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

HOXA1 Gene

protein-coding   GIFtS: 62
GCID: GC07M027099

homeobox A1

(Previous name: homeo box A1 )
(Previous symbols: HOX1F, HOX1)
 Explore 28 diseases affiliated with
HOXA1 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for HOXA1    

Aliases
for HOXA1 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Homeobox A11 2     Homeobox 1F2
HOX1F1 2 3 5     Homeobox Protein Hox-A12
HOX11 2     Hox 1.6-Like Protein2
Homeo Box A11 2     HOX A1 Homeodomain Protein2
Homeobox Protein Hox-1F2 3     Lab-Like Protein2
BSAS2 5     

External Ids:    HGNC: 50991   Entrez Gene: 31982   Ensembl: ENSG000001059917   OMIM: 1429555   UniProtKB: P496393   

Export aliases for HOXA1 gene to outside databases

Previous GC identifers: GC07M026776 GC07M026874 GC07M026905 GC07M027013


Summaries
for HOXA1 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 HOXA1:
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. The encoded protein may be involved in
the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. Two
transcript variants encoding two different isoforms have been found for this gene, with only one of the isoforms
containing the homeodomain region. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: HXA1_HUMAN, P49639
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. Acts on the anterior body structures. Seems to act
in the maintenance and/or generation of hindbrain segments

Gene Wiki entry for HOXA1 (Homeobox A1)


Genomic Views
for HOXA1 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 HOXA1 gene promoter:
         RelA   Nkx2-5   NF-kappaB   C/EBPalpha   GATA-2   AREB6   SRY   HSF2   Sox9   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: HOXA1 promoter sequence
   Search SABiosciences Chromatin IP Primers for HOXA1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HOXA1


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

Entrez Gene cytogenetic band: 7p15.3   Ensembl cytogenetic band:  7p15.2   HGNC cytogenetic band: 7p15.2

HOXA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXA1 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M027099:  view genomic region     (about GC identifiers)

Start:
 27,132,612 bp from pter      End:
 27,135,625 bp from pter
Size:
 3,014 bases      Orientation:
 minus strand

1 alternative location:
Chr7-,CRA_TCAG 27,183,765-27,186,778     

Proteins
for HOXA1 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: HXA1_HUMAN, P49639 (See protein sequence)
Recommended Name: Homeobox protein Hox-A1  
Size: 335 amino acids; 36641 Da
Subcellular location: Nucleus
Secondary accessions: A4D184 B2R8U7 O43363
Alternative splicing: 3 isoforms:  P49639-1   P49639-2   P49639-3   (Lacks the homeobox domain)

Explore the universe of human proteins at neXtProt for HOXA1: NX_P49639

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P49639

    • HOXA1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_005513.1  NP_705873.2  

    ENSEMBL proteins: 
     ENSP00000343246   ENSP00000347851  

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    Novus Biologicals HOXA1 Proteins
    Novus Biologicals HOXA1 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse ProSpec Recombinant Proteins
    Uscn Proteins for HOXA1

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

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


    HOXA1 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for HOXA1

    Protein Domains /
    Families
    for HOXA1 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HOXA1 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR020479 Homeobox_metazoa
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry P49639

    ProtoNet protein and cluster: P49639

    2 Blocks protein families:
    IPB000047 Lambda and other repressor helix-turn-helix signature
    IPB001827 Homeobox protein


    UniProtKB/Swiss-Prot: HXA1_HUMAN, P49639
    Similarity: Belongs to the Antp homeobox family. Labial subfamily
    Similarity: Contains 1 homeobox DNA-binding domain


    Function
    for HOXA1 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: HXA1_HUMAN, P49639
    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. Acts on the anterior body structures. Seems to act
    in the maintenance and/or generation of hindbrain segments

         Genatlas biochemistry entry for HOXA1:
    homeo box A1(1F),homologous to mouse Hox-1.6,Drosophila 1ab

    miRNA
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    hsa-mir-10a (MIRT001140), hsa-mir-210 (MIRT000152)

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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat HOXA1
    8/24 QIAGEN miScript miRNA Assays for microRNAs that regulate HOXA1 (see all 24):
    hsa-miR-181c hsa-miR-10b hsa-let-7a-2* hsa-miR-219-5p hsa-miR-216b hsa-miR-218 hsa-miR-508-3p hsa-let-7g*
    SwitchGear 3'UTR luciferase reporter plasmid: HOXA1 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for HOXA1 (see all 7)
    OriGene shRNA RFP: HOXA1
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    Gene Editing
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    Clone
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    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HOXA1 

    Cell Line
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    Search LifeMap BioReagents cell lines for HOXA1

    In Situ Assay
    Products:       
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    Gene Ontology (GO): 3 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:0005515protein binding IPI--
    GO:0043565sequence-specific DNA binding IEA--


    HOXA1 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for HOXA1:
     Synthetic lethal with c-Myc af 

    Animal Models:
         Mouse knock-outs for HOXA1: Hoxa1tm2Ipc Hoxa1tm1Ipc Hoxa1tm2Mrc Hoxa1tm1Mrc Hoxa1tm8.2Mrc
         15/18 MGI mutant phenotypes (inferred from 13 alleles) (MGI details for Hoxa1) (see all 18):
     behavior/neurological  cardiovascular system  cellular  craniofacial  digestive/alimentary 
     embryogenesis  endocrine/exocrine gland  hearing/vestibular/ear  hematopoietic system  homeostasis/metabolism 
     immune system  mortality/aging  muscle  nervous system  no phenotypic analysis 

    HOXA1 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for HOXA1 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

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Neural Crest Differentiation
    		Neural Crest Differentiation1.00


    1 BioSystems Pathway for HOXA1 
        Neural Crest Differentiation


    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for HOXA1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 17)

    5/22 Interacting proteins for HOXA1 (P496391, 2, 3 ENSP000003432464) via UniProtKB, MINT, STRING, and/or I2D (see all 22)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    TRAPPC6AO758652, 3, ENSP000000062754MINT-67909 I2D: score=5 STRING: ENSP00000006275
    EFEMP2O959672, 3, ENSP000003099534MINT-67847 I2D: score=4 STRING: ENSP00000309953
    LPXNO607112, 3MINT-67951 I2D: score=4 
    PRNPP041561, 3EBI-740785,EBI-977302 I2D: score=1 
    CHIC2Q9UKJ52, 3, ENSP000002639214MINT-66890 I2D: score=5 STRING: ENSP00000263921
    About this table

    Gene Ontology (GO): 5/31 biological process terms (GO ID links to tree view) (see all 31):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006357regulation of transcription from RNA polymerase II promoter ----
    GO:0007275multicellular organismal development TAS7622051
    GO:0007399nervous system development ----
    GO:0007605sensory perception of sound IDA16155570


    HOXA1 for ontologies           About GeneDecksing



    Drugs & Compounds
    for HOXA1 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

    HOXA1 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HOXA1
    3 Novoseek chemical compound relationships for HOXA1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoic acid 60.9 29 15722554 (3), 7488013 (2), 18512762 (2), 8105479 (2) (see all 13)
    retinoid 21.6 1 17663992 (1), 8838863 (1)
    histidine 5.1 6 17131398 (4), 16168961 (2)

    Search CenterWatch for drugs/clinical trials and news about HOXA1 / HXA1 

    Transcripts
    for HOXA1 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 HOXA1 gene (2 alternative transcripts): 
    NM_005522.4  NM_153620.2  

    Unigene Cluster for HOXA1:

    Homeobox A1
    Hs.67397  [show with all ESTs]
    Unigene Representative Sequence: S79869
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000343060(uc003syd.3 uc003sye.3) ENST00000355633

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat HOXA1
    8/24 QIAGEN miScript miRNA Assays for microRNAs that regulate HOXA1 (see all 24):
    hsa-miR-181c hsa-miR-10b hsa-let-7a-2* hsa-miR-219-5p hsa-miR-216b hsa-miR-218 hsa-miR-508-3p hsa-let-7g*
    SwitchGear 3'UTR luciferase reporter plasmid: HOXA1 3' UTR sequence
    Inhib. RNA
    Products:             		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for HOXA1 (see all 7)
    OriGene shRNA RFP: HOXA1
    OriGene siRNA: HOXA1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HOXA1
    Clone
    Products:             		 OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for HOXA1 (see all 4)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for HOXA1 (see all 2)
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector (see all 2): HOXA1 (NM_005522)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for HOXA1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat HOXA1 
    Primer
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    Browse OriGene validated miRNA SYBR primer pairs
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HOXA1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HOXA1

    Additional cDNA sequence: 

    AK308067.1 AK313514.1 BC032547.2 S69025.1 S79869.1 S79871.1 S79910.1 U10421.1 
    U37431.1 

    4 DOTS entries:

    DT.87046346  DT.92424753  DT.100754664  DT.312508 

    24/38 AceView cDNA sequences (see all 38):

    U10421 NM_153620 NM_005522 BC032547 S79869 AU128573 AU128846 S79910 
    BM838150 AU128022 AU132057 U37431 BF059441 AU128985 AU126484 BM462913 
    AU126166 AU127876 S79871 AU151383 AU129218 BF028399 AU129261 AU150283 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for HOXA1    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b
    SP1:                        
    SP2:                        


    ECgene alternative splicing isoforms for HOXA1

    Expression
    for HOXA1 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

    HOXA1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGTGTGAGTT

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

    HOXA1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    6 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    EpiblastEpiblastPrimordial Germ Cell PrecursorsGerm Cells
    AdiposeCervical Brown Adipose DepotCervical Brown Adipocyte CellsAdipose
    AdiposeLumbar Brown Adipose DepotLumbar Brown Adipocyte CellsAdipose
    AdiposeSacral Brown Adipose DepotSacral Brown Adipocyte CellsAdipose
    AdiposeThoracic Brown Adipose DepotThoracic Brown Adipocyte CellsAdipose
    SomiteThoracic Ventrolateral Dermomyotome LipMuscle Progenitor CellsSkeletal Muscle
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 2 LifeMap Cells 
    NameCategory
    Primordial germ cell-like cells (Reconstitution of mo...)
    Posterior foregut-like cells (A scalable, suspensi...)

    See HOXA1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HOXA1

    SOURCE GeneReport for Unigene cluster: Hs.67397
        SABiosciences Expression via Pathway-Focused PCR Arrays including HOXA1: 
              Stem Cell Transcription Factors in human mouse rat
              Homeobox (HOX) Genes in human mouse rat

    Primer
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HOXA1
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXA1

    Orthologs
    for HOXA1 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 HOXA1 gene from 6/20 species (see all 20)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves HOXA11 homeobox A1 74.52(n)
    72.93(a)    		   374051  XM_003640697.1  XP_003640745.1 
    lizard
    (Anolis carolinensis)    		 Reptilia HOXA16
    		 --
    		 97(a)
    		 1 ↔ 1
    		 GL343275.1(1541168-1543419)
    African clawed frog
    (Xenopus laevis)    		 Amphibia BC044984.12   -- 75.35(n)    BC044984.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii AJ306430.12   -- 78.67(n)   58051  AJ306430.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta lab6
    		 labial
    		 14(a)
    		 1 → many
    		 3R(2487149-2504312)
    worm
    (Caenorhabditis elegans)    		 Secernentea ceh-131 Protein CEH-13 51.05(n)
    54.95(a)    		   176069  NM_066254.4  NP_498655.1 


    ENSEMBL Gene Tree for HOXA1 (if available)
    TreeFam Gene Tree for HOXA1 (if available) 

    Paralogs
    for HOXA1 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HOXA1 gene
    GSX12  HOXA72  HOXD12  HOXA22  HOXB32  HOXC62  HOXB52  GSX22  
    HOXC52  HOXB42  HOXA52  HOXA42  HOXD32  HOXA62  HOXC82  HOXA32  
    HOXD82  HOXB12  HOXB62  HOXB82  HOXD42  HOXB22  HOXB72  PDX12  
    HOXC42  
    4 SIMAP similar genes for HOXA1 using alignment to 3 protein entries:     HXA1_HUMAN (see all proteins):
    HOXB1    HLX    HHEX    HOXD1

    HOXA1 for paralogs           About GeneDecksing



    Genomic Variants
    for HOXA1 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

    10/95 NCBI SNPs in HOXA1 are shown (see all 95)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 7 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1048940171,2
    		Cpathogenic27186601(-) GCCTAC/GCCCTC 4 Y * stg10--------
    rs1048940181,2
    		Cpathogenic27186609(-) CAGCCC/TGAGCC 4 R * stg10--------
    rs1420466471,2
    		--27132214(+) ACCTGG/TAAGTA 2 -- ds50010--------
    rs1458963381,2
    		--27132306(+) ATGACA/GGCTAT 2 -- ds50010--------
    rs1147968271,2
    		F,--27132714(+) CAAAAA/GTAAAT 2 -- ut311Minor allele frequency- G:0.02WA 118
    rs1861119021,2
    		--27132751(+) TTTTTG/TTCCAT 2 -- ut310--------
    rs1488277471,2
    		--27132831(+) ATATTC/TACCAC 2 -- ut310--------
    rs1905875741,2
    		--27133010(+) CAGAGC/TTGTTC 2 -- ut310--------
    rs1833423481,2
    		--27133336(+) AGCCGC/GGTTTC 2 -- ut310--------
    rs1170114041,2
    		--27133496(+) CTAAAC/GATTTC 2 -- ut311Minor allele frequency- G:0.01NA 120

    HapMap Linkage Disequilibrium report for HOXA1 (27132612 - 27135625 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for HOXA1: --
    Human Gene Mutation Database (HGMD): HOXA1

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HOXA1
    DNA2.0 Custom Variant and Variant Library Synthesis for HOXA1

    Disorders / Diseases
    for HOXA1 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    HOXA1 for disorders           About GeneDecksing

    OMIM gene information: 142955   
    OMIM disorders: 601536  
    UniProtKB/Swiss-Prot: HXA1_HUMAN, P49639
  • Defects in HOXA1 are the cause of Athabaskan brainstem dysgenesis syndrome (ABDS) [MIM:601536]; also known as
    • Narvajo brainstem syndrome. This syndrome is characterized by horizontal gaze palsy, sensorineural deafness, central
    hypoventilation, and developmental delay. Some patients had swallowing dysfunction, vocal cord paralysis, facial
    paresis, seizures, and cardiac outflow tract anomalies
  • Defects in HOXA1 are the cause of Bosley-Salih-Alorainy syndrome (BSAS) [MIM:601536]. Affected individuals
    • show horizontal gaze abnormalities, deafness, facial weakness, vascular malformations of the internal carotid arteries
    and cardiac outflow trac. Some patients manifest mental retardation and autism spectrum disorder. In contrast to
    individuals with ABSD, central hypoventilation is not observed in individuals with BSAS

    20/28 diseases for HOXA1 (see all 28):    About MalaCards
    bosley-salih-alorainy syndrome    athabaskan brainstem dysgenesis syndrome    tethered spinal cord syndrome    duane retraction syndrome
    gaze palsy    sensorineural hearing loss    hantavirus pulmonary syndrome    autism spectrum disorder
    hearing loss    cutaneous malignant melanoma    vascular malformations    teratocarcinoma
    aphasia    squamous cell carcinoma    cervical carcinoma    embryonal carcinoma
    cervicitis    carcinoma    breast cancer    lung adenocarcinoma

    1 disease from the University of Copenhagen DISEASES database for HOXA1:
    Tethered spinal cord syndrome

    10/14 Novoseek disease relationships for HOXA1 gene (see all 14)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    carcinoma embryonal 58.1 2 17663992 (2), 9438427 (1), 8105479 (1)
    teratocarcinoma 54.3 3 10942599 (1), 17663992 (1)
    autistic 54.1 2 17171652 (1), 12238024 (1)
    mental retardation 35 1 19018235 (1)
    congenital malformation 19.6 2 7956823 (1), 18412118 (1)
    cervical carcinoma 18.5 1 12824890 (1)
    genetic susceptibility 8.91 2 11091361 (1), 11840501 (1)
    leukemia 0 1 15722554 (1)
    carcinoma squamous cell 0 3 16525661 (2)
    breast cancer 0 11 8670198 (4), 7488013 (3)

    Genetic Association Database (GAD): HOXA1
    Human Genome Epidemiology (HuGE) Navigator: HOXA1 (10 documents)

    Export disorders for HOXA1 gene to outside databases

    Publications
    for HOXA1 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 HOXA1 gene, integrated from 9 sources (see all 102):
    (articles sorted by number of sources associating them with HOXA1)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Discovery of allelic variants of HOXA1 and HOXB1: genetic susceptibility to autism spectrum disorders. (PubMed id 11091361)1, 2, 9 Ingram J.L....Rodier P.M. (2000)
    2. Lack of association between HoxA1 and HoxB1 gene variants and autism in 110 multiplex families. (PubMed id 11840501)1, 4, 9 Li J....Myers R.M. (2002)
    3. Retinoic acid induces three newly cloned HOXA1 transcripts in MCF7 breast cancer cells. (PubMed id 7488013)1, 2, 9 Chariot A.... Castronovo V. (1995)
    4. Homozygous HOXA1 mutations disrupt human brainstem, inner ear, cardiovascular and cognitive development. (PubMed id 16155570)1, 2, 9 Tischfield M.A....Engle E.C. (2005)
    5. Association between the HOXA1 A218G polymorphism and increased head circumference in patients with autism. (PubMed id 14960295)1, 4, 9 Conciatori M....Persico A.M. (2004)
    6. The HOXA1 A218G polymorphism and autism: lack of association in white and black patients from the South Carolina Autism Project. (PubMed id 12908836)1, 4, 9 Collins J.S....Michaelis R.C. (2003)
    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. (2004)
    8. Human chromosome 7: DNA sequence and biology. (PubMed id 12690205)1, 2 Scherer S.W.... Tsui L.-C. (2003)
    9. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (2003)
    10. No evidence for linkage of liability to autism to HOXA1 in a sample from the CPEA network. (PubMed id 12210285)1, 4 Devlin B....Schellenberg G.D. (2002)

    External Searches for HOXA1 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
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    Genome Databases showing HOXA1 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 3198 HGNC: 5099 AceView: HOXA1 Ensembl:ENSG00000105991 euGenes: HUgn3198
    ECgene: HOXA1 H-InvDB: HOXA1

    Other Databases showing HOXA1 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing HOXA1 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 HOXA1 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/HOXA1

    Intellectual Property
    for HOXA1 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for HOXA1 gene:
    Search GeneIP for patents involving HOXA1

    GeneCards and IP:
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