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

TBC1D15 Gene

protein-coding   GIFtS: 48
GCID: GC12P072233

TBC1 domain family, member 15

  Search for TBC1D15
in our new
 Human Malady Compendium 
Biological research products
for TBC1D15
    

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

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
TBC1 Domain Family, Member 151 2     RAB7-GAP2
GAP For RAB72 3     TBC1 Domain Family Member 152
GTPase-Activating Protein RAB72 3     Tre-2-Budding Uninhibited By Benzimidazole-Cell Division Cycle 16 Domain,
Domain Family Member 152
DKFZp761D02231     Tre2/Bub2/Cdc16 Domain Family Member 152
FLJ120851     Rab7-GAP3

External Ids:    HGNC: 256941   Entrez Gene: 647862   Ensembl: ENSG000001217497   OMIM: 6126625   UniProtKB: Q8TC073   
ORGUL members:         
NONCODE:n407885    

Export aliases for TBC1D15 gene to outside databases

Previous GC identifers: GC12P070519 GC12P069283


(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 TBC1D15:
This gene encodes a member of the Ras-like proteins in brain-GTPase activating protein superfamily that share a
conserved Tre-2/Bub2/Cdc16 domain. The encoded protein interacts with Ras-like protein in brain 5A and may function as
a regulator of intracellular trafficking. Alternate splicing results in multiple transcript variants. (provided by
RefSeq, Apr 2009)

UniProtKB/Swiss-Prot: TBC15_HUMAN, Q8TC07
Function: Acts as a GTPase activating protein for RAB7A. Does not act on RAB4, RAB5 or RAB6 (By similarity)

Gene Wiki entry for TBC1D15


(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 TBC1D15 gene promoter:
         Nkx3-1   Egr-1   Nkx3-1 v1   Nkx2-5   LCR-F1   GATA-1   RORalpha1   IRF-7A   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTBC1D15 promoter sequence
   Search SABiosciences Chromatin IP Primers for TBC1D15

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TBC1D15


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

Entrez Gene cytogenetic band: 12q21.1   Ensembl cytogenetic band:  12q21.1   HGNC cytogenetic band: 12q15

TBC1D15 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D15 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P072233:  view genomic region     (about GC identifiers)

Start:
72,233,487 bp from pter      End:
72,320,629 bp from pter
Size:
87,143 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: TBC15_HUMAN, Q8TC07 (See protein sequence)
Recommended Name: TBC1 domain family member 15  
Size: 691 amino acids; 79491 Da
Subcellular location: Cytoplasm (By similarity)
Secondary accessions: B9A6L6 Q9HA83
Alternative splicing: 2 isoforms:  Q8TC07-1   Q8TC07-2   (Contains a phosphoserine at position 205)

Explore the universe of human proteins at neXtProt for TBC1D15: NX_Q8TC07

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8TC07

  • TBC1D15 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001139685.2  NP_001139686.1  NP_073608.4  

    ENSEMBL proteins: 
     ENSP00000449643   ENSP00000448182   ENSP00000417308   ENSP00000419365   ENSP00000418091  
     ENSP00000318262   ENSP00000418467   ENSP00000420678   ENSP00000420190   ENSP00000376986  

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    Uscn Proteins for TBC1D15

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--
    GO:0005622intracellular ----
    GO:0005737cytoplasm ISS--
    GO:0005739mitochondrion IEA--


    TBC1D15 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

    TBC1D15 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR000195 Rab-GTPase-TBC_dom
     IPR021935 DUF3548

    Graphical View of Domain Structure for InterPro Entry Q8TC07

    ProtoNet protein and cluster: Q8TC07

    1 Blocks protein family: IPB000195 RabGAP/TBC domain

    UniProtKB/Swiss-Prot: TBC15_HUMAN, Q8TC07
    Similarity: Contains 1 Rab-GAP TBC 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: TBC15_HUMAN, Q8TC07
    Function: Acts as a GTPase activating protein for RAB7A. Does not act on RAB4, RAB5 or RAB6 (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:0005097Rab GTPase activator activity ISS--
    GO:0005515protein binding IPI--


    TBC1D15 for ontologies           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 TBC1D15

    STRING Interaction Network Preview (showing 5 interactants - click image to see 6)

    5/12 Interacting proteins for TBC1D15 (Q8TC071, 3 ENSP000003182624) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GABARAPL1Q9H0R81, 3EBI-1048247,EBI-3240381 I2D: score=1 
    GABARAPL2P605201, 3EBI-1048247,EBI-2973440 I2D: score=1 
    MAP1LC3BQ9GZQ81, 3EBI-1048247,EBI-373144 I2D: score=1 
    GABARAPO951661, 3, ENSP000003068664EBI-1048247,EBI-712001 I2D: score=3 STRING: ENSP00000306866
    MEPCEQ7L2J03, ENSP000003085464I2D: score=1 STRING: ENSP00000308546
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0032313regulation of Rab GTPase activity ISS--
    GO:0032851positive regulation of Rab GTPase activity ----


    TBC1D15 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
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    Browse Tocris compounds for TBC1D15
    Search CenterWatch for drugs/clinical trials and news about TBC1D15 / TBC15 

    (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,
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    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 TBC1D15 gene (3 alternative transcripts): 
    NM_001146213.1  NM_001146214.1  NM_022771.4  

    Unigene Cluster for TBC1D15:

    TBC1 domain family, member 15
    Hs.284630  [show with all ESTs]
    Unigene Representative Sequence: NM_001146214
    18 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000482439 ENST00000550746(uc009zrv.2 uc001swu.3 uc010stt.2 uc001swv.3 uc001sww.3)
    ENST00000498482 ENST00000474468 ENST00000549402 ENST00000472611 ENST00000491063
    ENST00000319106 ENST00000462788 ENST00000485960 ENST00000468049 ENST00000546932
    ENST00000460818 ENST00000483828 ENST00000548679 ENST00000479971 ENST00000546450
    ENST00000393309

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    Inhib. RNA
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    Additional cDNA sequence: 

    AB449901.1 AK022147.1 AK225221.1 AK225747.1 AK292306.1 AK297626.1 AK307922.1 AL157464.1 
    AL833639.1 BC028352.2 NR_027449.1 

    17 DOTS entries:

    DT.443226  DT.97820282  DT.95273082  DT.121128159  DT.75101515  DT.100024976  DT.97824051  DT.40273168 
    DT.121128136  DT.40202512  DT.95273081  DT.121128078  DT.121128148  DT.75169358  DT.97859204  DT.99953406 
    DT.120734273 

    24/198 AceView cDNA sequences (see all 198):

    AA608723 BQ441869 AA524016 AI860580 AW105686 CA406704 AI291692 BM973597 
    AI082025 BU540713 AI290131 AI857368 BM810300 BG696214 BP371102 BU618659 
    AU136684 AL833639 BM765672 AA635017 BU608928 CA414859 AA732941 AI208402 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D15    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b
    SP1:                                                              -                       -                                             
    SP2:                                            -                 -                       -                                             
    SP3:                                -           -                 -                       -                                             
    SP4:                                                                                      -                                             
    SP5:                                                                                                                                    


    ECgene alternative splicing isoforms for TBC1D15

    (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

    TBC1D15 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CTTTAAGGTT

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

    About this image
    See TBC1D15 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TBC1D15

    SOURCE GeneReport for Unigene cluster: Hs.284630
        SABiosciences Custom PCR Arrays for TBC1D15
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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 eukaryotes.

    Orthologs for TBC1D15 gene from 8/27 species (see all 27)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves TBC1D151 TBC1 domain family, member 15 79.33(n)
    82.31(a)
      417857  NM_001012809.1  NP_001012827.1 
    lizard
    (Anolis carolinensis)
    Reptilia TBC1D156
    --
    78(a)
    1 ↔ 1
    5(38519337-38545372)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia BC063206.12   -- 76.92(n)    BC063206.1 
    zebrafish
    (Danio rerio)
    Actinopterygii 570503602   -- 75.27(n)    57050360 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG114906
    --
    26(a)
    1 → many
    2L(207179-210725)
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-156
    TBC (Tre-2/Bub2/Cdc16) domain family member (tbc-1...
    47(a)
    1 → many
    II(13437528-13441336)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT5G525806
    RabGAP/TBC domain-containing protein
    24(a)
    1 → many
    5(21337861-21342985)
    rice
    (Oryza sativa)
    Liliopsida --
    TBC domain containing protein, expressed
    24(a)
    1 → many
    2(29367149-29375222)


    ENSEMBL Gene Tree for TBC1D15 (if available)
    TreeFam Gene Tree for TBC1D15 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TBC1D15 gene
    SGSM12  TBC1D172  TBC1D212  SGSM22  TBC1D162  TBC1D252  
    4 SIMAP similar genes for TBC1D15 using alignment to 9 protein entries:     TBC15_HUMAN (see all proteins):
    DKFZp761D0223    TBC1D17    TBC1D16    TBC1D21

    TBC1D15 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

    10/1456 NCBI SNPs in TBC1D15 are shown (see all 1456    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1836787431,2
    --72231501(+) TAGGAA/GATTTT 4 -- us2k10--------
    rs1513385281,2
    --72231528(+) GATAAC/TGGCCC 4 -- us2k10--------
    rs757832801,2
    C,F,--72231529(+) ATAACG/AGCCCA 4 -- us2k11Minor allele frequency- A:0.02WA 118
    rs781626321,2
    F,--72231689(+) CTGTAG/TTTCTC 4 -- us2k11Minor allele frequency- T:0.03EA 120
    rs1878795231,2
    --72231814(+) CACATC/TAAAAT 4 -- us2k10--------
    rs1150764601,2
    F,--72231873(+) TGGGTC/TATCAG 4 -- us2k11Minor allele frequency- T:0.02WA 118
    rs3287601,2
    C,F,H,--72232107(-) GAGATT/CGCGTG 4 -- us2k17Minor allele frequency- C:0.08NS EA WA 542
    rs1161781001,2
    C,F,--72232159(+) CTTTCC/GTCACC 4 -- us2k11Minor allele frequency- G:0.03WA 118
    rs118316221,2
    C,F,H,--72232186(+) GTCACA/CTAACC 4 -- us2k121Minor allele frequency- C:0.06NS EA NA WA 2616
    rs3287611,2
    C,F,H,--72232292(-) GTCCAT/CTGAGG 4 -- us2k124Minor allele frequency- C:0.09NS EA NA WA 2770

    HapMap Linkage Disequilibrium report for TBC1D15 (72233487 - 72320629 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 5 variations for TBC1D15
         4 CNVs: 3894 9698 2990 8736
         1 Indel: 33564

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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

    TBC1D15 for disorders           About MalaCards

    TBC1D15 for disorders           About GeneDecksing

    OMIM gene information: 612662    OMIM disorders: --


    Export disorders for TBC1D15 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 TBC1D15 gene, integrated from 9 sources (see all 33):
    (articles sorted by number of sources associating them with TBC1D15)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. (PubMed id 19077034)1, 2 Ishibashi K.... Fukuda M. (2009)
    2. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (2006)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. 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)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    6. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    7. A high-throughput approach for measuring temporal chan ges in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (2012)
    8. The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (2012)
    9. Fis1 acts as mitochondrial recruitment factor for TBC1 D15 that involved in regulation of mitochondrial morphology. (PubMed id 23077178)1 Onoue K....Ishihara N. (2012)
    10. Global landscape of HIV-human protein complexes. (PubMed id 22190034)1 Jager S....Krogan N.J. (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: 64786 HGNC: 25694 AceView: TBC1D15 Ensembl:ENSG00000121749 euGenes: HUgn64786
    ECgene: TBC1D15 H-InvDB: TBC1D15

    (According to HUGE)
    About This Section
      --

    (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 TBC1D15 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 TBC1D15 gene:
    Search GeneIP for patents involving TBC1D15

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



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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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