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

HOXA6 Gene

protein-coding   GIFtS: 47
GCID: GC07M027185

homeobox A6

(Previous name: homeo box A6 )
(Previous symbols: HOX1B, HOX1)
  Search for HOXA6
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for HOXA6    

Aliases
for HOXA6 gene

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


Summaries
for HOXA6 gene

(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 HOXA6:
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: 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


Genomic Views
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 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 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 SABiosciences Chromatin IP Primers for HOXA6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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:
 27,192,217 bp from pter
Size:
 7,203 bases      Orientation:
 minus strand

1 alternative location:
Chr7-,CRA_TCAG 27,236,265-27,238,517     

Proteins
for HOXA6 gene

(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: HXA6_HUMAN, P31267 (See protein sequence)
Recommended Name: Homeobox protein Hox-A6  
Size: 233 amino acids; 26339 Da
Subcellular location: Nucleus
Secondary accessions: A4D192 Q2M3G3 Q9UPM0

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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P31267

    • HOXA6 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_076919.1  
    ENSEMBL proteins: 
     ENSP00000222728  

    Human Recombinant Protein Products: 
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    Uscn Proteins for HOXA6

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

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


    HOXA6 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for HOXA6

    Protein Domains /
    Families
    for HOXA6 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HOXA6 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 P31267

    ProtoNet protein and cluster: P31267

    1 Blocks protein family: IPB001827 Homeobox protein

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


    Function
    for HOXA6 gene

    (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: 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

    miRNA
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    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
    Products:       
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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--


    HOXA6 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Hoxa6tm1Mrc for HOXA6
         1 MGI mutant phenotype (inferred from 1 allele) (MGI details for Hoxa6):
     skeleton 

    HOXA6 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for HOXA6 gene

    (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:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HOXA6

    5/6 Interacting proteins for HOXA6 (P312673) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PBX1P404243I2D: score=1 
    PBX3P404263I2D: score=1 
    PKNOX2Q96KN33I2D: score=1 
    POLR2IP369543I2D: score=1 
    POU2F1P148593I2D: score=1 
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

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


    HOXA6 for ontologies           About GeneDecksing



    Drugs & Compounds
    for HOXA6 gene

    (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 HOXA6
    Search CenterWatch for drugs/clinical trials and news about HOXA6 / HXA6 

    Transcripts
    for HOXA6 gene

    (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 HOXA6 gene: 
    NM_024014.3  

    Unigene Cluster for HOXA6:

    Homeobox A6
    Hs.679517  [show with all ESTs]
    Unigene Representative Sequence: BC104917
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000222728(uc003syo.2) ENST00000521478 ENST00000498652(uc003syq.1)


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    Inhib. RNA
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    Clone
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HOXA6
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HOXA6

    Additional cDNA sequence: 

    BC069497.1 BC104915.1 BC104917.1 

    1 DOTS entry:

    DT.92068629 

    7 AceView cDNA sequences:

    NM_024014 BC069497 BE792613 BP871526 BG749730 BF820847 BF738660 

    GeneLoc Exon Structure


    Expression
    for HOXA6 gene

    (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

    HOXA6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

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

    HOXA6 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)
    Neural TubeNeural TubeSpinal Neural Tube CellsNeural Ectoderm
    BrainMedulla OblongataBrain
    Spinal CordPresumptive Spinal CordSpinal Cord
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    PureStem™ progenitor RASMO12 (Embryonic Progenitor Cell)

    See HOXA6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HOXA6

    SOURCE GeneReport for Unigene cluster: Hs.679517
        SABiosciences Custom PCR Arrays for HOXA6
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    In Situ
    Assay Products:     
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    Orthologs
    for HOXA6 gene

    (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 HOXA6 gene from 4/18 species (see all 18)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves LOC1008571631 homeobox protein Hox-A6-like 81.39(n)
    87.01(a)    		   100857163  XM_003640736.1  XP_003640784.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii hoxb6a6
    hoxb6b6
    		 homeo box B6b
    		 47(a)
    44(a)
    		 1 ↔ many
    possible ortholog
    		 3(23994945-23996987)
    12(28698170-28699799)
    fruit fly
    (Drosophila melanogaster)    		 Insecta Antp3 midgut development specific RNA polymerase
    II more    		 70(a)     --
    worm
    (Caenorhabditis elegans)    		 Secernentea lin-391 Protein LIN-39 44.32(n)
    45.25(a)    		   176068  NM_001025993.1  NP_001021164.1 


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

    Paralogs
    for HOXA6 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HOXA6 gene
    GSX12  HOXA72  HOXA12  HOXD12  HOXA22  HOXB32  HOXC62  HOXB52  
    GSX22  HOXC52  HOXB42  HOXA52  HOXA42  HOXD32  HOXC82  HOXA32  
    HOXD82  HOXB12  HOXB62  HOXB82  HOXD42  HOXB22  HOXB72  PDX12  
    HOXC42  
    13 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
    HOXB5

    HOXA6 for paralogs           About GeneDecksing



    Genomic Variants
    for HOXA6 gene

    (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

    10/68 NCBI SNPs in HOXA6 are shown (see all 68)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 7 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1887486271,2
    		C,--27185360(+) CATGCA/GGCGGT 4 R C int1 us2k1 mis10--------
    rs2020741801,2
    		C--27185473(+) CCAGCT/GCCAGT 4 /E /A mis1 us2k1 int11Minor allele frequency- G:0.00EU 1323
    rs175008631,2
    		C,F,--27185520(+) CCATGG/ACTCCC 4 /S syn1 us2k1 int1 ese36Minor allele frequency- A:0.08NA WA CSA EU 6055
    rs2017658741,2
    		--27185541(+) CCTACA/GAGCAG 3 -- int1 us2k10--------
    rs751655721,2
    		C,--27185634(+) AAACCA/CCCCCG 3 -- int1 us2k10--------
    rs1430588641,2
    		--27185712(+) CAAGCA/GAGATG 3 -- int1 us2k10--------
    rs1387288841,2
    		--27185722(+) GTTTTC/GCACCT 3 -- int1 us2k10--------
    rs47198851,2
    		C,F,A,H,--27185723(+) TTTTCC/GACCTA 3 -- int1 us2k131Minor allele frequency- N:0.00EA NA NS 3166
    rs1450270791,2
    		C,--27185870(+) GTGTT-/TGTGTGT 3 -- int1 us2k10--------
    rs566887721,2
    		C--27185872(+) GTGTC-/GTTGGGG 3 -- int1 us2k12Minor allele frequency- GT:0.25NA 4

    HapMap Linkage Disequilibrium report for HOXA6 (27185015 - 27192217 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for HOXA6: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HOXA6
    DNA2.0 Custom Variant and Variant Library Synthesis for HOXA6

    Disorders / Diseases
    for HOXA6 gene

    (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
    HOXA6 for disorders           About MalaCards

    HOXA6 for disorders           About GeneDecksing

    OMIM gene information: 142951    OMIM disorders: --

    Human Genome Epidemiology (HuGE) Navigator: HOXA6 (2 documents)

    Export disorders for HOXA6 gene to outside databases

    Publications
    for HOXA6 gene

    (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 HOXA6 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with HOXA6)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. 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. (2004)
    2. Human chromosome 7: DNA sequence and biology. (PubMed id 12690205)1, 2 Scherer S.W.... Tsui L.-C. (2003)
    3. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (2003)
    4. Vertebrate homeobox gene nomenclature. (PubMed id 1358459)1, 3 Scott M.P. (1992)
    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. 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 Yerges L.M....Zmuda J.M. (2009)
    8. Hoxa6 potentiates short-term hemopoietic cell proliferation and extended self-renewal. (PubMed id 19157684)1 Dickson G.J....Thompson A. (2009)
    9. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    10. Complete mutation analysis panel of the 39 human HOX genes. (PubMed id 11857506)1 Kosaki K.... Matsuo N. (2002)

    External Searches for HOXA6 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing HOXA6 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 3203 HGNC: 5107 AceView: HOXA6 Ensembl:ENSG00000106006 euGenes: HUgn3203
    ECgene: HOXA6 H-InvDB: HOXA6

    Other Databases showing HOXA6 gene

    (According to HUGE)
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    Specialized Databases showing HOXA6 gene

    (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 HOXA6 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for HOXA6 gene

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

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