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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HOXA4 Gene

protein-coding   GIFtS: 52
GCID: GC07M027170

homeobox A4

(Previous name: homeo box A4 )
(Previous symbols: HOX1D, HOX1)
 Explore 12 diseases affiliated with
HOXA4 via our new
 Human Malady Compendium 
Biological research products
for HOXA4
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Homeobox A41 2     Homeobox Protein Hox-1D2 3
HOX1D1 2 3 5     Dfd-Like Protein2
HOX11 2     Homeobox Protein Hox-A42
Homeo Box A41 2     Hox-1.4-Like Protein2
Homeobox Protein Hox-1.42 3     

External Ids:    HGNC: 51051   Entrez Gene: 32012   Ensembl: ENSG000001975767   OMIM: 1429535   UniProtKB: Q000563   

Export aliases for HOXA4 gene to outside databases

Previous GC identifers: GC07M026810 GC07M026911 GC07M026912 GC07M026941 GC07M027134 GC07M027048


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for HOXA4:
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)

UniProtKB/Swiss-Prot: HXA4_HUMAN, Q00056
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'

Gene Wiki entry for HOXA4


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NC_018918.1  NT_007819.17  NT_079592.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HOXA4 gene promoter:
         Sp1   c-Myb   AP-2beta   AP-2alpha   AP-2gamma   FOXO1   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHOXA4 promoter sequence
   Search SABiosciences Chromatin IP Primers for HOXA4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HOXA4


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

HOXA4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXA4 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M027170:  view genomic region     (about GC identifiers)

Start:
27,168,126 bp from pter      End:
27,170,418 bp from pter
Size:
2,293 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 27,219,281-27,221,554     

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: HXA4_HUMAN, Q00056 (See protein sequence)
Recommended Name: Homeobox protein Hox-A4  
Size: 320 amino acids; 34499 Da
Subcellular location: Nucleus
Secondary accessions: A4D180 O43366

Explore the universe of human proteins at neXtProt for HOXA4: NX_Q00056

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q00056

  • HOXA4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_002132.3  
    ENSEMBL proteins: 
     ENSP00000353151   ENSP00000447955   ENSP00000447249   ENSP00000448015   ENSP00000408845  

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    Uscn Proteins for HOXA4

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--


    HOXA4 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    HOXA4 for domains           About GeneDecksing

    5/6 InterPro domains/families (see all 6):
     IPR001827 Homeobox_Antennapedia_CS
     IPR020479 Homeobox_metazoa
     IPR017995 Homeobox_antennapedia
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain

    Graphical View of Domain Structure for InterPro Entry Q00056

    ProtoNet protein and cluster: Q00056

    1 Blocks protein family: IPB001827 Homeobox protein

    UniProtKB/Swiss-Prot: HXA4_HUMAN, Q00056
    Similarity: Belongs to the Antp homeobox family. Deformed subfamily
    Similarity: Contains 1 homeobox DNA-binding domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: HXA4_HUMAN, Q00056
    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 entry for HOXA4:
    homeo box A4(1D),homologous to mouse Hox-1.4,Drosophila Dfd

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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0043565sequence-specific DNA binding IEA--


    HOXA4 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for HOXA4:
     Increased S DNA content 

    Animal Models:
         Mouse knock-outs for HOXA4: Hoxa4tm1Bhr Hoxa4tm1Mrc
         4 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Hoxa4):
     behavior/neurological  mortality/aging  nervous system  skeleton 

    HOXA4 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for HOXA4

    1 Interacting protein for HOXA4 (Q000563) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NFE2Q166213I2D: score=1 
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0007275multicellular organismal development ----
    GO:0009653anatomical structure morphogenesis TAS1675427
    GO:0009952anterior/posterior pattern specification IEA--
    GO:0048704embryonic skeletal system morphogenesis IEA--


    HOXA4 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HOXA4
    Search CenterWatch for drugs/clinical trials and news about HOXA4 / HXA4 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HOXA4 gene: 
    NM_002141.4  

    Unigene Cluster for HOXA4:

    Homeobox A4
    Hs.533357  [show with all ESTs]
    Unigene Representative Sequence: NM_002141
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000360046(uc003sym.4) ENST00000552601 ENST00000548581 ENST00000511914
    ENST00000428284

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    Additional cDNA sequence: 

    BC126993.1 BC126994.1 M74297.1 

    4 DOTS entries:

    DT.99946118  DT.121115460  DT.86851017  DT.40285593 

    24/81 AceView cDNA sequences (see all 81):

    BF593069 BM824037 NM_153631 AA947856 AW015589 NM_030661 AW849525 BF435327 
    NM_153632 AW166311 AI831660 AI627633 AA534436 AA863038 W69170 BM984688 
    BF939880 AI768663 BG413439 BG768698 AW080161 AI660911 BP872792 BM758409 

    GeneLoc Exon Structure


    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HOXA4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGCTAAGAAT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    HOXA4 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    3 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    SomiteCervical Mesenchymal SclerotomeCervical Sclerotome CellsBone, Cartilage, Tendons & Ligaments
    BoneMaxillary ProcessBone
    LimbLimb BudLimb
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 4 LifeMap Cells 
    NameCategory
    Human umbilical vein endothelial cells (HUVEC) (Primary Cell)Endothelium
    PureStem™ progenitor RASMO12 (Embryonic Progenitor Cell)
    PureStem™ progenitor W10 (Embryonic Progenitor Cell)
    Beating cell clusters (Spontaneous differen...)

    See HOXA4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HOXA4

    SOURCE GeneReport for Unigene cluster: Hs.533357

    UniProtKB/Swiss-Prot: HXA4_HUMAN, Q00056
    Tissue specificity: Embryonic nervous system

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    In Situ
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    (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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for HOXA4 gene from 5/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves F1NMG4_CHICK6
    homeobox protein
    51(a)
    1 ↔ 1
    2(32543955-32546257)
    lizard
    (Anolis carolinensis)
    Reptilia HOXD46
    HOXA46
    --
    52(a)
    46(a)
    possible ortholog
    1 ↔ 1
    GL343356.1(478136-480351)
    GL343275.1(1489989-1492053)
    zebrafish
    (Danio rerio)
    Actinopterygii hoxa4a6
    homeo box A4a
    52(a)
    1 ↔ 1
    19(19233312-19235118)
    fruit fly
    (Drosophila melanogaster)
    Insecta Dfd3 induction of apoptosis transcription factor 73(a)
    (best of 2)
      3 84A5   --
    worm
    (Caenorhabditis elegans)
    Secernentea lin-396
    Homeobox protein lin-39
    23(a)
    possible ortholog
    III(7528603-7536567)


    ENSEMBL Gene Tree for HOXA4 (if available)
    TreeFam Gene Tree for HOXA4 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HOXA4 gene
    GSX12  HOXA72  HOXA12  HOXD12  HOXA22  HOXB32  HOXC62  HOXB52  
    GSX22  HOXC52  HOXB42  HOXA52  HOXD32  HOXA62  HOXC82  HOXA32  
    HOXD82  HOXB12  HOXB62  HOXB82  HOXD42  HOXB22  HOXB72  PDX12  
    HOXC42  
    18/65 SIMAP similar genes for HOXA4 using alignment to 5 protein entries:     HXA4_HUMAN (see all proteins) (see all similar genes):
    HOX B6    HOXA6    HOXB6    HOXC6    HOXB8    HOXB4
    BARX2    MNX1    HOXD12    HOXA5    HOXC13    MEOX2
    HOXA11    BARX1    HOXA10    HOXD8    HOXA7    HOXB7

    HOXA4 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/62 NCBI SNPs in HOXA4 are shown (see all 62    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs47226621,2
    C,F,A,H,--27168719(+) CTTTTT/CACCAA 1 -- ut31 ese312Minor allele frequency- C:0.04EA NS NA WA 668
    rs1112568301,2
    --27168723(+) TCACCG/AATTTG 1 -- ut311Minor allele frequency- A:0.00CSA 1
    rs1880974111,2
    --27168744(+) GGTGTC/TTATTA 1 -- ut310--------
    rs1479235651,2
    C,--27168848(+) ATTATA/GTGGAG 2 T I mis10--------
    rs175007571,2
    C,H--27168858(+) GGAGGG/AAACGG 2 /P /S mis1 ese3 trp36Minor allele frequency- A:0.00NS EA NA 392
    rs2016597671,2
    C,--27168882(+) CGGGTC/G/TGGGGT 3 N H D mis11EU 587
    rs1398084841,2
    C--27168896(+) GATGGA/CGGTGT 2 R L mis11Minor allele frequency- C:0.00NA 4550
    rs2007256701,2
    --27168927(+) CCCTGG/TTGGGC 2 T P mis10--------
    rs1998976901,2
    C,--27168938(+) CGGCAC/GAGGCC 2 S C mis10--------
    rs69768471,2
    C,F,H--27169056(+) GAGCGT/GGTGGG 2 /T /P mis1 ese310Minor allele frequency- G:0.07NS EA NA 1040

    HapMap Linkage Disequilibrium report for HOXA4 (27168126 - 27170418 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for HOXA4: --
    Human Gene Mutation Database (HGMD): HOXA4

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for HOXA4

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

    HOXA4 for disorders           About GeneDecksing

    OMIM gene information: 142953    OMIM disorders: --

    12 diseases for HOXA4:    About MalaCards
    abdominal aortic aneurysm    aortic aneurysm    megacolon    acute myeloid leukemia
    myeloid leukemia    hirschsprung's disease    hypospadias    teratocarcinoma
    ovarian cancer    leukemia    neuroblastoma    pancreatitis

    Human Genome Epidemiology (HuGE) Navigator: HOXA4 (3 documents)

    Export disorders for HOXA4 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)
    About This Section

    PubMed articles for HOXA4 gene, integrated from 9 sources (see all 28):
    (articles sorted by number of sources associating them with HOXA4)
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    1. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (2003)
    2. Vertebrate homeobox gene nomenclature. (PubMed id 1358459)1, 3 Scott M.P. (1992)
    3. Alteration of homeobox gene expression by N-ras transformation of PA- 1 human teratocarcinoma cells. (PubMed id 1675427)1, 2 Buettner R.... Tainsky M.A. (1991)
    4. Expression of HOX homeogenes in human neuroblastoma cell culture lines. (PubMed id 1981366)1, 2 Peverali F.A.... Boncinelli E. (1990)
    5. Nomenclature for human homeobox genes. (PubMed id 1973146)1, 3 McAlpine P.J. and Shows T.B. (1990)
    6. Organization of human class I homeobox genes. (PubMed id 2576652)1, 2 Boncinelli E.... Simeone A. (1989)
    7. Isolation, chromosomal localization, and nucleotide sequence of the human HOX 1.4 homeobox. (PubMed id 2571574)1, 2 Ferguson-Smith A.C.... Ruddle F.H. (1989)
    8. HOX genes in pancreatic development and cancer. (PubMed id 21546695)1 Gray S....Morgan R. (2011)
    9. Regional expression of HOXA4 along the aorta and its potential role in human abdominal aortic aneurysms. (PubMed id 21627813)1 Lillvis J.H....Kuivaniemi H. (2011)
    10. The combined expression of HOXA4 and MEIS1 is an inde pendent prognostic factor in patients with AML. (PubMed id 19563517)1 Zangenberg M....Hokland P. (2009)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 3201 HGNC: 5105 AceView: HOXA4andHOXA3 Ensembl:ENSG00000197576 euGenes: HUgn3201
    ECgene: HOXA4 H-InvDB: HOXA4

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HOXA4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HOXA4 gene:
    Search GeneIP for patents involving HOXA4

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