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Aliases for HOXA4 Gene

Aliases for HOXA4 Gene

  • Homeobox A4 2 3 5
  • Homeobox Protein Hox-1.4 3 4
  • Homeobox Protein Hox-1D 3 4
  • Homeo Box A4 2 3
  • HOX1D 3 4
  • Homeobox Protein Hox-A4 3
  • Hox-1.4-Like Protein 3
  • Dfd-Like Protein 3
  • HOX1 3

External Ids for HOXA4 Gene

Previous HGNC Symbols for HOXA4 Gene

  • HOX1D
  • HOX1

Previous GeneCards Identifiers for HOXA4 Gene

  • GC07M026810
  • GC07M026911
  • GC07M026912
  • GC07M026941
  • GC07M027134
  • GC07M027048
  • GC07M027170

Summaries for HOXA4 Gene

Entrez Gene Summary for HOXA4 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. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXA4 Gene

HOXA4 (Homeobox A4) is a Protein Coding gene. Diseases associated with HOXA4 include Hypospadias. 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 HOXB4.

UniProtKB/Swiss-Prot for HOXA4 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. Binds to sites in the 5-flanking sequence of its coding region with various affinities. The consensus sequences of the high and low affinity binding sites are 5-TAATGA[CG]-3 and 5-CTAATTTT-3.

Gene Wiki entry for HOXA4 Gene

Additional gene information for HOXA4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXA4 Gene

Genomics for HOXA4 Gene

GeneHancer (GH) Regulatory Elements for HOXA4 Gene

Promoters and enhancers for HOXA4 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 3.4 VISTA UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 653.8 -7.4 -7396 86.3 MLX FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 NFYC SSRP1 ZNF610 HOXA2 HOXA9 HOXA10 HOXA1 HOXA3 HOXA6 HOXA4 HOXA5 HOXA7 HNRNPA2B1
GH07J026862 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.8 +266.7 266685 3.1 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SKAP2 HOTAIRM1 HMGB3P20 TPM3P4 RPL23P7 PSMC1P2 HNRNPA2B1 HOXA-AS3 HOXA4 HOXA3
GH07J026855 Enhancer 1.3 Ensembl ENCODE dbSUPER 12.2 +273.3 273251 4.8 HDAC1 PKNOX1 FEZF1 ZBTB40 TCF12 GLIS2 EGR1 ZNF366 EGR2 ZNF362 HOTAIRM1 HOXA5 HOXA-AS3 HOXA4 HOXA3 HOXA6 HOXA1 HOXA2 HOXA-AS2 SKAP2
GH07J026853 Enhancer 0.8 ENCODE dbSUPER 12 +276.8 276822 0.2 CTCF ZNF654 PRDM6 ZSCAN4 SMC3 BMI1 RAD21 SP7 HOXA5 HOXA-AS3 HOXA4 HOXA3 HOXA6 HOTAIRM1 HOXA1 GC07P026846 RPL7AP38 SKAP2
GH07J026860 Enhancer 0.7 ENCODE dbSUPER 11.8 +270.3 270262 0.2 ELF3 CTCF JUND ZNF654 SMC3 RAD21 MIXL1 HOXA-AS3 HOXA4 HOXA5 HOXA3 HOXA6 HOXA2 HOTAIRM1 HOXA1 HOXA-AS2 GC07P026846
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXA4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXA4 gene promoter:
  • Sp1
  • AP-2gamma
  • AP-2beta
  • AP-2alphaA
  • AP-2alpha
  • c-Myb
  • FOXO1

Genomic Locations for HOXA4 Gene

Genomic Locations for HOXA4 Gene
chr7:27,128,507-27,130,799
(GRCh38/hg38)
Size:
2,293 bases
Orientation:
Minus strand
chr7:27,168,126-27,170,418
(GRCh37/hg19)
Size:
2,293 bases
Orientation:
Minus strand

Genomic View for HOXA4 Gene

Genes around HOXA4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXA4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXA4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXA4 Gene

Proteins for HOXA4 Gene

  • Protein details for HOXA4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q00056-HXA4_HUMAN
    Recommended name:
    Homeobox protein Hox-A4
    Protein Accession:
    Q00056
    Secondary Accessions:
    • A4D180
    • O43366

    Protein attributes for HOXA4 Gene

    Size:
    320 amino acids
    Molecular mass:
    34499 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXA4 Gene

Post-translational modifications for HOXA4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXA4 Gene

No data available for DME Specific Peptides for HOXA4 Gene

Domains & Families for HOXA4 Gene

Gene Families for HOXA4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for HOXA4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q00056

UniProtKB/Swiss-Prot:

HXA4_HUMAN :
  • Belongs to the Antp homeobox family. Deformed subfamily.
Family:
  • Belongs to the Antp homeobox family. Deformed subfamily.
genes like me logo Genes that share domains with HOXA4: view

Function for HOXA4 Gene

Molecular function for HOXA4 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. Binds to sites in the 5-flanking sequence of its coding region with various affinities. The consensus sequences of the high and low affinity binding sites are 5-TAATGA[CG]-3 and 5-CTAATTTT-3.
GENATLAS Biochemistry:
homeo box A4(1D),homologous to mouse Hox-1.4,Drosophila Dfd

Phenotypes From GWAS Catalog for HOXA4 Gene

Gene Ontology (GO) - Molecular Function for HOXA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXA4: view
genes like me logo Genes that share phenotypes with HOXA4: view

Animal Models for HOXA4 Gene

MGI Knock Outs for HOXA4:

Animal Model Products

miRNA for HOXA4 Gene

miRTarBase miRNAs that target HOXA4

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXA4 Gene

Localization for HOXA4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXA4 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 HOXA4 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HOXA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with HOXA4: view

Pathways & Interactions for HOXA4 Gene

genes like me logo Genes that share pathways with HOXA4: view

Gene Ontology (GO) - Biological Process for HOXA4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
GO:0009653 anatomical structure morphogenesis TAS 1675427
genes like me logo Genes that share ontologies with HOXA4: view

No data available for SIGNOR curated interactions for HOXA4 Gene

Drugs & Compounds for HOXA4 Gene

No Compound Related Data Available

Transcripts for HOXA4 Gene

mRNA/cDNA for HOXA4 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(50) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HOXA4 Gene

Homeobox A4:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXA4 Gene

No ASD Table

Relevant External Links for HOXA4 Gene

GeneLoc Exon Structure for
HOXA4
ECgene alternative splicing isoforms for
HOXA4

Expression for HOXA4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXA4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXA4 Gene

This gene is overexpressed in Esophagus - Muscularis (x7.3) and Esophagus - Gastroesophageal Junction (x6.8).

Protein differential expression in normal tissues from HIPED for HOXA4 Gene

This gene is overexpressed in Neutrophil (23.8), Tlymphocyte (12.9), Nasal epithelium (10.8), and Blymphocyte (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HOXA4 Gene



Protein tissue co-expression partners for HOXA4 Gene

NURSA nuclear receptor signaling pathways regulating expression of HOXA4 Gene:

HOXA4

SOURCE GeneReport for Unigene cluster for HOXA4 Gene:

Hs.533357

mRNA Expression by UniProt/SwissProt for HOXA4 Gene:

Q00056-HXA4_HUMAN
Tissue specificity: Embryonic nervous system.
genes like me logo Genes that share expression patterns with HOXA4: view

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXA4 Gene

Orthologs for HOXA4 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXA4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HOXA4 34 33
  • 99.37 (n)
OneToOne
dog
(Canis familiaris)
Mammalia HOXA4 34 33
  • 91.59 (n)
OneToOne
cow
(Bos Taurus)
Mammalia HOXA4 34 33
  • 90.22 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC100360577 33
  • 83.99 (n)
mouse
(Mus musculus)
Mammalia Hoxa4 16 34 33
  • 83.27 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HOXA4 34
  • 66 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HOXA4 34
  • 55 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC100858429 33
  • 94.44 (n)
HOXA4 34 34
  • 60 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia HOXA4 34
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxa4 33
  • 66.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta Scr 35
  • 60 (a)
Dfd 34 35
  • 20 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 28 (a)
OneToMany
Species where no ortholog for HOXA4 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 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)
  • zebrafish (Danio rerio)

Evolution for HOXA4 Gene

ENSEMBL:
Gene Tree for HOXA4 (if available)
TreeFam:
Gene Tree for HOXA4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HOXA4: view image

Paralogs for HOXA4 Gene

Variants for HOXA4 Gene

Sequence variations from dbSNP and Humsavar for HOXA4 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
VAR_036266 A breast cancer sample p.Gly37Asp
rs1001379085 -- 27,128,387(-) T/A downstream_transcript_variant
rs1001544497 -- 27,128,830(-) A/G 3_prime_UTR_variant
rs1002143143 -- 27,128,852(-) T/A 3_prime_UTR_variant
rs1002822603 -- 27,132,201(-) G/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXA4 Gene

Variant ID Type Subtype PubMed ID
dgv1094n67 CNV gain 20364138
dgv11244n54 CNV loss 21841781
nsv5674 CNV deletion 18451855
nsv606464 CNV loss 21841781
nsv606465 CNV loss 21841781
nsv7393 OTHER inversion 18451855
nsv824042 CNV gain 20364138

Variation tolerance for HOXA4 Gene

Residual Variation Intolerance Score: 73.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.09; 80.48% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXA4 Gene

Human Gene Mutation Database (HGMD)
HOXA4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOXA4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXA4 Gene

Disorders for HOXA4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for HOXA4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
hypospadias
  • familial hypospadias
- elite association - COSMIC cancer census association via MalaCards
Search HOXA4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HOXA4

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 HOXA4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HOXA4 Gene

Publications for HOXA4 Gene

  1. 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 44 58
  2. Mutation screening of BMP4, BMP7, HOXA4 and HOXB6 genes in Chinese patients with hypospadias. (PMID: 17003840) Chen T … Shen Y (European journal of human genetics : EJHG 2007) 3 44 58
  3. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier LW … Wilson RK (Nature 2003) 3 4 58
  4. Vertebrate homeobox gene nomenclature. (PMID: 1358459) Scott MP (Cell 1992) 2 3 58
  5. Alteration of homeobox gene expression by N-ras transformation of PA-1 human teratocarcinoma cells. (PMID: 1675427) Buettner R … Tainsky MA (Molecular and cellular biology 1991) 3 4 58

Products for HOXA4 Gene

Sources for HOXA4 Gene

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