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TBC1D3B Gene

protein-coding   GIFtS: 33
GCID: GC17M034492

TBC1 Domain Family, Member 3B

(Previous names: TBC1 domain family, member 3I)
(Previous symbol: TBC1D3I)
  See related diseases
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 3B1 2     Prostate Cancer Gene 17 Duplicate2
TBC1D3I1 2 3     Rab GTPase-Activating Protein PRC17 Duplicate2
TBC1 Domain Family, Member 3I1 2     TBC1 Domain Family Member 3B2
PRC172 5     TBC1 Domain Family Member 3B/I2

External Ids:    HGNC: 270111   Entrez Gene: 4140592   Ensembl: ENSG000002242267   OMIM: 6101445   UniProtKB: A6NDS43   

Export aliases for TBC1D3B gene to outside databases

Previous GC identifer: GC17M031519


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for TBC1D3B Gene:
This gene encodes a protein that is similar to TBC1 domain family, member 3. This protein contains a TBC (Tre-2,
Bub2p, and Cdc16p) domain, which is found in proteins involved in RAB GTPase signaling and vesicle trafficking.
There are multiple copies of this gene located within a cluster of chemokine genes on chromosome 17q. (provided
by RefSeq, Apr 2009)

GeneCards Summary for TBC1D3B Gene:
TBC1D3B (TBC1 domain family, member 3B) is a protein-coding gene. Diseases associated with TBC1D3B include prostate cancer, and prostatitis. GO annotations related to this gene include Rab GTPase activator activity. An important paralog of this gene is TBC1D3H.

UniProtKB/Swiss-Prot: TBC3B_HUMAN, A6NDS4
Function: Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11 (By similarity)




(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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RefSeq DNA sequence:
NC_000017.11  NT_010783.16  NT_187614.1  NC_018928.2  NT_187661.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the TBC1D3B gene promoter:
         Pbx1a   CUTL1   LCR-F1   C/EBPalpha   MEF-2A   MZF-1   HSF2   c-Myb   aMEF-2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for TBC1D3B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TBC1D3B


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

Entrez Gene cytogenetic band: 17q12   Ensembl cytogenetic band:  17q12   HGNC cytogenetic band: 17q21.1

TBC1D3B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D3B gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M034492:  view genomic region     (about GC identifiers)

Start:
34,493,061 bp from pter      End:
34,503,996 bp from pter
Size:
10,936 bases      Orientation:
minus strand

1 alternative location:
Chr17-,NW_003315949 50,441-61,368     

(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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: TBC3B_HUMAN, A6NDS4 (See protein sequence)
Recommended Name: TBC1 domain family member 3B  
Size: 549 amino acids; 62315 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
Secondary accessions: A8K892

Explore the universe of human proteins at neXtProt for TBC1D3B: NX_A6NDS4

Explore proteomics data for TBC1D3B 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 TBC1D3B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001001417.5  
    ENSEMBL proteins: 
     ENSP00000390852   ENSP00000466792   ENSP00000464888   ENSP00000466703   ENSP00000381781  

    TBC1D3B Human Recombinant Protein Products:

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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 A6NDS4

    ProtoNet protein and cluster: A6NDS4

    UniProtKB/Swiss-Prot: TBC3B_HUMAN, A6NDS4
    Similarity: Contains 1 Rab-GAP TBC domain


    TBC1D3B for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TBC3B_HUMAN, A6NDS4
    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--
         
    TBC1D3B for ontologies           About GeneDecksing


    Animal Models:
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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
    TBC3B_HUMAN, A6NDS4: Cell membrane; Lipid-anchor (By similarity). Note=Associated with lipid rafts (By
    similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2

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

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

    TBC1D3B for ontologies           About GeneDecksing


    (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 TBC1D3B
    Interactions:

        Search GeneGlobe Interaction Network for TBC1D3B

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

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

    TBC1D3B for ontologies           About GeneDecksing



    (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 TBC1D3B (TBC3B)



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for TBC1D3B gene: 
    NM_001001417.5  

    Unigene Cluster for TBC1D3B:

    TBC1 domain family, member 3B
    Hs.105891  [show with all ESTs]
    Unigene Representative Sequence: NM_001001417
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000454519(uc002hky.2) ENST00000588574 ENST00000586369 ENST00000589443
    ENST00000589139 ENST00000398801
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat TBC1D3B
      QuantiFast Probe-based Assays in human, mouse, rat TBC1D3B

    Additional mRNA sequence: AK292257.1 

    19 DOTS entries:

    DT.92042803  DT.102843582  DT.97771291  DT.120948306  DT.91828704  DT.95298563  DT.102843998  DT.120994618 
    DT.212833  DT.120894916  DT.120894920  DT.120948289  DT.100742312  DT.100787971  DT.120910090  DT.120948285 
    DT.120948301  DT.91767081  DT.95298566 

    Selected AceView cDNA sequences (see all 48):

    CA394892 BX281608 BU542901 AX775947 BI519993 AK095385 BG718044 BX279913 
    BM846014 BC075809 BF091359 CD653466 BI832051 BF809416 BX644661 BM762465 
    AX775949 AA350665 BQ920917 BQ923700 BM914524 BI828272 BM563571 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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    TBC1D3B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    TBC1D3B Expression
    About this image

    TBC1D3B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TBC1D3B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.105891
        Custom PCR Arrays for TBC1D3B
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TBC1D3B

    (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 TBC1D3B 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)
    33(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 TBC1D3B (if available)
    TreeFam Gene Tree for TBC1D3B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TBC1D3B gene
    LOC101060321  TBC1D3H1 2  TBC1D31 2  LOC101060389  TBC1D3C1 2  TBC1D3F1 2  LOC102724862  LOC101060351  
    LOC101060376  LOC102723859  TBC1D262  ENSG000002487512  GRTP12  TBC1D10C2  TBC1D10A2  TBC1D3G2  
    TBC1D10B2  USP6NL2  TBC1D282  
    13 SIMAP similar genes for TBC1D3B using alignment to 2 protein entries:     TBC3B_HUMAN (see all proteins):
    TBC1D3F    TBC1D3C    TBC1D3H    TBC1D3    TBC1D3G    USP6-short
    tre    TRE17    USP6    LOC440419    TBC1D26    TBC1D28
    TBC1D29

    TBC1D3B for paralogs           About GeneDecksing



    (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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    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for TBC1D3B (see all 25):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2664544CNV Deletion23128226
    esv2715876CNV Deletion23290073
    dgv12n31CNV Duplication19718026
    esv33107CNV Loss17666407
    nsv2040CNV Loss18451855
    esv29998CNV Loss17803354
    dgv3150n71CNV Gain21882294
    dgv122e55CNV Gain17911159
    nsv526727CNV Gain19592680
    dgv3147n71CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing TBC1D3B
    DNA2.0 Custom Variant and Variant Library Synthesis for TBC1D3B

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 610144    OMIM disorders: --

    2 diseases for TBC1D3B:    
    About MalaCards
    prostate cancer    prostatitis


    TBC1D3B for disorders           About GeneDecksing


    Export disorders for TBC1D3B 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 TBC1D3B gene integrated from 10 sources:
    (articles sorted by number of sources associating them with TBC1D3B)
        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, 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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Diversity of human copy number variation and multicopy genes. (PubMed id 21030649)2 Sudmant P.H.... Eichler E.E. (Science 2010)
    5. PRC17, a novel oncogene encoding a Rab GTPase-activating protein, is amplified in prostate cancer. (PubMed id 12359748)3 Pei L.... Li J. (Cancer Res. 2002)
    6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 414059 HGNC: 27011 AceView: TBC1D3.2 Ensembl:ENSG00000224226 euGenes: HUgn414059
    ECgene: TBC1D3B H-InvDB: TBC1D3B

    (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 TBC1D3B 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 TBC1D3B gene:
    Search GeneIP for patents involving TBC1D3B

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    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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