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

ALX1 Gene

protein-coding   GIFtS: 50
GCID: GC12P085674

ALX homeobox 1

(Previous name: cartilage paired-class homeoprotein 1 )
(Previous symbol: CART1)
 Explore 7 diseases affiliated with
ALX1 via our new
 Human Malady Compendium 
Biological research products
for ALX1
    

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

Aliases
ALX Homeobox 11 2     FND32 5
CART11 2 3 5     ALX Homeobox Protein 12
Cartilage Paired-Class Homeoprotein 11 2     Cartilage Homeoprotein 13
CART-12 3     

External Ids:    HGNC: 14941   Entrez Gene: 80922   Ensembl: ENSG000001803187   OMIM: 6015275   UniProtKB: Q156993   

Export aliases for ALX1 gene to outside databases

Previous GC identifers: GC12P084198 GC12P082731


(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 ALX1:
The specific function of this gene has yet to be determined in humans; however, in rodents, it is necessary for
survival of the forebrain mesenchyme and may also be involved in development of the cervix. Mutations in the mouse
gene lead to neural tube defects such as acrania and meroanencephaly. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: ALX1_HUMAN, Q15699
Function: Transcriptional activator that acts at a palindromic recognition sequence to enhance the activity of the SV40
and TK promoters. Functions as a repressor with the prolactin promoter in vivo. May play a role in chondrocyte
differentiation and may also influence cervix development

Gene Wiki entry for ALX1


(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_000012.11  NC_018923.1  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ALX1 gene promoter:
         STAT5B   TBP   LHX3b/Lhx3b   CUTL1   XBP-1   Arnt   HNF-1A   HNF-1   LHX3a/Lhx3a   Zic3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidALX1 promoter sequence
   Search SABiosciences Chromatin IP Primers for ALX1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ALX1


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

Entrez Gene cytogenetic band: 12q21.31   Ensembl cytogenetic band:  12q21.31   HGNC cytogenetic band: 12q21.31

ALX1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ALX1 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P085674:  view genomic region     (about GC identifiers)

Start:
85,673,885 bp from pter      End:
85,695,562 bp from pter
Size:
21,678 bases      Orientation:
plus strand

(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: ALX1_HUMAN, Q15699 (See protein sequence)
Recommended Name: ALX homeobox protein 1  
Size: 326 amino acids; 36961 Da
Subunit: Interacts (via homeobox domain) with EP300 (By similarity)
Subcellular location: Nucleus
Secondary accessions: Q546C8 Q96FH4

Explore the universe of human proteins at neXtProt for ALX1: NX_Q15699

Post-translational modifications:

  • Acetylated at Lys-131 by EP300, leading to increased interaction with EP300 and enhances transcriptional activation
  • activity (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q15699

  • ALX1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_008913.2  
    ENSEMBL proteins: 
     ENSP00000315417  

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    Uscn Proteins for ALX1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA9753625
    GO:0005667transcription factor complex IEA--


    ALX1 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

    ALX1 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR003654 OAR_dom
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry Q15699

    ProtoNet protein and cluster: Q15699

    1 Blocks protein family: IPB003654 Paired-like homeodomain protein

    UniProtKB/Swiss-Prot: ALX1_HUMAN, Q15699
    Similarity: Belongs to the paired homeobox family
    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: ALX1_HUMAN, Q15699
    Function: Transcriptional activator that acts at a palindromic recognition sequence to enhance the activity of the SV40
    and TK promoters. Functions as a repressor with the prolactin promoter in vivo. May play a role in chondrocyte
    differentiation and may also influence cervix development

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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat ALX1
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    Inhib. RNA
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    Gene Ontology (GO): 5 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:0003714transcription corepressor activity TAS8756334
    GO:0005515protein binding IPI16189514
    GO:0043565sequence-specific DNA binding IEA--
    GO:0046982protein heterodimerization activity IEA--


    ALX1 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Alx1tm1Crm for ALX1
         14 MGI mutant phenotypes (inferred from 1 allele(MGI details for Alx1):
     behavior/neurological  craniofacial  digestive/alimentary  embryogenesis  growth/size 
     hearing/vestibular/ear  homeostasis/metabolism  limbs/digits/tail  mortality/aging  nervous system 
     normal  respiratory system  skeleton  vision/eye 

    ALX1 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:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ALX1

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for ALX1 (Q156991, 2, 3 ENSP000003154174) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    IPO13O948291, 2, 3, ENSP000003614184EBI-750671,EBI-747310 MINT-67873 I2D: score=6 STRING: ENSP00000361418
    ALX4Q9H1613, ENSP000003327444I2D: score=1 STRING: ENSP00000332744
    CREBBPQ927933, ENSP000002623674I2D: score=1 STRING: ENSP00000262367
    EP300Q094723, ENSP000002632534I2D: score=1 STRING: ENSP00000263253
    About this table

    Gene Ontology (GO): 5/15 biological process terms (GO ID links to tree view) (see all 15):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IDA8756334
    GO:0001502cartilage condensation TAS8756334
    GO:0001843neural tube closure IEA--
    GO:0006351transcription, DNA-dependent ----
    GO:0006355regulation of transcription, DNA-dependent ----


    ALX1 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 ALX1
    Search CenterWatch for drugs/clinical trials and news about ALX1 

    (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 ALX1 gene: 
    NM_006982.2  

    Unigene Cluster for ALX1:

    ALX homeobox 1
    Hs.41683  [show with all ESTs]
    Unigene Representative Sequence: U31986
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000316824(uc001tae.4)

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    hsa-miR-590-5p hsa-miR-320e hsa-miR-501-5p hsa-miR-205* hsa-miR-664 hsa-miR-3692 hsa-miR-646 hsa-miR-21
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    Inhib. RNA
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    Clone
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    Additional cDNA sequence: 

    BC010923.1 U31986.1 

    1 DOTS entry:

    DT.410563 

    21 AceView cDNA sequences:

    BC010923 BM459110 AA418118 CB159197 NM_006982 BQ217398 BF666634 U31986 
    AA425489 AA476766 AA425284 N20106 AA476763 BM016562 BG204483 BE895307 
    AW439142 BF669405 BQ432264 BE958505 BF669718 

    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

    ALX1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGCCAGTCTC

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

    About this image

    ALX1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    5 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    KidneyMetanephric MesenchymeMetanephric Mesenchyme CellsKidney
    BoneMaxillary ProcessBone
    Head MesenchymeFrontonasal ProcessHead Mesenchyme
    KidneyInterstitial StromaKidney
    LimbLimb BudLimb
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 4 LifeMap Cells 
    NameCategory
    PureStem™ mesenchymal Progenitor SK11 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)Lateral Plate Mesoderm, Neural Crest
    PureStem™ progenitor SM22 (Embryonic Progenitor Cell)
    Embryoid bodies (Generation of adipoc...)

    See ALX1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ALX1

    SOURCE GeneReport for Unigene cluster: Hs.41683

    UniProtKB/Swiss-Prot: ALX1_HUMAN, Q15699
    Tissue specificity: Cartilage and cervix tissue

        SABiosciences Expression via Pathway-Focused PCR Array including ALX1: 
              Homeobox (HOX) Genes in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ALX1

    (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 chordates.

    Orthologs for ALX1 gene from 4/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves ALX11 ALX homeobox 1 84.76(n)
    93.56(a)
      427871  XM_425445.3  XP_425445.3 
    lizard
    (Anolis carolinensis)
    Reptilia ALX16
    --
    83(a)
    1 ↔ 1
    5(34785534-34835750)
    African clawed frog
    (Xenopus laevis)
    Amphibia cart1-A2 cartilage paired-class homeoprotein 1 80.39(n)    U15276.1 
    zebrafish
    (Danio rerio)
    Actinopterygii cart11 cartilage paired-class homeoprotein 1 69.01(n)
    74.44(a)
      565176  NM_001045074.1  NP_001038539.1 


    ENSEMBL Gene Tree for ALX1 (if available)
    TreeFam Gene Tree for ALX1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ALX1 gene
    PITX12  PHOX2B2  RAX2  ARX2  VSX12  PRRX12  DRGX2  PITX22  
    PHOX2A2  VSX22  ISX2  ALX42  RAX22  PITX32  ALX32  PRRX22  
    4 SIMAP similar genes for ALX1 using alignment to 1 protein entry:     ALX1_HUMAN:
    ALX4    RAX2    ALX3    DUX2

    ALX1 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

    10/375 NCBI SNPs in ALX1 are shown (see all 375    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1407685131,2
    --85672170(+) AGGCCA/TCACTG 1 -- us2k10--------
    rs116112741,2
    C,H--85672268(+) GCCAGA/CTGATC 1 -- us2k1 tfbs31Minor allele frequency- C:0.00NA 2
    rs1501478841,2
    --85672310(+) TTAAGC/GCCGAC 1 -- us2k10--------
    rs1386907281,2
    --85672316(+) CCGACC/GCTGCC 1 -- us2k10--------
    rs1417056421,2
    --85672341(+) AAGGAA/GCAGCT 1 -- us2k10--------
    rs1462752531,2
    --85672395(+) CCTGGG/TCAGGT 1 -- us2k10--------
    rs1380812971,2
    --85672658(+) CCTGTA/CTGGCT 1 -- us2k10--------
    rs1408776241,2
    C,--85672689(+) GCTTA-/GGGTGC 1 -- us2k10--------
    rs1870585571,2
    --85672707(+) AAATGA/CGATTT 1 -- us2k10--------
    rs775392111,2
    F,--85672749(+) AGCGCC/AGCGGG 1 -- us2k11Minor allele frequency- A:0.14WA 118

    HapMap Linkage Disequilibrium report for ALX1 (85673885 - 85695562 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for ALX1: --
    Human Gene Mutation Database (HGMD): ALX1

    SABiosciences Cancer Mutation 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.)
    About This Section

    ALX1 for disorders           About GeneDecksing

    OMIM gene information: 601527   
    OMIM disorders: 613456  
    UniProtKB/Swiss-Prot: ALX1_HUMAN, Q15699
  • Defects in ALX1 are the cause of frontonasal dysplasia type 3 (FND3) [MIM:613456]. The term frontonasal
  • dysplasia describes an array of abnormalities affecting the eyes, forehead and nose and linked to midfacial dysraphia.
    The clinical picture is highly variable. Major findings include true ocular hypertelorism; broadening of the nasal
    root; median facial cleft affecting the nose and/or upper lip and palate; unilateral or bilateral clefting of the alae
    nasi; lack of formation of the nasal tip; anterior cranium bifidum occultum; a V-shaped or widow's peak frontal
    hairline

    7 diseases for ALX1:    About MalaCards
    frontonasal dysplasia    frontonasal dysplasia 3    neural tube defect    spina bifida
    microphthalmia    breast carcinoma    carcinoma

    Human Genome Epidemiology (HuGE) Navigator: ALX1 (1 document)

    Export disorders for ALX1 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 ALX1 gene, integrated from 9 sources (see all 14):
    (articles sorted by number of sources associating them with ALX1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Human Cart-1: structural organization, chromosomal localization, and functional analysis of a cartilage-specific homeodomain cDNA. (PubMed id 8756334)1, 2, 3, 9 Gordon D.F....Gutierrez-Hartmann A. (1996)
    2. Disruption of ALX1 causes extreme microphthalmia and severe facial clefting: expanding the spectrum of autosomal-recessive ALX-relat ed frontonasal dysplasia. (PubMed id 20451171)1, 2 Uz E....Akarsu N.A. (2010)
    3. 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)
    4. Human CART1, a paired-class homeodomain protein, activates transcription through palindromic binding sites. (PubMed id 9753625)1, 2 Cai R.L. (1998)
    5. Presence of a new conserved domain in CART1, a novel member of the tumor necrosis factor receptor-associated protein family, which is expressed in breast carcinoma. (PubMed id 7592751)1, 3 Regnier C.H.... Rio M.-C. (1995)
    6. Prenatal folic acid treatment suppresses acrania and meroanencephaly in mice mutant for the Cart1 homeobox gene. (PubMed id 8673125)1, 9 Zhao Q....de Crombrugghe B. (1996)
    7. The steroid receptor RNA activator protein is recruit ed to promoter regions and acts as a transcriptional repressor. (PubMed id 20398657)1 Chooniedass-Kothari S....Leygue E. (2010)
    8. Genes encoding critical transcriptional activators fo r murine neural tube development and human spina bifida: a case-control study. (PubMed id 20932315)1 Lu W....Zhu H. (2010)
    9. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    10. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 8092 HGNC: 1494 AceView: CART1 Ensembl:ENSG00000180318 euGenes: HUgn8092
    ECgene: ALX1 H-InvDB: ALX1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for ALX1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ALX1 gene:
    Search GeneIP for patents involving ALX1

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