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 g... See more...

Aliases for HOXA1 Gene

Aliases for HOXA1 Gene

  • Homeobox A1 2 3 5
  • Homeobox Protein Hox-A1 3 4
  • Homeobox Protein Hox-1F 3 4
  • Homeo Box A1 2 3
  • HOX1F 3 4
  • HOX A1 Homeodomain Protein 3
  • Hox 1.6-Like Protein 3
  • Lab-Like Protein 3
  • Homeobox 1F 3
  • HOXA1 5
  • 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 Microtia, Hearing Impairment, And Cleft Palate. Among its related pathways are Signaling pathways regulating pluripotency of stem cells and Mesodermal Commitment Pathway. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXB1.

UniProtKB/Swiss-Prot Summary for HOXA1 Gene

  • Sequence-specific transcription factor (By similarity). Regulates multiple developmental processes including brainstem, inner and outer ear, abducens nerve and cardiovascular development and morphogenesis as well as cognition and behavior (PubMed:16155570). Also 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 (By similarity). Activates transcription in the presence of PBX1A and PKNOX1 (By similarity).

Gene Wiki entry for HOXA1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HOXA1 Gene

Genomics for HOXA1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HOXA1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXA1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HOXA1

Top Transcription factor binding sites by QIAGEN in the HOXA1 gene promoter:
  • AREB6
  • C/EBPalpha
  • GATA-2
  • HSF2
  • NF-kappaB
  • Nkx2-5
  • RelA
  • Sox9
  • SRY

Genomic Locations for HOXA1 Gene

Latest Assembly
chr7:27,092,993-27,096,000
(GRCh38/hg38)
Size:
3,008 bases
Orientation:
Minus strand

Previous Assembly
chr7:27,132,612-27,135,619
(GRCh37/hg19 by Entrez Gene)
Size:
3,008 bases
Orientation:
Minus strand

chr7:27,132,612-27,135,615
(GRCh37/hg19 by Ensembl)
Size:
3,004 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:
    • Interacts with OGT (via TPR repeats domain); the interaction takes place mainly in the nucleus.
    Miscellaneous:
    • [Isoform 1]: Lacks the homeobox domain.
    • [Isoform 2]: Lacks the homeobox domain.

    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:

Antibodies for research

  • Abcam antibodies for HOXA1
  • Santa Cruz Biotechnology (SCBT) Antibodies for HOXA1

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

Protein Domains for HOXA1 Gene

InterPro:
Blocks:
  • Lambda and other repressor helix-turn-helix signature
  • Homeobox protein, antennapedia type

Suggested Antigen Peptide Sequences for HOXA1 Gene

GenScript: Design optimal peptide antigens:
  • Homeo box A1 (A4D185_HUMAN)
  • Homeobox protein Hox-1F (HXA1_HUMAN)

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

UniProtKB/Swiss-Prot Function:
Sequence-specific transcription factor (By similarity). Regulates multiple developmental processes including brainstem, inner and outer ear, abducens nerve and cardiovascular development and morphogenesis as well as cognition and behavior (PubMed:16155570). Also 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 (By similarity). Activates transcription in the presence of PBX1A and PKNOX1 (By similarity).
GENATLAS Biochemistry:
homeo box A1(1F),homologous to mouse Hox-1.6,Drosophila 1ab

Phenotypes From GWAS Catalog for HOXA1 Gene

Gene Ontology (GO) - Molecular Function for HOXA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific IEA,ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 15665309
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 16189514
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:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXA1

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 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for HOXA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IEA,IBA 21873635
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

SIGNOR curated interactions for HOXA1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for HOXA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA,IBA 21873635
GO:0007275 multicellular organism development TAS 7622051
GO:0007605 sensory perception of sound IDA 16155570
GO:0007634 optokinetic behavior IDA 16155570
genes like me logo Genes that share ontologies with HOXA1: view

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

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXA1

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

Expression for HOXA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HOXA1

SOURCE GeneReport for Unigene cluster for HOXA1 Gene:

Hs.67397

Evidence on tissue expression from TISSUES for HOXA1 Gene

  • Skin(4.3)

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

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

Primer products for research

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 29 30
  • 99.3 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia HOXA1 29 30
  • 92.56 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia HOXA1 29 30
  • 92.09 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia HOXA1 30
  • 91 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Hoxa1 29 16 30
  • 90.9 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC100911406 29
  • 90.65 (n)
Oppossum
(Monodelphis domestica)
Mammalia HOXA1 30
  • 84 (a)
OneToOne
Chicken
(Gallus gallus)
Aves HOXA1 29 30
  • 74.86 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia HOXA1 30
  • 68 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia hoxa1 29
  • 70.56 (n)
Zebrafish
(Danio rerio)
Actinopterygii hoxa1a 29 30
  • 60.71 (n)
OneToOne
-- 29
Fruit Fly
(Drosophila melanogaster)
Insecta zen2 30
  • 21 (a)
ManyToMany
Species where no ortholog for HOXA1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for HOXA1: view image
Alliance of Genome Resources:
Additional Orthologs for HOXA1

Paralogs for HOXA1 Gene

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

  • HXA1_HUMAN
  • A4D185_HUMAN
  • E7ERT8_HUMAN
genes like me logo Genes that share paralogs with HOXA1: view

Variants for HOXA1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HOXA1 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
701069 Benign: not provided 27,095,695(-) C/.
NM_005522.5(HOXA1):c.218= (p.Arg73=)
NO_SEQUENCE_ALTERATION
908469 Benign: Human HOXA1 syndromes 27,093,350(-) G/A
NM_005522.5(HOXA1):c.*1090C>T
THREE_PRIME_UTR
908470 Uncertain Significance: Human HOXA1 syndromes 27,093,382(-) A/T
NM_005522.5(HOXA1):c.*1058T>A
THREE_PRIME_UTR
908471 Uncertain Significance: Human HOXA1 syndromes 27,093,460(-) G/C
NM_005522.5(HOXA1):c.*980C>G
THREE_PRIME_UTR
908472 Uncertain Significance: Human HOXA1 syndromes 27,093,620(-) T/C
NM_005522.5(HOXA1):c.*820A>G
THREE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for HOXA1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for HOXA1 Gene

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

SNP Genotyping and Copy Number Assays for research

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

Disorders for HOXA1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for HOXA1 Gene - From: OMI, CVR, GTR, ORP, COP, and GCD

Disorder Aliases PubMed IDs
athabaskan brainstem dysgenesis syndrome
  • abds
microtia, hearing impairment, and cleft palate
  • microtia with or without hearing impairment
embryonal carcinoma
  • primary extragonadal embryonal carcinoma
accommodative esotropia
  • esotropia with accommodative compensation
autism
  • autistic disorder
- 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 variants 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 variants affecting the gene represented in this entry.

Additional Disease Information for HOXA1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with HOXA1: view

No data available for Genatlas for HOXA1 Gene

Publications for HOXA1 Gene

  1. Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development. (PMID: 16155570) Tischfield MA … Engle EC (Nature genetics 2005) 3 4 22 72
  2. 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 40
  3. Polymorphisms of coding trinucleotide repeats of homeogenes in neurodevelopmental psychiatric disorders. (PMID: 19018235) Laroche F … Robel L (Psychiatric genetics 2008) 3 22 40
  4. 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 40
  5. Clinical characterization of the HOXA1 syndrome BSAS variant. (PMID: 17875913) Bosley TM … Engle EC (Neurology 2007) 3 22 72

Products for HOXA1 Gene

Sources for HOXA1 Gene