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

SNX27 Gene

protein-coding   GIFtS: 51
GCID: GC01P151585

sorting nexin family member 27

  Search for SNX27
in our new
 Human Malady Compendium 
Biological research products
for SNX27
    

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

Aliases
Sorting Nexin Family Member 271 2     MGC204711
MY0141 2     Methamphetamine-Responsive Transcript 12
KIAA04881 3     Sorting Nexin-272
MRT12 5     

External Ids:    HGNC: 200731   Entrez Gene: 816092   Ensembl: ENSG000001433767   OMIM: 6115415   UniProtKB: Q96L923   

Export aliases for SNX27 gene to outside databases

Previous GC identifers: GC01P147367 GC01P148359 GC01P148801 GC01P148397 GC01P149851 GC01P122961


(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 SNX27:
This gene encodes a member of the sorting nexin family, a diverse group of cytoplasmic and membrane-associated proteins
involved in endocytosis of plasma membrane receptors and protein trafficking through these compartments. All members
of this protein family contain a phosphoinositide binding domain (PX domain). A highly similar protein in mouse is
responsible for the specific recruitment of an isoform of serotonin 5-hydroxytryptamine 4 receptor into early
endosomes, suggesting the analogous role for the human protein. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: SNX27_HUMAN, Q96L92
Function: Involved in endocytic trafficking (By similarity). In T lymphocytes, participates in endocytic recycling
pathway. Recruits PSCDBP and HT4R to early endosomes (By similarity)

Gene Wiki entry for SNX27


(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_000001.10  NC_018912.1  NT_004487.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SNX27 gene promoter:
         RFX1   AML1a   Pax-5   Nkx2-5   Nkx5-1   MEF-2A   SRY   c-Myb   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSNX27 promoter sequence
   Search SABiosciences Chromatin IP Primers for SNX27

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SNX27


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

Entrez Gene cytogenetic band: 1q21.3   Ensembl cytogenetic band:  1q21.3   HGNC cytogenetic band: 1q21.3

SNX27 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNX27 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P151585:  view genomic region     (about GC identifiers)

Start:
151,584,541 bp from pter      End:
151,671,567 bp from pter
Size:
87,027 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: SNX27_HUMAN, Q96L92 (See protein sequence)
Recommended Name: Sorting nexin-27  
Size: 541 amino acids; 61265 Da
Subunit: Interacts with PSCDBP. Isoforms 1 and 2 directly interact with DGKZ. Isoforms 1 and 2 interact with HT4R
isoform 5-HTA(A) (By similarity). Interacts with MCC
Subcellular location: Cytoplasm, cytosol. Early endosome. Note=In T-lymphocytes, recruited from the cytosol to sorting
endosomes by phosphoinositide-3-kinase products
Sequence caution: Sequence=AAG43127.1; Type=Erroneous initiation;
Secondary accessions: Q32Q36 Q4AEJ5 Q5VWB0 Q5VWB1 Q5VWB2 Q6IPP6 Q86UB1 Q96D79 Q9H3K8
Alternative splicing: 4 isoforms:  Q96L92-1   Q96L92-3   Q96L92-2   Q96L92-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SNX27: NX_Q96L92

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96L92

  • SNX27 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_112180.4  
    ENSEMBL proteins: 
     ENSP00000357834   ENSP00000400333   ENSP00000357836   ENSP00000357831  

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    Uscn Proteins for SNX27

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--
    GO:0005769early endosome IEA--
    GO:0005829cytosol IEA--


    SNX27 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

    SNX27 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR001478 PDZ
     IPR001683 Phox
     IPR000159 Ras-assoc

    Graphical View of Domain Structure for InterPro Entry Q96L92

    ProtoNet protein and cluster: Q96L92

    3 Blocks protein families:
    IPB000159 RA domain
    IPB001478 PDZ/DHR/GLGF domain
    IPB001683 Phox-like


    UniProtKB/Swiss-Prot: SNX27_HUMAN, Q96L92
    Domain: The PDZ domain mediates the interaction with DGKZ, PSCDBP and HT4R and is responsible for vesicular
    localization (By similarity)
    Similarity: Belongs to the sorting nexin family
    Similarity: Contains 1 PDZ (DHR) domain
    Similarity: Contains 1 PX (phox homology) domain
    Similarity: Contains 1 Ras-associating 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: SNX27_HUMAN, Q96L92
    Function: Involved in endocytic trafficking (By similarity). In T lymphocytes, participates in endocytic recycling
    pathway. Recruits PSCDBP and HT4R to early endosomes (By similarity)

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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:0005515protein binding IPI19555689
    GO:0035091phosphatidylinositol binding IEA--


    SNX27 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Snx27tm1Lslo for SNX27
         8 MGI mutant phenotypes (inferred from 1 allele(MGI details for Snx27):
     cardiovascular system  cellular  digestive/alimentary  growth/size  hematopoietic system 
     immune system  liver/biliary system  mortality/aging 

    SNX27 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SNX27

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    5/21 Interacting proteins for SNX27 (Q96L922, 3 ENSP000003578364) via UniProtKB, MINT, STRING, and/or I2D (see all 21)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PHLPP2Q6ZVD83, ENSP000003486114I2D: score=2 STRING: ENSP00000348611
    MCCP235082, ENSP000003862274MINT-7211237 STRING: ENSP00000386227
    SCRIBQ141602MINT-7211237 MINT-7211267
    PHLPP1O603463I2D: score=2 
    CYTH1Q154383I2D: 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:0007165signal transduction IEA--
    GO:0008333endosome to lysosome transport IEA--
    GO:0015031protein transport IEA--
    GO:0042493response to drug ----


    SNX27 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 SNX27
    Search CenterWatch for drugs/clinical trials and news about SNX27 

    (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 SNX27 gene: 
    NM_030918.5  

    Unigene Cluster for SNX27:

    Sorting nexin family member 27
    Hs.192326  [show with all ESTs]
    Unigene Representative Sequence: NM_030918
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000368841(uc001eyo.3) ENST00000458013(uc001eyp.3) ENST00000368843(uc001eyn.1)
    ENST00000368838 ENST00000482791

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    hsa-miR-323-3p hsa-miR-140-5p hsa-miR-193a-3p hsa-miR-3607-3p hsa-miR-607 hsa-miR-300 hsa-miR-376b hsa-miR-200a
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    Additional cDNA sequence: 

    AF060509.1 AJ009640.1 AK001395.1 AY044866.1 BC012184.1 BC051817.1 BC071825.1 BC100998.1 
    BC100999.1 BC101000.1 BC101822.1 BC101824.1 BC107862.1 BC127853.1 BC127854.1 

    13 DOTS entries:

    DT.100009569  DT.443740  DT.100749458  DT.40234407  DT.40107009  DT.121404701  DT.97817778  DT.100749455 
    DT.217541  DT.121502720  DT.91731716  DT.92019059  DT.97764375 

    24/267 AceView cDNA sequences (see all 267):

    BU951018 AV726824 BU676479 BU623265 R81952 BG570901 BU952464 AI678358 
    AA633943 BM704187 BM314517 AW271766 BC012184 CA439434 AB054889 BM980059 
    AA283733 NM_030918 AI089923 BQ008510 AY044866 AV708925 BG291397 BM849526 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for SNX27    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14
    SP1:                    -                                         -                                             
    SP2:              -     -                                         -                                             
    SP3:                                                              -                                             
    SP4:                                                              -                             -     -         
    SP5:                                                                                                            


    ECgene alternative splicing isoforms for SNX27

    (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

    SNX27 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CACATTTAAT

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

    About this image
    See SNX27 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SNX27

    SOURCE GeneReport for Unigene cluster: Hs.192326

    UniProtKB/Swiss-Prot: SNX27_HUMAN, Q96L92
    Tissue specificity: Expressed in cells of hematopoietic origin (at protein level)

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for SNX27 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 SNX271 sorting nexin family member 27 80.89(n)
    94.84(a)
      425666  NM_001031346.1  NP_001026517.1 
    lizard
    (Anolis carolinensis)
    Reptilia SNX276
    --
    84(a)
    1 ↔ 1
    GL343554.1(25173-52965)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.98862 Xenopus laevis transcribed sequence with strong similarity more 80.06(n)    CA788990.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc660942 hypothetical protein MGC66094 76.91(n)   393512  BC056315.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG327581 CG32758 56.97(n)
    54.58(a)
      31493  NM_167045.1  NP_727023.1 
    worm
    (Caenorhabditis elegans)
    Secernentea snx-271 Protein SNX-27 52.51(n)
    45.19(a)
      172937  NM_060357.3  NP_492758.1 


    ENSEMBL Gene Tree for SNX27 (if available)
    TreeFam Gene Tree for SNX27 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SNX27 gene
    SNX172  SNX312  
    2 SIMAP similar genes for SNX27 using alignment to 2 protein entries:     SNX27_HUMAN (see all proteins):
    SNX17    ARHGAP23

    SNX27 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

    10/1493 NCBI SNPs in SNX27 are shown (see all 1493    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1865385031,2
    --151582676(+) TGAAGA/CGATCC 1 -- us2k10--------
    rs1904967561,2
    --151582712(+) GGGACG/TACAGG 1 -- us2k10--------
    rs1117994721,2
    C--151582757(+) TTTTAG/TATATA 1 -- us2k10--------
    rs1384713621,2
    --151582874(+) GGTCTC/GCCAAA 1 -- us2k10--------
    rs1413657501,2
    --151582911(+) CACACA/CCAGCC 1 -- us2k10--------
    rs1816123161,2
    --151583052(+) TTAATG/TTTATG 1 -- us2k10--------
    rs1451076621,2
    --151583102(+) CACAAA/GCATAG 1 -- us2k10--------
    rs1389057111,2
    --151583321(+) ACCAGC/GTTGGC 1 -- us2k10--------
    rs1861944671,2
    --151583386(+) GTGGCA/GCATGC 1 -- us2k10--------
    rs1150975321,2
    F,--151583399(+) TTAATC/TGCAAG 1 -- us2k11Minor allele frequency- T:0.03WA 118

    HapMap Linkage Disequilibrium report for SNX27 (151584541 - 151671567 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SNX27: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SNX27
    DNA2.0 Custom Variant and Variant Library Synthesis for SNX27

    (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

    SNX27 for disorders           About MalaCards

    SNX27 for disorders           About GeneDecksing

    OMIM gene information: 611541    OMIM disorders: --

    Human Genome Epidemiology (HuGE) Navigator: SNX27 (1 document)

    Export disorders for SNX27 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 SNX27 gene, integrated from 9 sources (see all 31):
    (articles sorted by number of sources associating them with SNX27)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Proteomics identification of sorting nexin 27 as a diacylglycerol kinase zeta-associated protein: new diacylglycerol kinase roles in endocytic recycling. (PubMed id 17351151)1, 2, 9 Rincon E.... Merida I. (2007)
    2. Sorting nexin 27 interacts with the Cytohesin associated scaffolding protein (CASP) in lymphocytes. (PubMed id 17577583)1, 2, 9 MacNeil A.J.... Pohajdak B. (2007)
    3. MCC, a new interacting protein for Scrib, is required for cell migration in epithelial cells. (PubMed id 19555689)1, 2 Arnaud C....Lecine P. (2009)
    4. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    5. New sorting nexin (SNX27) and NHERF specifically interact with the 5-HT4a receptor splice variant: roles in receptor targeting. (PubMed id 15466885)1, 2 Joubert L....Bockaert J. (2004)
    6. Sorting out the cellular functions of sorting nexins. (PubMed id 12461558)1, 3 Worby C.A. and Dixon J.E. (2002)
    7. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PubMed id 9455484)1, 2 Seki N.... Ohara O. (1997)
    8. A unique sorting nexin regulates trafficking of potassium channels via a PDZ domain interaction. (PubMed id 17828261)1, 9 Lunn M.L....Slesinger P.A. (2007)
    9. Subunit-specific regulation of Kir3 channels by sorting nexin 27. (PubMed id 18690037)1, 9 Nassirpour R. and Slesinger P.A. (2007)
    10. Sorting nexin 27 interacts with multidrug resistance-a ssociated protein 4 (MRP4) and mediates internalization of MRP4. (PubMed id 22411990)1 Hayashi H....Sugiyama Y. (2012)

    (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: 81609 HGNC: 20073 AceView: SNX27 Ensembl:ENSG00000143376 euGenes: HUgn81609
    ECgene: SNX27 H-InvDB: SNX27

    (According to HUGE)
    About This Section
    HUGE: KIAA0488

    (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 SNX27 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SNX27 gene:
    Search GeneIP for patents involving SNX27

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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