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Aliases for HOXA9 Gene

Aliases for HOXA9 Gene

  • Homeobox A9 2 3 5
  • Homeobox Protein Hox-1G 3 4
  • HOX1G 3 4
  • Homeodomain Protein HOXA9 3
  • Homeobox Protein Hox-A9 3
  • Homeo Box A9 2
  • HOX1.7 3
  • ABD-B 3
  • HOX1 3

External Ids for HOXA9 Gene

Previous HGNC Symbols for HOXA9 Gene

  • HOX1G
  • HOX1

Previous GeneCards Identifiers for HOXA9 Gene

  • GC07U990049
  • GC07M026844
  • GC07M026910
  • GC07M026945
  • GC07M026946
  • GC07M026975
  • GC07M027168
  • GC07M027213
  • GC07M027214
  • GC07M027219
  • GC07M027230
  • GC07M027254

Summaries for HOXA9 Gene

Entrez Gene Summary for HOXA9 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. This gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila. A specific translocation event which causes a fusion between this gene and the NUP98 gene has been associated with myeloid leukemogenesis. Read-through transcription exists between this gene and the upstream homeobox A10 (HOXA10) gene.[provided by RefSeq, Mar 2011]

GeneCards Summary for HOXA9 Gene

HOXA9 (Homeobox A9) is a Protein Coding gene. Diseases associated with HOXA9 include Myeloid Leukemia and Myelodysplastic Syndrome. Among its related pathways are Transcriptional misregulation in cancer. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding and enzyme binding. An important paralog of this gene is HOXB9.

UniProtKB/Swiss-Prot for HOXA9 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. Required for induction of E-selectin and VCAM-1, on the endothelial cells surface at sites of inflammation.

Gene Wiki entry for HOXA9 Gene

Additional gene information for HOXA9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXA9 Gene

Genomics for HOXA9 Gene

GeneHancer (GH) Regulatory Elements for HOXA9 Gene

Promoters and enhancers for HOXA9 Gene
GeneHancer (GH) Identifier GH Type GH
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 668 +37.0 36985 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 10.7 +311.1 311066 3.1 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SKAP2 HOTAIRM1 HMGB3P20 TPM3P4 RPL23P7 PSMC1P2 HNRNPA2B1 HOXA-AS3 HOXA4 HOXA3
GH07J026372 Promoter/Enhancer 1.9 UCNEbase Ensembl ENCODE 12 +800.2 800245 5.6 HDGF ARID4B SIN3A FEZF1 ZNF2 ZNF143 ZNF548 SP3 REST ZNF662 LOC105375304 HNRNPA2B1 RPL23P7 TPM3P4 HMGB3P20 ENSG00000227386 HOXA10-AS HOXA9 CBX3 KIAA0087
GH07J027920 Enhancer 1 Ensembl ENCODE 10.7 -746.1 -746135 0.6 MZF1 SIN3A BMI1 FEZF1 ZNF2 RAD21 RFX5 ZNF335 ZNF213 ZSCAN5C ENSG00000253508 HOTTIP HOXA13 HOXA11 HOXA11-AS HOXA10 HOXA9 ENSG00000253308 EVX1 EVX1-AS
GH07J028082 Enhancer 1.1 FANTOM5 Ensembl ENCODE 9.7 -908.5 -908503 2.6 FOXA2 RXRA CEBPB REST EP300 RFX5 YY1 SP1 JUND ATF3 JAZF1 JAZF1-AS1 HOXA11 HOXA11-AS HOXA10 HOXA9 HOXA13 ENSG00000253508 HOTTIP EVX1-AS
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXA9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXA9 gene promoter:
  • p53
  • c-Myb
  • Sp1
  • MyoD

Genomic Locations for HOXA9 Gene

Genomic Locations for HOXA9 Gene
12,746 bases
Minus strand
8,064 bases
Minus strand

Genomic View for HOXA9 Gene

Genes around HOXA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXA9 Gene

Proteins for HOXA9 Gene

  • Protein details for HOXA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-A9
    Protein Accession:
    Secondary Accessions:
    • O43369
    • O43429
    • Q99820

    Protein attributes for HOXA9 Gene

    272 amino acids
    Molecular mass:
    30172 Da
    Quaternary structure:
    • Transiently interacts with PRMT5 in TNF-alpha stimulated endothelial cells.
    • Sequence=AAC50364.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for HOXA9 Gene

Post-translational modifications for HOXA9 Gene

  • Methylated on Arg-140 by PRMT5; methylation is critical for E-selectin induction.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXA9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXA9 Gene

Domains & Families for HOXA9 Gene

Gene Families for HOXA9 Gene

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

Suggested Antigen Peptide Sequences for HOXA9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Abd-B homeobox family.
  • Belongs to the Abd-B homeobox family.
genes like me logo Genes that share domains with HOXA9: view

Function for HOXA9 Gene

Molecular function for HOXA9 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. Required for induction of E-selectin and VCAM-1, on the endothelial cells surface at sites of inflammation.
GENATLAS Biochemistry:
homeo box A9(1G),with two alternatively spliced isoforms,including either exon AB or CD,homologous to mouse Hox-1.7,Drosophila abd-B,fused with NUP98 in acute myeloid leukemia with translocation t(7;11),see AML2

Phenotypes From GWAS Catalog for HOXA9 Gene

Gene Ontology (GO) - Molecular Function for HOXA9 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:0005515 protein binding IPI 16189514
GO:0019899 enzyme binding IPI 22269951
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXA9: view
genes like me logo Genes that share phenotypes with HOXA9: view

Animal Models for HOXA9 Gene

MGI Knock Outs for HOXA9:

Animal Model Products

miRNA for HOXA9 Gene

miRTarBase miRNAs that target HOXA9

Transcription Factor Targets for HOXA9 Gene

Selected GeneGlobe predicted Target genes for HOXA9
Targeted motifs for HOXA9 Gene
HOMER Transcription Factor Regulatory Elements motif HOXA9
  • Consensus sequence: GGCCATAAATCA Submotif: canonical Cell Type: HSC GEO ID: GSE33509

Clone Products

  • Addgene plasmids for HOXA9

No data available for Enzyme Numbers (IUBMB) and Human Phenotype Ontology for HOXA9 Gene

Localization for HOXA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXA9 Gene

Subcellular locations from

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 HOXA9 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HOXA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA --
genes like me logo Genes that share ontologies with HOXA9: view

Pathways & Interactions for HOXA9 Gene

genes like me logo Genes that share pathways with HOXA9: view

Pathways by source for HOXA9 Gene

1 KEGG pathway for HOXA9 Gene

SIGNOR curated interactions for HOXA9 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for HOXA9 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,TAS --
GO:0042118 endothelial cell activation IMP 22269951
genes like me logo Genes that share ontologies with HOXA9: view

Drugs & Compounds for HOXA9 Gene

(2) Drugs for HOXA9 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with HOXA9: view

Transcripts for HOXA9 Gene

mRNA/cDNA for HOXA9 Gene

Clone Products

  • Addgene plasmids for HOXA9

Alternative Splicing Database (ASD) splice patterns (SP) for HOXA9 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c
SP1: - -

Relevant External Links for HOXA9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXA9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXA9 Gene

This gene is overexpressed in Kidney - Cortex (x5.8) and Fallopian Tube (x5.4).

NURSA nuclear receptor signaling pathways regulating expression of HOXA9 Gene:


Evidence on tissue expression from TISSUES for HOXA9 Gene

  • Bone marrow(4.6)
  • Intestine(4.3)
  • Blood(2)
genes like me logo Genes that share expression patterns with HOXA9: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXA9 Gene

Orthologs for HOXA9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HOXA9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXA9 34 33
  • 99.14 (n)
(Canis familiaris)
Mammalia -- 34
  • 97 (a)
HOXA9 33
  • 94.24 (n)
(Bos Taurus)
Mammalia HOXA9 34 33
  • 93.87 (n)
(Mus musculus)
Mammalia Hoxa9 16 34 33
  • 92.87 (n)
(Rattus norvegicus)
Mammalia Hoxa9l 33
  • 92.62 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 71 (a)
(Gallus gallus)
Aves -- 34
  • 89 (a)
-- 34
  • 81 (a)
-- 34
  • 81 (a)
LOC100858870 33
  • 79.23 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 95 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxa9 33
  • 71.79 (n)
African clawed frog
(Xenopus laevis)
Amphibia hoxa9-A 33
(Danio rerio)
Actinopterygii hoxa9b 34
  • 48 (a)
hoxa9a 34 34
  • 42 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 18 (a)
Species where no ortholog for HOXA9 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • oppossum (Monodelphis domestica)
  • 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 HOXA9 Gene

Gene Tree for HOXA9 (if available)
Gene Tree for HOXA9 (if available)
Evolutionary constrained regions (ECRs) for HOXA9: view image

Paralogs for HOXA9 Gene

(5) SIMAP similar genes for HOXA9 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with HOXA9: view

Variants for HOXA9 Gene

Sequence variations from dbSNP and Humsavar for HOXA9 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs35991882 uncertain-significance, not provided 27,163,754(-) T/G coding_sequence_variant, missense_variant
rs1000950303 -- 27,165,162(-) G/A coding_sequence_variant, missense_variant
rs1001052090 -- 27,167,291(-) G/A upstream_transcript_variant
rs1001381193 -- 27,165,360(-) C/G/T coding_sequence_variant, missense_variant
rs1002348742 -- 27,163,080(-) C/T 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXA9 Gene

Variant ID Type Subtype PubMed ID
dgv1094n67 CNV gain 20364138
nsv606465 CNV loss 21841781
nsv606468 CNV loss 21841781
nsv7393 OTHER inversion 18451855
nsv824042 CNV gain 20364138

Variation tolerance for HOXA9 Gene

Residual Variation Intolerance Score: 61.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.97; 36.49% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXA9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXA9 Gene

Disorders for HOXA9 Gene

MalaCards: The human disease database

(6) MalaCards diseases for HOXA9 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
myeloid leukemia
  • leukemia myelogenous
myelodysplastic syndrome
  • mds
clivus chordoma
  • chordoma of clivus
leukemia, chronic myeloid
  • cml
hematologic cancer
  • blood cancer
- elite association - COSMIC cancer census association via MalaCards
Search HOXA9 in MalaCards View complete list of genes associated with diseases


  • Note=A chromosomal aberration involving HOXA9 is found in a form of acute myeloid leukemia. Translocation t(7;11)(p15;p15) with NUP98.
  • Note=A chromosomal aberration involving HOXA9 may contribute to disease progression in chronic myeloid leukemia. Translocation t(7;17)(p15;q23) with MSI2.

Additional Disease Information for HOXA9

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HOXA9: view

No data available for Genatlas for HOXA9 Gene

Publications for HOXA9 Gene

  1. A novel gene, MSI2, encoding a putative RNA-binding protein is recurrently rearranged at disease progression of chronic myeloid leukemia and forms a fusion gene with HOXA9 as a result of the cryptic t(7;17)(p15;q23). (PMID: 12649177) Barbouti A … Fioretos T (Cancer research 2003) 3 4 22 58
  2. The t(7;11)(p15;p15) translocation in acute myeloid leukaemia fuses the genes for nucleoporin NUP98 and class I homeoprotein HOXA9. (PMID: 8563754) Borrow J … Housman DE (Nature genetics 1996) 3 4 22 58
  3. HOXA9 methylation by PRMT5 is essential for endothelial cell expression of leukocyte adhesion molecules. (PMID: 22269951) Bandyopadhyay S … Dicorleto PE (Molecular and cellular biology 2012) 3 4 58
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  5. Reversing HOXA9 oncogene activation by PI3K inhibition: epigenetic mechanism and prognostic significance in human glioblastoma. (PMID: 20068170) Costa BM … Costello JF (Cancer research 2010) 3 22 58

Products for HOXA9 Gene

Sources for HOXA9 Gene

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