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HOXA6 Gene

protein-coding   GIFtS: 49
GCID: GC07M027185

Homeobox A6

(Previous name: homeo box A6)
(Previous symbols: HOX1B, HOX1)
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(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 A61 2     HOX1.22
HOX1B1 2 3 5     Homeo Box 1B2
HOX11 2     Homeobox Protein Hox-A62
Homeo Box A61 2     Homeobox Protein HOXA62
Homeobox Protein Hox-1B2 3     

External Ids:    HGNC: 51071   Entrez Gene: 32032   Ensembl: ENSG000001060067   OMIM: 1429515   UniProtKB: P312673   

Export aliases for HOXA6 gene to outside databases

Previous GC identifers: GC07M026827 GC07M026927 GC07M026958 GC07M027151 GC07M027065


(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 HOXA6 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 HOXA6 Gene:
HOXA6 (homeobox A6) is a protein-coding gene. GO annotations related to this gene include sequence-specific DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is HOXA7.

UniProtKB/Swiss-Prot: HXA6_HUMAN, P31267
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

Gene Wiki entry for HOXA6 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 HOXA6 gene promoter:
         Sp1   p53   AP-2beta   c-Myb   AP-2alpha   AP-2gamma   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): HOXA6 promoter sequence
   Search Chromatin IP Primers for HOXA6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HOXA6


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

HOXA6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXA6 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M027185:  view genomic region     (about GC identifiers)

Start:
27,185,015 bp from pter      End:
27,190,222 bp from pter
Size:
5,208 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 27,236,351-27,238,542     

(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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: HXA6_HUMAN, P31267 (See protein sequence)
Recommended Name: Homeobox protein Hox-A6  
Size: 233 amino acids; 26339 Da
Secondary accessions: A4D192 Q2M3G3 Q9UPM0

Explore the universe of human proteins at neXtProt for HOXA6: NX_P31267

Explore proteomics data for HOXA6 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys172
  • Modification sites at PhosphoSitePlus

  • See HOXA6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_076919.1  
    ENSEMBL proteins: 
     ENSP00000222728  

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    (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):
     IPR001827 Homeobox_Antennapedia_CS
     IPR020479 Homeobox_metazoa
     IPR017995 Homeobox_antennapedia
     IPR017970 Homeobox_CS
     IPR001356 Homeobox_dom

    Graphical View of Domain Structure for InterPro Entry P31267

    ProtoNet protein and cluster: P31267

    1 Blocks protein domain: IPB001827 Homeobox protein

    UniProtKB/Swiss-Prot: HXA6_HUMAN, P31267
    Similarity: Belongs to the Antp homeobox family
    Similarity: Contains 1 homeobox DNA-binding domain


    Find genes that share domains with HOXA6           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HXA6_HUMAN, P31267
    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 entry for HOXA6:
    homeo box A6(1B),homologous to mouse Hox-1.2,Drosophila Antp,Ubx,abd-A

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0043565sequence-specific DNA binding IEA--
         
    Find genes that share ontologies with HOXA6           About GenesLikeMe


    Phenotypes:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Hoxa6):
     skeleton 

    Find genes that share phenotypes with HOXA6           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Hoxa6tm1Mrc for HOXA6

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for HOXA6
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for HOXA6

    miRNA
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    miRTarBase miRNAs that target HOXA6:
    hsa-mir-296-3p (MIRT038338), hsa-let-7a-5p (MIRT052543)

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    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat HOXA6

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    (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
    HXA6_HUMAN, P31267: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    Find genes that share ontologies with HOXA6           About GenesLikeMe


    (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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for HOXA6
    Interactions:

        Search GeneGlobe Interaction Network for HOXA6

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    Selected Interacting proteins for HOXA6 (P312673 ENSP000002227284) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PBX1P404243, ENSP000004058904I2D: score=1 STRING: ENSP00000405890
    PBX3P404263, ENSP000003625884I2D: score=1 STRING: ENSP00000362588
    PKNOX2Q96KN33I2D: score=1 
    POLR2IP369543I2D: score=1 
    POU2F1P148593I2D: score=1 
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0009952anterior/posterior pattern specification IEA--
    GO:0048704embryonic skeletal system morphogenesis IEA--
    GO:0048706embryonic skeletal system development ----

    Find genes that share ontologies with HOXA6           About GenesLikeMe



    (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 HOXA6 (HXA6)



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for HOXA6 gene: 
    NM_024014.3  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000222728(uc003syo.2) ENST00000521478
    miRNA
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    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat HOXA6
      QuantiFast Probe-based Assays in human, mouse, rat HOXA6

    7 AceView cDNA sequences:

    NM_024014 BC069497 BP871526 BG749730 BE792613 BF820847 BF738660 

    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™, 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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    HOXA6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    HOXA6 Expression
    About this image


    HOXA6 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Brain (Nervous System)    fully expand to see all 5 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Liver (Hepatobiliary System)
             Hepatocytes Liver Lobule
     
     Bone (Muscoskeletal System)
             Bone Marrow
    HOXA6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    HOXA6 Protein Expression
        Custom PCR Arrays for HOXA6
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    In Situ
    Assay Products:
     

     
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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)
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    This gene was present in the common ancestor of animals.

    Orthologs for HOXA6 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hoxa61 , 5 homeobox A61, 5 92.96(n)1
    96.55(a)1
      6 (25.40 cM)5
    154031  NM_010454.11  NP_034584.11 
     522054315 
    chicken
    (Gallus gallus)
    Aves LOC1008584341 homeobox protein Hox-A6-like 81.39(n)
    87.01(a)
      100858434  XM_003640700.2  XP_003640748.2 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia hoxa61 homeobox A6 68.54(n)
    72.73(a)
      100485428  XM_002933395.2  XP_002933441.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta Antp3 midgut development specific RNA
    polymerase II more
    70(a)     --


    ENSEMBL Gene Tree for HOXA6 (if available)
    TreeFam Gene Tree for HOXA6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for HOXA6 gene
    HOXA72  HOXB52  HOXC62  HOXC52  HOXB42  HOXA52  ENSG000002732662  HOXA42  
    HOXC82  ENSG000002730492  HOXD82  HOXB62  HOXB82  HOXD42  HOXB72  HOXC42  
    12 SIMAP similar genes for HOXA6 using alignment to 1 protein entry:     HXA6_HUMAN:
    HOXA4    HOXB6    HOXC6    HOXA5    HOXC9    HOXD8
    HOXB7    HOXC8    HOXA7    HOXB8    HOXC4    HOXC5

    Find genes that share paralogs with HOXA6           About GenesLikeMe



    (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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    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for HOXA6 (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv887856CNV Loss21882294
    nsv887876CNV Loss21882294
    nsv5674CNV Loss18451855
    dgv7233n71CNV Loss21882294
    dgv7231n71CNV Loss21882294
    nsv526526CNV Loss19592680
    dgv7235n71CNV Loss21882294
    dgv7236n71CNV Loss21882294
    dgv7234n71CNV Loss21882294
    dgv7232n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
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    (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.)
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    OMIM gene information: 142951    OMIM disorders: --


    Find genes that share disorders with HOXA6           About GenesLikeMe

    Genetic Association Database (GAD): HOXA6
    Human Genome Epidemiology (HuGE) Navigator: HOXA6 (2 documents)

    Export disorders for HOXA6 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 HOXA6 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with HOXA6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    2. 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)
    3. Human chromosome 7: DNA sequence and biology. (PubMed id 12690205)1, 2 Scherer S.W.... Tsui L.-C. (Science 2003)
    4. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (Nature 2003)
    5. Vertebrate homeobox gene nomenclature. (PubMed id 1358459)1, 3 Scott M.P. (Cell 1992)
    6. Nomenclature for human homeobox genes. (PubMed id 1973146)1, 3 McAlpine P.J. and Shows T.B. (Genomics 1990)
    7. Organization of human class I homeobox genes. (PubMed id 2576652)1, 2 Boncinelli E.... Simeone A. (Genome 1989)
    8. DNA methylation in the malignant transformation of meningiomas. (PubMed id 23349797)1 Gao F....Wang K. (PLoS ONE 2013)
    9. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    10. Hoxa6 potentiates short-term hemopoietic cell proliferation and extended self-renewal. (PubMed id 19157684)1 Dickson G.J....Thompson A. (Exp. Hematol. 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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)
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    Entrez Gene: 3203 HGNC: 5107 AceView: HOXA6 Ensembl:ENSG00000106006 euGenes: HUgn3203
    ECgene: HOXA6 H-InvDB: HOXA6

    (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)
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    NameDescription
    PharmGKB entry for HOXA6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for HOXA6 gene:
    Search GeneIP for patents involving HOXA6

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