-Prot for HOXA1 Gene

  • Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Acts on the anterior body structures. Seems to act in the maintenance and/or generation of hindbrain segments.

Gene Wiki entry for HOXA1 Gene

Additional gene information for HOXA1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXA1 Gene

Genomics for HOXA1 Gene

Regulatory Elements for HOXA1 Gene

Enhancers for HOXA1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07H027095 3.3 VISTA FANTOM5 Ensembl ENCODE dbSUPER 12.2 -42.2 -42190 86 MLX FEZF1 DMAP1 YY1 ZNF143 SP3 NFYC ZC3H11A SSRP1 ZNF610 HNRNPA2B1 HOTAIRM1 HOXA10-AS HOXA2 HOXA-AS2 CBX3 HOXA9 HOXA11-AS HOXA10 TPM3P4
GH07H026855 1.4 Ensembl ENCODE dbSUPER 11.7 +238.5 238459 4 HDAC1 PKNOX1 FEZF1 ZBTB40 TCF12 GLIS2 GATA2 EGR1 ZNF366 EGR2 HOTAIRM1 HOXA5 HOXA-AS3 HOXA4 HOXA3 HOXA6 HOXA1 HOXA2 HOXA-AS2 SKAP2
GH07H026862 1.4 ENCODE dbSUPER 11.5 +231.9 231892 3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF766 HOTAIRM1 HNRNPA2B1 HMGB3P20 TPM3P4 RPL23P7 PSMC1P2 HOXA-AS3 HOXA4 HOXA3 HOXA6
GH07H027030 1 Ensembl ENCODE 11.3 +64.5 64489 2 PKNOX1 RB1 L3MBTL2 CEBPB CEBPG FEZF1 ELF1 ZNF384 REST EP300 HOTAIRM1 SKAP2 HOXA1 HOXA2 HOXA-AS2 HOXA3 TPM3P4 NHP2P2
GH07H026853 0.9 ENCODE dbSUPER 11.7 +242.0 242030 0 CTCF ZNF654 ZSCAN4 BMI1 RAD21 PRDM6 SMC3 REPIN1 SP7 HOXA5 HOXA-AS3 HOXA4 HOXA3 HOXA6 HOXA1 HOTAIRM1 GC07P026846 RPL7AP38
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HOXA1 on UCSC Golden Path with GeneCards custom track

Promoters for HOXA1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000325311 -1394 3601 PKNOX1 ARNT SIN3A FEZF1 ZNF2 GLIS2 SP3 NFYC TSHZ1 ZNF488

Genomic Location for HOXA1 Gene

Chromosome:
7
Start:
27,092,993 bp from pter
End:
27,096,006 bp from pter
Size:
3,014 bases
Orientation:
Minus strand

Genomic View for HOXA1 Gene

Genes around HOXA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXA1 Gene

Proteins for HOXA1 Gene

  • Protein details for HOXA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P49639-HXA1_HUMAN
    Recommended name:
    Homeobox protein Hox-A1
    Protein Accession:
    P49639
    Secondary Accessions:
    • A4D184
    • B2R8U7
    • O43363

    Protein attributes for HOXA1 Gene

    Size:
    335 amino acids
    Molecular mass:
    36641 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for HOXA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HOXA1 Gene

Post-translational modifications for HOXA1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXA1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXA1 Gene

Domains & Families for HOXA1 Gene

Gene Families for HOXA1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for HOXA1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P49639

UniProtKB/Swiss-Prot:

HXA1_HUMAN :
  • Belongs to the Antp homeobox family. Labial subfamily.
Family:
  • Belongs to the Antp homeobox family. Labial subfamily.
genes like me logo Genes that share domains with HOXA1: view

Function for HOXA1 Gene

Molecular function for HOXA1 Gene

GENATLAS Biochemistry:
homeo box A1(1F),homologous to mouse Hox-1.6,Drosophila 1ab
UniProtKB/Swiss-Prot Function:
Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Acts on the anterior body structures. Seems to act in the maintenance and/or generation of hindbrain segments.

Phenotypes From GWAS Catalog for HOXA1 Gene

Gene Ontology (GO) - Molecular Function for HOXA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding IC --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0042802 identical protein binding IPI 21516116
GO:0043565 sequence-specific DNA binding IDA 23332764
genes like me logo Genes that share ontologies with HOXA1: view
genes like me logo Genes that share phenotypes with HOXA1: view

Human Phenotype Ontology for HOXA1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HOXA1 Gene

MGI Knock Outs for HOXA1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for HOXA1
  • Applied Biological Materials Clones for HOXA1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for HOXA1 Gene

Localization for HOXA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXA1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HOXA1 gene
Compartment Confidence
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for HOXA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with HOXA1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HOXA1 Gene

Pathways & Interactions for HOXA1 Gene

genes like me logo Genes that share pathways with HOXA1: view

Gene Ontology (GO) - Biological Process for HOXA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0007275 multicellular organism development TAS 7622051
GO:0007605 sensory perception of sound IDA 16155570
genes like me logo Genes that share ontologies with HOXA1: view

No data available for SIGNOR curated interactions for HOXA1 Gene

Drugs & Compounds for HOXA1 Gene

(1) Drugs for HOXA1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for HOXA1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HOXA1: view

Transcripts for HOXA1 Gene

mRNA/cDNA for HOXA1 Gene

Unigene Clusters for HOXA1 Gene

Homeobox A1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for HOXA1
  • Applied Biological Materials Clones for HOXA1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for HOXA1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b
SP1:
SP2:

Relevant External Links for HOXA1 Gene

GeneLoc Exon Structure for
HOXA1
ECgene alternative splicing isoforms for
HOXA1

Expression for HOXA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXA1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXA1 Gene

This gene is overexpressed in Bladder (x7.2) and Esophagus - Mucosa (x5.4).

NURSA nuclear receptor signaling pathways regulating expression of HOXA1 Gene:

HOXA1

SOURCE GeneReport for Unigene cluster for HOXA1 Gene:

Hs.67397

Evidence on tissue expression from TISSUES for HOXA1 Gene

  • Skin(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXA1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • nervous
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • cerebellum
  • eye
  • head
genes like me logo Genes that share expression patterns with HOXA1: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for HOXA1 Gene

Orthologs for HOXA1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HOXA1 33 34
  • 99.3 (n)
dog
(Canis familiaris)
Mammalia HOXA1 33 34
  • 92.56 (n)
cow
(Bos Taurus)
Mammalia HOXA1 33 34
  • 92.09 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HOXA1 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hoxa1 33 16 34
  • 90.9 (n)
rat
(Rattus norvegicus)
Mammalia LOC100911406 33
  • 90.65 (n)
oppossum
(Monodelphis domestica)
Mammalia HOXA1 34
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves HOXA1 33 34
  • 74.86 (n)
lizard
(Anolis carolinensis)
Reptilia HOXA1 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxa1 33
  • 70.56 (n)
zebrafish
(Danio rerio)
Actinopterygii hoxa1a 33 34
  • 60.71 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta zen2 34
  • 21 (a)
ManyToMany
Species where no ortholog for HOXA1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HOXA1 Gene

ENSEMBL:
Gene Tree for HOXA1 (if available)
TreeFam:
Gene Tree for HOXA1 (if available)

Paralogs for HOXA1 Gene

Paralogs for HOXA1 Gene

(3) SIMAP similar genes for HOXA1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with HOXA1: view

Variants for HOXA1 Gene

Sequence variations from dbSNP and Humsavar for HOXA1 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs104894017 Pathogenic 27,095,829(-) GCCTA(C/G)CCCTC upstream-variant-2KB, reference, stop-gained
rs104894018 Pathogenic 27,095,837(-) CAGCC(C/G/T)GAGCC upstream-variant-2KB, reference, missense
rs2074398 Likely benign 27,095,700(+) tgatg(A/G)tggtg upstream-variant-2KB, reference, synonymous-codon
rs368428758 Likely benign 27,095,695(+) GGTGG(-/CGA)TGGTG upstream-variant-2KB, cds-indel
rs45571645 Likely benign 27,095,477(+) CTGGT(G/T)GTGGT intron-variant, upstream-variant-2KB, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for HOXA1 Gene

Variant ID Type Subtype PubMed ID
dgv1094n67 CNV gain 20364138
dgv11244n54 CNV loss 21841781
nsv7393 OTHER inversion 18451855

Variation tolerance for HOXA1 Gene

Residual Variation Intolerance Score: 33.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.56; 44.59% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HOXA1 Gene

Human Gene Mutation Database (HGMD)
HOXA1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOXA1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXA1 Gene

Disorders for HOXA1 Gene

MalaCards: The human disease database

(9) MalaCards diseases for HOXA1 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
athabaskan brainstem dysgenesis syndrome
  • bosley-salih-alorainy syndrome
hoxa1-related disorders
autism spectrum disorder
  • pervasive developmental disorder
duane retraction syndrome
  • duane's syndrome
pneumonic plague
  • primary pneumonic plague
- elite association - COSMIC cancer census association via MalaCards
Search HOXA1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HXA1_HUMAN
  • Athabaskan brainstem dysgenesis syndrome (ABDS) [MIM:601536]: Characterized by horizontal gaze palsy, sensorineural deafness, central hypoventilation, and developmental delay. Some patients had swallowing dysfunction, vocal cord paralysis, facial paresis, seizures, and cardiac outflow tract anomalies. {ECO:0000269 PubMed:16155570}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Bosley-Salih-Alorainy syndrome (BSAS) [MIM:601536]: A disease characterized by horizontal gaze abnormalities, deafness, facial weakness, vascular malformations of the internal carotid arteries and cardiac outflow trac. Some patients manifest mental retardation and autism spectrum disorder. Affected individuals do not suffer from central hypoventilation. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for HOXA1

Genetic Association Database (GAD)
HOXA1
Human Genome Epidemiology (HuGE) Navigator
HOXA1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HOXA1
genes like me logo Genes that share disorders with HOXA1: view

No data available for Genatlas for HOXA1 Gene

Publications for HOXA1 Gene

  1. HOXA1 A218G polymorphism is associated with smaller cerebellar volume in healthy humans. (PMID: 19018953) Canu E … Frisoni GB (Journal of neuroimaging : official journal of the American Society of Neuroimaging 2009) 3 22 45 60
  2. Polymorphisms of coding trinucleotide repeats of homeogenes in neurodevelopmental psychiatric disorders. (PMID: 19018235) Laroche F … Robel L (Psychiatric genetics 2008) 3 22 45 60
  3. HOXA1 gene variants influence head growth rates in humans. (PMID: 17171652) Muscarella LA … Persico AM (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2007) 3 22 45 60
  4. Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development. (PMID: 16155570) Tischfield MA … Engle EC (Nature genetics 2005) 3 4 22 60
  5. Association between the HOXA1 A218G polymorphism and increased head circumference in patients with autism. (PMID: 14960295) Conciatori M … Persico AM (Biological psychiatry 2004) 3 22 45 60

Products for HOXA1 Gene

  • Addgene plasmids for HOXA1

Sources for HOXA1 Gene

Content
Loading form....