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HOXA9 Gene

protein-coding   GIFtS: 56
GCID: GC07M027254

Homeobox A9

(Previous name: homeo box A9)
(Previous symbols: HOX1G, HOX1)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Homeobox A91 2     ABD-B2
HOX1G1 2 3 5     HOX1.72
HOX11 2     Homeobox Protein Hox-A92
Homeobox Protein Hox-1G2 3     Homeodomain Protein HOXA92
Homeo Box A91     

External Ids:    HGNC: 51091   Entrez Gene: 32052   Ensembl: ENSG000000783997   OMIM: 1429565   UniProtKB: P312693   

Export aliases for HOXA9 gene to outside databases

Previous GC identifers: GC07U990049 GC07M026844 GC07M026910 GC07M026945 GC07M026946 GC07M026975 GC07M027168 GC07M027213 GC07M027214 GC07M027219 GC07M027230


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 mn1, and acute leukemia. GO annotations related to this gene include enzyme binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is HOXD11.

UniProtKB/Swiss-Prot: HXA9_HUMAN, P31269
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

Gene Wiki entry for HOXA9 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the HOXA9 gene promoter:
         Sp1   p53   MyoD   c-Myb   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): HOXA9 promoter sequence
   Search Chromatin IP Primers for HOXA9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HOXA9


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 7p15.2   Ensembl cytogenetic band:  7p15.2   HGNC cytogenetic band: 7p15.2

HOXA9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXA9 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M027254:  view genomic region     (about GC identifiers)

Start:
27,202,054 bp from pter      End:
27,210,117 bp from pter
Size:
8,064 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 27,253,232-27,256,324     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: HXA9_HUMAN, P31269 (See protein sequence)
Recommended Name: Homeobox protein Hox-A9  
Size: 272 amino acids; 30172 Da
Subunit: Transiently interacts with PRMT5 in TNF-alpha stimulated endothelial cells
Sequence caution: Sequence=AAC50364.1; Type=Erroneous initiation;
Secondary accessions: O43369 O43429 Q99820

Explore the universe of human proteins at neXtProt for HOXA9: NX_P31269

Explore proteomics data for HOXA9 at MOPED

Post-translational modifications: 

  • Methylated on Arg-140 by PRMT5; methylation is critical for E-selectin induction1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See HOXA9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689952.1  
    ENSEMBL proteins: 
     ENSP00000343619   ENSP00000379634  

    HOXA9 Human Recombinant Protein Products:

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    Novus Biologicals HOXA9 Protein
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    Browse Sino Biological Cell Lysates
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    Cloud-Clone Corp. Proteins for HOXA9

    HOXA9 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of HOXA9
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    LSBio Antibodies in human, mouse, rat for HOXA9

    HOXA9 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for HOXA9
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    Cloud-Clone Corp. ELISAs for HOXA9
    Cloud-Clone Corp. CLIAs for HOXA9


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    HOXL: Homeoboxes / ANTP class : HOXL subclass

    Selected InterPro protein domains (see all 6):
     IPR020479 Homeobox_metazoa
     IPR006711 Hox9_activation_N
     IPR017112 Homeobox_Hox9
     IPR017970 Homeobox_CS
     IPR001356 Homeobox_dom

    Graphical View of Domain Structure for InterPro Entry P31269

    ProtoNet protein and cluster: P31269

    2 Blocks protein domains:
    IPB000047 Lambda and other repressor helix-turn-helix signature
    IPB006711 Hox9 activation region


    UniProtKB/Swiss-Prot: HXA9_HUMAN, P31269
    Similarity: Belongs to the Abd-B homeobox family
    Similarity: Contains 1 homeobox DNA-binding domain


    HOXA9 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HXA9_HUMAN, P31269
    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 entry for HOXA9:
    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

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0005515protein binding IPI16189514
    GO:0019899enzyme binding IPI--
    GO:0043565sequence-specific DNA binding IEA--
         
    HOXA9 for ontologies           About GeneDecksing


    Phenotypes:
         8 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Hoxa9):
     endocrine/exocrine gland  growth/size/body  hematopoietic system  immune system  integument 
     limbs/digits/tail  reproductive system  skeleton 

    HOXA9 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for HOXA9: Hoxa9tm1Mrc Hoxa9tm1Ipc

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HOXA9
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for HOXA9

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for HOXA9
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HOXA9

    Transcription Factor Targeting: 
    Targeting motifs: HOMER Transcription Factor Regulatory Elements motif viewer 
                                          Consensus sequence:  GGCCATAAATCA 

    miRNA
    Products:
        
    miRTarBase miRNAs that target HOXA9:
    hsa-mir-340-5p (MIRT019591), hsa-mir-324-5p (MIRT043225), hsa-mir-210-3p (MIRT000149), hsa-mir-18a-5p (MIRT031333), hsa-mir-33a-5p (MIRT028225), hsa-mir-145-5p (MIRT001917), hsa-mir-26b-5p (MIRT030092), hsa-mir-101-3p (MIRT027337), hsa-mir-96-5p (MIRT027927), hsa-mir-21-5p (MIRT030986), hsa-mir-769-3p (MIRT039078), hsa-mir-126-3p (MIRT001918), hsa-mir-652-3p (MIRT016142)

    Block miRNA regulation of human, mouse, rat HOXA9 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HOXA9 (see all 39):
    hsa-miR-124* hsa-let-7d hsa-miR-300 hsa-miR-139-5p hsa-miR-128 hsa-miR-3142 hsa-let-7g hsa-miR-548m
    SwitchGear 3'UTR luciferase reporter plasmidHOXA9 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for HOXA9
    Predesigned siRNA for gene silencing in human, mouse, rat HOXA9

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for HOXA9

    Clone
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    OriGene clones in human, mouse for HOXA9 (see all 7)
    OriGene ORF clones in mouse, rat for HOXA9
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: HOXA9 (NM_152739)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HOXA9
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HOXA9

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for HOXA9 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXA9


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    HXA9_HUMAN, P31269: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005667transcription factor complex ----
    GO:0005737cytoplasm ----

    HOXA9 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for HOXA9 About    
    See pathways by source

    SuperPathContained pathways About
    1Transcriptional misregulation in cancer
    Transcriptional misregulation in cancer
    2TGF-beta Receptor Signaling Pathway
    TGF-beta Receptor Signaling Pathway

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for HOXA9
        TGF-beta Receptor Signaling Pathway


    1 Kegg Pathway  (Kegg details for HOXA9):
        Transcriptional misregulation in cancer


    HOXA9 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including HOXA9: 
              Stem Cell Transcription Factors in human mouse rat
              Homeobox (HOX) Genes in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for HOXA9

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for HOXA9 (P312691, 3 ENSP000003436194) via UniProtKB, MINT, STRING, and/or I2D (see all 60)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TRIP6Q156541, 3, ENSP000002004574EBI-742314,EBI-742327 I2D: score=4 STRING: ENSP00000200457
    ENSG00000225987P404253, ENSP000004039484I2D: score=3 STRING: ENSP00000403948
    PBX2P404253, ENSP000003641904I2D: score=3 STRING: ENSP00000364190
    ENSG00000206315P404253I2D: score=3 
    ENSG00000224952P404253I2D: score=3 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0007275multicellular organismal development IEA--
    GO:0009952anterior/posterior pattern specification ----
    GO:0009954proximal/distal pattern formation ----

    HOXA9 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for HOXA9 (HXA9)

    2 Novoseek inferred chemical compound relationships for HOXA9 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    estradiol 0 1 10834931 (1)
    tyrosine 0 3 16518848 (1), 14764452 (1), 15681849 (1)



    HOXA9 for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for HOXA9 gene: 
    NM_152739.3  

    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000343483(uc003syt.3 uc022aar.1) ENST00000497089 ENST00000487384
    ENST00000396345 ENST00000489695
    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat HOXA9 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate HOXA9 (see all 39):
    hsa-miR-124* hsa-let-7d hsa-miR-300 hsa-miR-139-5p hsa-miR-128 hsa-miR-3142 hsa-let-7g hsa-miR-548m
    SwitchGear 3'UTR luciferase reporter plasmidHOXA9 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for HOXA9
    Predesigned siRNA for gene silencing in human, mouse, rat HOXA9
    Clone
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    GenScript: all cDNA clones in your preferred vector: HOXA9 (NM_152739)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HOXA9
    Primer
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    OriGene qPCR primer pairs and template standards for HOXA9
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat HOXA9
      QuantiTect SYBR Green Assays in human, mouse, rat HOXA9
      QuantiFast Probe-based Assays in human, mouse, rat HOXA9

    Selected AceView cDNA sequences (see all 182):

    NM_152739 AA613299 NM_002142 BM920206 BE292889 AL080006 NM_153715 AA599729 
    AW612608 AI738605 BM796352 AA577580 BE328694 BU624206 AW770908 AW452853 
    BU624249 BQ422016 BX104119 BC006537 CA442923 CR606804 BF434948 AA195633 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for HOXA9    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c
    SP1:        -     -                           
    SP2:                                          
    SP3:                                          


    ECgene alternative splicing isoforms for HOXA9

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    HOXA9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    HOXA9 Expression
    About this image


    HOXA9 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 20) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Lumbar Sclerotome Cells Lumbar Mesenchymal Sclerotome
             Bone Marrow
     
     Mesoderm (Gastrulation Derivatives)
             Limb Bud Mesenchyme Cells Limb Bud
     
     Cartilage (Muscoskeletal System)
             Lumbar Sclerotome Cells Lumbar Mesenchymal Sclerotome
     
     Somite (Muscoskeletal System)
             Lumbar Sclerotome Cells Lumbar Mesenchymal Sclerotome
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
    HOXA9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HOXA9 Protein Expression
        Pathway & Disease-focused RT2 Profiler PCR Arrays including HOXA9: 
              Stem Cell Transcription Factors in human mouse rat
              Homeobox (HOX) Genes in human mouse rat

    Primer
    Products:
    OriGene qPCR primer pairs and template standards for HOXA9
    OriGene qSTAR qPCR primer pairs in human, mouse for HOXA9
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat HOXA9
    QuantiTect SYBR Green Assays in human, mouse, rat HOXA9
    QuantiFast Probe-based Assays in human, mouse, rat HOXA9
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXA9

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for HOXA9 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hoxa91 , 5 homeobox A91, 5 92.87(n)1
    98.15(a)1
      6 (25.40 cM)5
    154051  NM_010456.31  NP_034586.11 
     522230975 
    chicken
    (Gallus gallus)
    Aves LOC1008588701 homeobox protein Hox-A9-like 79.23(n)
    78.08(a)
      100858870  XM_003640706.2  XP_003640754.1 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    95(a)
    1 → many
    GL343275.1(1440520-1440768)
    African clawed frog
    (Xenopus laevis)
    Amphibia hoxa9-A2 homeo box A9 80.34(n)    AJ319749.1 
    zebrafish
    (Danio rerio)
    Actinopterygii hoxa9b6
    hoxa9a6
    (see all 3)
    homeo box A9a
    (see all 3)
    48(a)
    42(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    16(22999749-23002014) ENSDARG00000056819
    19(19213175-19217890) ENSDARG00000009461


    ENSEMBL Gene Tree for HOXA9 (if available)
    TreeFam Gene Tree for HOXA9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HOXA9 gene
    HOXD112  ENSG000002571842  HOXD102  HOXC132  HOXC102  HOXD122  HOXA132  HOXC92  
    HOXB132  HOXC122  HOXC112  HOXD132  HOXA112  HOXB92  HOXD92  HOXA102  
    5 SIMAP similar genes for HOXA9 using alignment to 2 protein entries:     HXA9_HUMAN (see all proteins):
    HOXA-9    HOXC9    HOXB9    HOXA10    HOXC10

    HOXA9 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for HOXA9 (see all 143)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
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    ----------
    rs1927455791,2
    --27167441(+) GCAAGA/CCCCCA 1 -- ds50010--------
    rs1847420391,2
    --27167447(+) CCCCAA/GAATGT 1 -- ds50010--------
    rs353357611,2
    C--27167979(+) TCAAC-/ACAACAAT 1 -- cds10--------
    rs1901226101,2
    --27168038(+) GTTCAA/GTCTGA 1 -- ut310--------
    rs1817376851,2
    --27168155(+) ATTTCA/CTCCAA 1 -- ut310--------
    rs102596201,2
    C,F,A,H--27168159(+) CCTCCG/AATTAA 1 -- ut31 ese338Minor allele frequency- A:0.30NS EA NA WA CSA 3733
    rs1490012661,2
    --27168210(+) GTATAA/GCTCCG 1 -- ut310--------
    rs1459058651,2
    C--27168223(+) TTTCCC/TCACTG 1 -- ut310--------
    rs1864363141,2
    --27168332(+) GATAAC/TGGACA 1 -- ut310--------
    rs125373911,2
    C,H--27168405(+) TTAAAA/TTTTTT 1 -- ut314Minor allele frequency- T:0.00NS EA 412

    HapMap Linkage Disequilibrium report for HOXA9 (27202054 - 27210117 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for HOXA9:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv887856CNV Loss21882294
    dgv7236n71CNV Loss21882294
    dgv7234n71CNV Loss21882294
    dgv7233n71CNV Loss21882294
    dgv7232n71CNV Loss21882294
    dgv7231n71CNV Loss21882294
    dgv1094n67CNV Gain20364138
    nsv824042CNV Gain20364138
    nsv7393OTHER Inversion18451855

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing HOXA9
    DNA2.0 Custom Variant and Variant Library Synthesis for HOXA9

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 142956    OMIM disorders: --

    UniProtKB/Swiss-Prot: HXA9_HUMAN, P31269
  • 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

  • Selected diseases for HOXA9 (see all 31):    
    About MalaCards
    mn1    acute leukemia    chronic myelomonocytic leukemia    acute monocytic leukemia
    chronic myeloid leukemia    clubfoot    monocytic leukemia    myelodysplastic syndromes
    acute lymphocytic leukemia    acute myeloid leukemia    myeloid leukemia    testicular cancer
    hirschsprung's disease    esophageal squamous cell carcinoma    lymphoblastic leukemia    conjunctivitis
    esophageal cancer    esophagitis    endotheliitis    leukemia

    1 disease from the University of Copenhagen DISEASES database for HOXA9:
    Leukemia

    HOXA9 for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for HOXA9 gene (see all 11)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    leukemogenesis 79 6 15755900 (2), 17379095 (1), 10698505 (1), 11830496 (1) (see all 5)
    leukemia 64 45 19056693 (4), 8563753 (3), 15755900 (3), 12358913 (2) (see all 23)
    myeloid leukemia 63.2 7 10602420 (2), 10996203 (1), 14713950 (1), 11687616 (1) (see all 6)
    acute leukemia 58.8 7 16102826 (2), 16518848 (1), 18337761 (1), 15160920 (1) (see all 5)
    myelodysplastic syndromes 40.8 3 15982348 (2), 17178874 (1)
    myeloid leukemia chronic 33 4 11830496 (1), 12649177 (1), 10602420 (1), 16630659 (1)
    lymphoblastic leukemia acute 31.6 3 11314021 (1), 16102826 (1), 18337761 (1)
    chromosomal aberrations 17.1 2 11314021 (1), 10565304 (1)
    cancer 4.05 2 19621443 (1), 15709170 (1)
    hematologic malignancies 1.9 1 12461755 (1)

    Genetic Association Database (GAD): HOXA9
    Human Genome Epidemiology (HuGE) Navigator: HOXA9 (4 documents)

    Export disorders for HOXA9 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for HOXA9 gene, integrated from 10 sources (see all 214):
    (articles sorted by number of sources associating them with HOXA9)
        Utopia: connect your pdf to the dynamic
    world of online information

    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). (PubMed id 12649177)1, 2, 9 Barbouti A.... Fioretos T. (Cancer Res. 2003)
    2. The t(7;11)(p15;p15) translocation in acute myeloid leukaemia fuses the genes for nucleoporin NUP98 and class I homeoprotein HOXA9. (PubMed id 8563754)1, 2, 9 Borrow J.... Housman D.E. (Nat. Genet. 1996)
    3. HOXA9 methylation by PRMT5 is essential for endothelial cell expression of leukocyte adhesion molecules. (PubMed id 22269951)1, 2 Bandyopadhyay S.... Dicorleto P.E. (Mol. Cell. Biol. 2012)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    5. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PubMed id 19453261)1, 4 Yerges L.M....Zmuda J.M. (J. Bone Miner. Res. 2009)
    6. Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. (PubMed id 19938081)1, 4 Ester A.R....Hecht J.T. (Am. J. Med. Genet. A 2009)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (Nature 2003)
    9. Endothelial cells express a novel, tumor necrosis factor-alpha- regulated variant of HOXA9. (PubMed id 9880515)1, 2 Patel C.V.... DiCorleto P.E. (J. Biol. Chem. 1999)
    10. Vertebrate homeobox gene nomenclature. (PubMed id 1358459)1, 3 Scott M.P. (Cell 1992)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section

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    Entrez Gene: 3205 HGNC: 5109 AceView: HOXA9andHOXA10 Ensembl:ENSG00000078399 euGenes: HUgn3205
    ECgene: HOXA9 Kegg: 3205 H-InvDB: HOXA9

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for HOXA9 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for HOXA9 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for HOXA9 gene:
    Search GeneIP for patents involving HOXA9

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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