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TBC1D3F Gene

protein-coding   GIFtS: 41
GCID: GC17P036283

TBC1 Domain Family, Member 3F

  See TBC1D3F-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
TBC1 Domain Family, Member 3F1 2     TBC1 Domain Family Member 32
TBC1D32     TBC1 Domain Family Member 3F2
Prostate Cancer Gene 17 Protein2     TBC1D3E3
Protein TRE17-Alpha2     

External Ids:    HGNC: 182571   Entrez Gene: 842182   Ensembl: ENSG000001851287   OMIM: 6108095   UniProtKB: A6NER03   

Export aliases for TBC1D3F gene to outside databases

Previous GC identifers: GC17M031607 GC17U900818 GC17P033363 GC17M033595 GC17M030678


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TBC1D3F Gene:
TBC1D3F (TBC1 domain family, member 3F) is a protein-coding gene. Diseases associated with TBC1D3F include prostate cancer. GO annotations related to this gene include Rab GTPase activator activity. An important paralog of this gene is TBC1D3H.

UniProtKB/Swiss-Prot: TBC3F_HUMAN, A6NER0
Function: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11 (By similarity)

Gene Wiki entry for TBC1D3F (TBC1D3) 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the TBC1D3F gene promoter:
         NF-1/L   NF-1   HTF   Lmo2   ATF   Egr-4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTBC1D3F promoter sequence
   Search Chromatin IP Primers for TBC1D3F

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TBC1D3F


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

Entrez Gene cytogenetic band: 17q12   Ensembl cytogenetic band:  17q12   HGNC cytogenetic band: 17q12

TBC1D3F Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D3F gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P036283:  view genomic region     (about GC identifiers)

Start:
36,283,960 bp from pter      End:
36,294,915 bp from pter
Size:
10,956 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TBC3F_HUMAN, A6NER0 (See protein sequence)
Recommended Name: TBC1 domain family member 3F  
Size: 549 amino acids; 62156 Da
Miscellaneous: TBC1D3 is encoded by a collection of very similar paralogs with multiple copies of each paralog,
some human genomes encoding well over 50 copies depending on ethnic origin of the donor

Explore the universe of human proteins at neXtProt for TBC1D3F: NX_A6NER0

Explore proteomics data for TBC1D3F at MOPED

Post-translational modifications: 

  • Ubiquitinated by a CUL7-based E3 ligase, which leads to proteasomal degradation (By similarity)1
  • Palmitoylation is required for membrane localization and protects TBC1D3 from ubiquination (By similarity)1
  • Modification sites at neXtProt

  • See TBC1D3F Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_115634.2  
    ENSEMBL proteins: 
     ENSP00000329256   ENSP00000467535   ENSP00000421962   ENSP00000367416   ENSP00000443859  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR000195 Rab-GTPase-TBC_dom

    Graphical View of Domain Structure for InterPro Entry A6NER0

    ProtoNet protein and cluster: A6NER0

    UniProtKB/Swiss-Prot: TBC3F_HUMAN, A6NER0
    Similarity: Contains 1 Rab-GAP TBC domain


    Find genes that share domains with TBC1D3F           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TBC3F_HUMAN, A6NER0
    Function: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11 (By similarity)

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IEA--
         
    Find genes that share ontologies with TBC1D3F           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TBC1D3F
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    TBC3F_HUMAN, A6NER0: Cell membrane; Lipid-anchor (By similarity). Note=Associated with lipid rafts (By
    similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    cytoskeleton1
    endosome1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--

    Find genes that share ontologies with TBC1D3F           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TBC1D3F
    Interactions:

        Search GeneGlobe Interaction Network for TBC1D3F

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

    5 Interacting proteins for TBC1D3F (A6NER03 ENSP000003292564) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    YWHAEP622583, ENSP000002643354I2D: score=1 STRING: ENSP00000264335
    RAB5AP203393, ENSP000002730474I2D: score=1 STRING: ENSP00000273047
    CDC42P609533, ENSP000003144584I2D: score=2 STRING: ENSP00000314458
    RAC1P630003, ENSP000003484614I2D: score=2 STRING: ENSP00000348461
    COL4A3BPENSP000003698624STRING: ENSP00000369862
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

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

    Find genes that share ontologies with TBC1D3F           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for TBC1D3F (TBC3F)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for TBC1D3F gene: 
    NM_032258.3  

    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000327454(uc002hoo.2 uc010cvf.1) ENST00000442786(uc002hop.2 uc010wdj.1)
    ENST00000513862 ENST00000505415(uc002hoq.2) ENST00000378174 ENST00000539424(uc010wdk.1)

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    Selected AceView cDNA sequences (see all 48):

    BX281608 CA394892 BM842932 BM846014 BU526609 BI827136 AV650439 BQ923700 
    BM914524 BI520522 BI753688 BX644661 BM563571 BQ942166 AA350665 BC033670 
    AX775949 AX775945 BQ920917 BF809416 BM842553 BX279913 AX775951 BM553146 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    TBC1D3F expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTTGAAATA
    TBC1D3F Expression
    About this image

    TBC1D3F Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TBC1D3F Protein Expression

    UniProtKB/Swiss-Prot: TBC3F_HUMAN, A6NER0
    Tissue specificity: Expressed in most tissues including pancreas, thymus and testis

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    In Situ
    Assay Products:
     

     
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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)
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    This gene was present in the common ancestor of animals.

    Orthologs for TBC1D3F gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia --
    --
    (see all 9)
    Uncharacterized protein
    (see all 9)
    36(a)
    34(a)
    (see all 9)
    many ↔ many
    many ↔ many
    (see all 9)
    4(35158703-35165770)
    22(89476-95800)
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    32(a)
    1 → many
    5(15411217-15475247)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    36(a)
    1 → many
    1(74862925-74883710)
    zebrafish
    (Danio rerio)
    Actinopterygii TBC1D3G6
    TBC1 domain family, member 3G
    14(a)
    1 → many
    25(16824916-16909191) ENSDARG00000086840
    fruit fly
    (Drosophila melanogaster)
    Insecta RN-tre6
    tre oncogene-related protein
    21(a)
    1 → many
    2R(9872320-9878215)
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-176
    Protein TBC-17, isoform d (tbc-17) mRNA, complete ...
    14(a)
    1 → many
    II(12694412-12725483) WBGene00012894


    ENSEMBL Gene Tree for TBC1D3F (if available)
    TreeFam Gene Tree for TBC1D3F (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TBC1D3F gene
    TBC1D31 2  LOC101060389  LOC101060376  TBC1D3C1 2  LOC102724862  TBC1D3H1 2  LOC101060321  LOC101060351  
    LOC102723859  TBC1D3B1 2  TBC1D262  ENSG000002487512  GRTP12  TBC1D10C2  TBC1D10A2  TBC1D3G2  
    TBC1D10B2  USP6NL2  TBC1D282  
    15 SIMAP similar genes for TBC1D3F using alignment to 3 protein entries:     TBC3F_HUMAN (see all proteins):
    TBC1D3B    TBC1D3H    TBC1D3    TBC1D3G    TBC1D3C    USP6-short
    USP6    tre    TRE17    CDH11/USP6 fusion oncogene    LOC440419    TBC1D26
    TBC1D28    TBC1D29    TBC1D10A

    Find genes that share paralogs with TBC1D3F           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for TBC1D3F (see all 28)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs29447441,2
    --36282020(-) TCTTGC/TAGCTC 1 -- us2k10--------
    rs3761673281,2
    C--36282084(+) GAATTA/GAATCC 1 -- us2k10--------
    rs1445262481,2
    --36282171(+) GCGCGA/GGAGTT 1 -- us2k10--------
    rs1453932651,2
    --36286613(+) GTGGCC/TCGGGT 1 -- int10--------
    rs115507501,2
    C--36288278(+) TGAAGA/TTGAAA 2 M L mis10--------
    rs2013301881,2
    --36290307(+) GACGC-/CCTCCTCC 1 -- int10--------
    rs2008766531,2
    --36294118(+) AGGCCC/TCTCCA 2 P S mis10--------
    rs2000298371,2
    --36294478(+) CACCCA/GGCACT 2 S G mis10--------
    rs3711912531,2
    ----36282095(+) CTCCTG/TGTCAA 1 -- us2k10--------
    rs3727107591,2
    ----36282408(+) CTCCTC/TGGCAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TBC1D3F (36283960 - 36294915 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for TBC1D3F:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv471398CNV Duplication19718026
    nsv820624CNV Duplication20802225
    nsv908172CNV Loss21882294
    nsv833435CNV Gain+Loss17160897
    dgv957e1CNV Complex17122850

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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.)
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    OMIM gene information: 610809    OMIM disorders: --

    1 disease for TBC1D3F:    
    About MalaCards
    prostate cancer


    Find genes that share disorders with TBC1D3F           About GenesLikeMe


    Export disorders for TBC1D3F 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 TBC1D3F gene, integrated from 10 sources (see all 19):
    (articles sorted by number of sources associating them with TBC1D3F)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. TBC1D3, a hominoid oncoprotein, is encoded by a cluster of paralogues located on chromosome 17q12. (PubMed id 16863688)1, 2, 3 Hodzic D....Stahl P.D. (Genomics 2006)
    2. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)1, 2 Zody M.C.... Nusbaum C. (Nature 2006)
    3. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. (PubMed id 23535730)1 Pharoah P.D....Sellers T.A. (Nat. Genet. 2013)
    4. Diversity of human copy number variation and multicopy genes. (PubMed id 21030649)2 Sudmant P.H.... Eichler E.E. (Science 2010)
    5. A human MAP kinase interactome. (PubMed id 20936779)1 Bandyopadhyay S....Ideker T. (Nat. Methods 2010)
    6. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. (PubMed id 19077034)1 Ishibashi K.... Fukuda M. (Genes Cells 2009)
    7. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (Nucleic Acids Res. 2006)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)1 Wiemann S....Poustka A. (Genome Res. 2004)
    10. The TRE17 oncogene encodes a component of a novel effector pathway for Rho GTPases Cdc42 and Rac1 and stimulates actin remodeling. (PubMed id 12612085)1 Masuda-Robens J.M.... Chou M.M. (Mol. Cell. Biol. 2003)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 84218 HGNC: 18257 AceView: TBC1D3.2 Ensembl:ENSG00000185128 euGenes: HUgn84218
    ECgene: TBC1D3F H-InvDB: TBC1D3F

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for TBC1D3F Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for TBC1D3F gene:
    Search GeneIP for patents involving TBC1D3F

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



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