HOXA2 Gene (Protein Coding)

Homeobox A2

GC07M027100
GIFtS:
39
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 HOXA2 Gene

Aliases for HOXA2 Gene

  • Homeobox A2 2 3 5
  • Homeobox Protein Hox-1K 3 4
  • Homeobox Protein Hox-A2 3 4
  • HOX1K 3 4
  • Homeo Box A2 2
  • MCOHI 3

External Ids for HOXA2 Gene

Previous HGNC Symbols for HOXA2 Gene

  • HOX1K

Previous GeneCards Identifiers for HOXA2 Gene

  • GC07M026782
  • GC07M026881
  • GC07M026882
  • GC07M026913
  • GC07M027106
  • GC07M027020

Summaries for HOXA2 Gene

Entrez Gene Summary for HOXA2 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. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXA2 Gene

HOXA2 (Homeobox A2) is a Protein Coding gene. Diseases associated with HOXA2 include Microtia, Hearing Impairment, And Cleft Palate and Microtia. Among its related pathways are Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Developmental Biology. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is HOXB2.

UniProtKB/Swiss-Prot Summary for HOXA2 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.

Gene Wiki entry for HOXA2 Gene

Additional gene information for HOXA2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HOXA2 Gene

Genomics for HOXA2 Gene

GeneHancer (GH) Regulatory Elements for HOXA2 Gene

Promoters and enhancers for HOXA2 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH07J027095 Promoter/Enhancer 3 VISTA UCNEbase EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 526.2 -35.4 -35386 86.3 EP300 HNRNPK ZNF217 CTCF ZSCAN5C TCF12 POLR2G USF1 NCOR1 PHF8 HOXA2 HOXA9 HOXA10 HOXA1 HOXA3 HOXA6 HOXA4 HOXA5 HOXA7 HNRNPA2B1
GH07J026862 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 11.1 +239.0 238975 4 ZNF217 TCF12 SIN3A NRF1 USF1 POLR2G SP1 GTF2E2 PHF8 PHB2 SKAP2 lnc-EVX1-8 lnc-HOXA1-1 HOTAIRM1 HOXA5 HOXA-AS3 HOXA4 HOXA3 HOXA6 HOXA1
GH07J026855 Promoter/Enhancer 1.3 Ensembl ENCODE dbSUPER 11.7 +245.2 245227 4.8 CTBP1 ZNF341 NCOR1 NFIC ZBTB17 ZNF384 MAFF ZFHX2 TAL1 MAFK HOTAIRM1 HOXA5 HOXA-AS3 HOXA4 HOXA3 HOXA6 HOXA1 HOXA2 HOXA-AS2 SKAP2
GH07J026947 Enhancer 1 Ensembl ENCODE 10.8 +153.4 153375 6 NCOR1 TEAD4 TCF7 SKI TEAD1 TBX3 HDAC2 POLR2A FOXA2 TCF7L2 piR-57460-602 HOTAIRM1 SKAP2 HOXA1 HOXA2 HOXA-AS2 HOXA3 piR-33804-081 piR-32214-619
GH07J027066 Enhancer 0.8 Ensembl ENCODE 12 +35.6 35574 3.2 USF1 EP300 ZEB1 CEBPB FOS JUN EZH2 JUND NFYB PRDM1 HOTAIRM1 SKAP2 HOXA1 HOXA2 HOXA-AS2 HOXA3 piR-56037-047
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXA2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HOXA2

Top Transcription factor binding sites by QIAGEN in the HOXA2 gene promoter:
  • AREB6
  • C/EBPalpha
  • GATA-2
  • HNF-4alpha1
  • HNF-4alpha2
  • HSF2
  • Nkx2-5
  • Sox9
  • SRY

Genomic Locations for HOXA2 Gene

Genomic Locations for HOXA2 Gene
chr7:27,100,354-27,102,775
(GRCh38/hg38)
Size:
2,422 bases
Orientation:
Minus strand
chr7:27,139,721-27,142,430
(GRCh37/hg19)
Size:
2,710 bases
Orientation:
Minus strand

Genomic View for HOXA2 Gene

Genes around HOXA2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXA2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXA2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HOXA2 Gene

Proteins for HOXA2 Gene

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  1. Antibody
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  3. Assay

  • Protein details for HOXA2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43364-HXA2_HUMAN
    Recommended name:
    Homeobox protein Hox-A2
    Protein Accession:
    O43364
    Secondary Accessions:
    • A1L4K3
    • B2RMW3

    Protein attributes for HOXA2 Gene

    Size:
    376 amino acids
    Molecular mass:
    41002 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXA2 Gene

Post-translational modifications for HOXA2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXA2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXA2 Gene

Domains & Families for HOXA2 Gene

Gene Families for HOXA2 Gene

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

Protein Domains for HOXA2 Gene

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

Suggested Antigen Peptide Sequences for HOXA2 Gene

GenScript: Design optimal peptide antigens:
  • Homeobox protein Hox-1K (HXA2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O43364

UniProtKB/Swiss-Prot:

HXA2_HUMAN :
  • Belongs to the Antp homeobox family. Proboscipedia subfamily.
Family:
  • Belongs to the Antp homeobox family. Proboscipedia subfamily.
genes like me logo Genes that share domains with HOXA2: view

Function for HOXA2 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
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Molecular function for HOXA2 Gene

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.
GENATLAS Biochemistry:
homeo box A2(1K),homologous to mouse Hox-1.11,Drosophila pb

Phenotypes From GWAS Catalog for HOXA2 Gene

Gene Ontology (GO) - Molecular Function for HOXA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IEA,IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IBA 21873635
genes like me logo Genes that share ontologies with HOXA2: view
genes like me logo Genes that share phenotypes with HOXA2: view

Human Phenotype Ontology for HOXA2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HOXA2 Gene

MGI Knock Outs for HOXA2:

Animal Model Products

CRISPR Products

miRNA for HOXA2 Gene

miRTarBase miRNAs that target HOXA2
Targeted motifs for HOXA2 Gene
HOMER Transcription Factor Regulatory Elements motif HOXA2
  • Consensus sequence: GYCATCMATCAT Submotif: canonical Cell Type: mES

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXA2

Clone Products

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targets for HOXA2 Gene

Localization for HOXA2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXA2 Gene

Nucleus.

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 HOXA2 gene
Compartment Confidence
nucleus 5
extracellular 2
cytoskeleton 2
plasma membrane 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HOXA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with HOXA2: view

Pathways & Interactions for HOXA2 Gene

genes like me logo Genes that share pathways with HOXA2: view

Gene Ontology (GO) - Biological Process for HOXA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IBA 21873635
GO:0001709 cell fate determination IEA --
GO:0002076 osteoblast development IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with HOXA2: view

No data available for SIGNOR curated interactions for HOXA2 Gene

Drugs & Compounds for HOXA2 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for HOXA2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for HOXA2 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXA2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXA2 Gene

No ASD Table

Relevant External Links for HOXA2 Gene

GeneLoc Exon Structure for
HOXA2

Expression for HOXA2 Gene

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  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HOXA2 Gene

mRNA expression in normal human tissues for HOXA2 Gene
mRNA expression by BioGPS for HOXA2 GenemRNA expression by GTEx for HOXA2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXA2 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x4.6).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HOXA2

SOURCE GeneReport for Unigene cluster for HOXA2 Gene:

Hs.592177

Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXA2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • skeleton
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • head
  • inner ear
  • middle ear
  • mouth
  • outer ear
  • skull
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with HOXA2: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for HOXA2 Gene

Orthologs for HOXA2 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXA2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HOXA2 31 30
  • 99.91 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia HOXA2 31 30
  • 95.88 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia HOXA2 31 30
  • 95.72 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia LOC100911443 30
  • 93.6 (n)
mouse
(Mus musculus)
 Mammalia Hoxa2 17 31 30
  • 93.33 (n)
oppossum
(Monodelphis domestica)
 Mammalia HOXA2 31
  • 90 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia HOXA2 31
  • 88 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves HOXA2 31 30
  • 85.61 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia HOXA2 31
  • 81 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hoxa2 30
  • 79.16 (n)
Str.13271 30
African clawed frog
(Xenopus laevis)
 Amphibia hoxa2b-A 30
zebrafish
(Danio rerio)
 Actinopterygii hoxa2b 31 30 30
  • 73.94 (n)
 OneToOne
fruit fly
(Drosophila melanogaster)
 Insecta pb 31
  • 14 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 58 (a)
 OneToMany
Species where no ortholog for HOXA2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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 HOXA2 Gene

ENSEMBL:
Gene Tree for HOXA2 (if available)
TreeFam:
Gene Tree for HOXA2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HOXA2: view image

Paralogs for HOXA2 Gene

Paralogs for HOXA2 Gene

(1) SIMAP similar genes for HOXA2 Gene using alignment to 1 proteins:

  • HXA2_HUMAN
genes like me logo Genes that share paralogs with HOXA2: view

Variants for HOXA2 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HOXA2 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
rs10951154 Benign: Microtia, hearing impairment, and cleft palate 27,095,695(-) C/T MISSENSE_VARIANT,NO_SEQUENCE_ALTERATION
rs117630421 Likely Benign: Athabaskan brainstem dysgenesis; Bosley-Salih-Alorainy syndrome; Microtia, hearing impairment, and cleft palate 27,100,618(-) G/A THREE_PRIME_UTR_VARIANT
rs119489104 Pathogenic: Microtia, hearing impairment, and cleft palate. Microtia, hearing impairment, and cleft palate (MHICP) [MIM:612290] 27,101,301(-) G/Tp.Gln186Lys MISSENSE_VARIANT
rs139504171 Uncertain Significance: Microtia, hearing impairment, and cleft palate 27,101,463(-) A/T MISSENSE_VARIANT
rs141414600 Uncertain Significance: Microtia, hearing impairment, and cleft palate 27,100,410(-) A/G THREE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for HOXA2 Gene

Structural Variations from Database of Genomic Variants (DGV) for HOXA2 Gene

Variant ID Type Subtype PubMed ID
dgv1094n67 CNV gain 20364138
dgv11244n54 CNV loss 21841781
esv3612654 CNV loss 21293372
nsv606464 CNV loss 21841781
nsv7393 OTHER inversion 18451855

Variation tolerance for HOXA2 Gene

Residual Variation Intolerance Score: 38.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.08; 22.09% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXA2 Gene

Human Gene Mutation Database (HGMD)
HOXA2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOXA2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXA2 Gene

Disorders for HOXA2 Gene

MalaCards: The human disease database

(13) MalaCards diseases for HOXA2 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search HOXA2 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HXA2_HUMAN
  • Microtia, hearing impairment, and cleft palate (MHICP) [MIM:612290]: A disease characterized by microtia, mixed symmetric severe to profound hearing impairment, and partial cleft palate. Microtia is a congenital deformity of the outer ear that is small and abnormally shaped. In classic microtia, the pinna is essentially absent, except for a vertical sausage-shaped skin remnant. The superior aspect of this sausage-shaped skin remnant consists of underlying unorganized cartilage, and the inferior aspect of this remnant consists of a relatively well-formed lobule. Syndromic forms of microtia occur in conjunction with other abnormalities including cleft palate, a congenital fissure of the soft and/or hard palate due to faulty fusion. {ECO:0000269 PubMed:18394579}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Microtia with or without hearing impairment (MCRT) [MIM:612290]: Microtia is a congenital deformity of the outer ear that is small and abnormally shaped. In classic microtia, the pinna is essentially absent, except for a vertical sausage-shaped skin remnant. The superior aspect of this sausage-shaped skin remnant consists of underlying unorganized cartilage, and the inferior aspect of this remnant consists of a relatively well-formed lobule. {ECO:0000269 PubMed:23775976}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HOXA2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HOXA2: view

No data available for Genatlas for HOXA2 Gene

Publications for HOXA2 Gene

  1. HOXA2 haploinsufficiency in dominant bilateral microtia and hearing loss. (PMID: 23775976) Brown KK … Seidman CE (Human mutation 2013) 3 4 54
  2. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges LM … MrOS Research Group (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009) 3 41 54
  3. Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. (PMID: 19938081) Ester AR … Hecht JT (American journal of medical genetics. Part A 2009) 3 41 54
  4. A mutation in HOXA2 is responsible for autosomal-recessive microtia in an Iranian family. (PMID: 18394579) Alasti F … Van Camp G (American journal of human genetics 2008) 3 4 54
  5. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer SW … Tsui LC (Science (New York, N.Y.) 2003) 3 4 54

ExternalLinks

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