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TBC1D17 Gene

protein-coding   GIFtS: 46
GCID: GC19P050380

TBC1 Domain Family, Member 17

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(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 171 2
TBC1 Domain Family Member 172

External Ids:    HGNC: 256991   Entrez Gene: 797352   Ensembl: ENSG000001049467   UniProtKB: Q9HA653   

Export aliases for TBC1D17 gene to outside databases

Previous GC identifers: GC19P055072 GC19P046757


(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 TBC1D17 Gene:
TBC1D17 (TBC1 domain family, member 17) is a protein-coding gene. GO annotations related to this gene include Rab GTPase activator activity. An important paralog of this gene is SGSM1.

UniProtKB/Swiss-Prot: TBC17_HUMAN, Q9HA65
Function: May act as a GTPase-activating protein for Rab family protein(s)




(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 at NCBI GenBank:
NC_000019.9  NT_011109.17  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TBC1D17 gene promoter:
         p53   Sp1   SREBP-1c   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTBC1D17 promoter sequence
   Search Chromatin IP Primers for TBC1D17

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TBC1D17


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

Entrez Gene cytogenetic band: 19q13.33   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.33

TBC1D17 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D17 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P050380:  view genomic region     (about GC identifiers)

Start:
50,380,682 bp from pter      End:
50,392,007 bp from pter
Size:
11,326 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TBC17_HUMAN, Q9HA65 (See protein sequence)
Recommended Name: TBC1 domain family member 17  
Size: 648 amino acids; 72728 Da
Secondary accessions: B4DT12 F5H1W7
Alternative splicing: 2 isoforms:  Q9HA65-1   Q9HA65-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TBC1D17: NX_Q9HA65

Explore proteomics data for TBC1D17 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys23
  • Modification sites at PhosphoSitePlus

  • See TBC1D17 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001161694.1  NP_078958.2  

    ENSEMBL proteins: 
     ENSP00000221543   ENSP00000446323   ENSP00000469010   ENSP00000472647   ENSP00000469747  

    TBC1D17 Human Recombinant Protein Products:

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    antibodies-online kits for TBC1D17 (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR000195 Rab-GTPase-TBC_dom
     IPR021935 DUF3548

    Graphical View of Domain Structure for InterPro Entry Q9HA65

    ProtoNet protein and cluster: Q9HA65

    1 Blocks protein domain: IPB000195 RabGAP/TBC domain

    UniProtKB/Swiss-Prot: TBC17_HUMAN, Q9HA65
    Similarity: Contains 1 Rab-GAP TBC domain


    Find genes that share domains with TBC1D17           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: TBC17_HUMAN, Q9HA65
    Function: May act as a GTPase-activating protein for Rab family protein(s)

         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 TBC1D17           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for TBC1D17:
     Increased gamma-H2AX phosphory 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for TBC1D17

    miRNA
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    miRTarBase miRNAs that target TBC1D17:
    hsa-mir-335-5p (MIRT018707)

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    hsa-miR-519d hsa-miR-20a hsa-miR-106a hsa-miR-106b hsa-miR-223 hsa-miR-93 hsa-miR-20b hsa-miR-17
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TBC1D17


    (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 COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    endosome1
    golgi apparatus1

    (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 TBC1D17
    Interactions:

        Search GeneGlobe Interaction Network for TBC1D17

    STRING Interaction Network Preview (showing 5 interactants - click image to see 11)

    Selected Interacting proteins for TBC1D17 (Q9HA652, 3 ENSP000002215434) via UniProtKB, MINT, STRING, and/or I2D (see all 23)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CALCOCO1Q9P1Z22, 3, ENSP000002620594MINT-65533 I2D: score=4 STRING: ENSP00000262059
    DHX29Q7Z4782, 3, ENSP000002516364MINT-64771 I2D: score=3 STRING: ENSP00000251636
    ASCC2Q9H1I82, 3MINT-65483 I2D: score=4 
    CCT5P486432, 3MINT-63776 I2D: score=4 
    FBLP220872, 3MINT-63595 I2D: score=4 
    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 TBC1D17           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 TBC1D17 (TBC17)



    (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 TBC1D17 gene (2 alternative transcripts): 
    NM_001168222.1  NM_024682.2  

    Unigene Cluster for TBC1D17:

    TBC1 domain family, member 17
    Hs.631587  [show with all ESTs]
    Unigene Representative Sequence: AY129013
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000221543(uc010enn.2 uc002pqo.3 uc002pqp.3) ENST00000535102(uc010ybg.2 uc002pqr.3)
    ENST00000594996 ENST00000598789 ENST00000599049 ENST00000596243 ENST00000594984
    ENST00000600354
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate TBC1D17 (see all 9):
    hsa-miR-519d hsa-miR-20a hsa-miR-106a hsa-miR-106b hsa-miR-223 hsa-miR-93 hsa-miR-20b hsa-miR-17
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      QuantiFast Probe-based Assays in human, mouse, rat TBC1D17

    Additional mRNA sequence: 

    AB449903.1 AK022230.1 AK090606.1 AK092924.1 AK300007.1 AK309412.1 AY129013.1 BC003516.1 

    Selected DOTS entries (see all 28):

    DT.410596  DT.92353955  DT.100775177  DT.95332891  DT.100016076  DT.100878770  DT.100878776  DT.100701463 
    DT.86848830  DT.95136694  DT.95333212  DT.95333198  DT.121429374  DT.75161880  DT.121429289  DT.121429294 
    DT.121429325  DT.434746  DT.95333211  DT.97855753  DT.121429313  DT.121429409  DT.121429480  DT.91664413 

    Selected AceView cDNA sequences (see all 269):

    BX378124 AI669742 BI198535 CA443888 BE900296 AI304680 AK022230 AI869317 
    BM714721 BM840199 CA420725 CR598900 BU739364 CR613490 AI685621 CD722617 
    BG280753 BM545258 BQ645612 CK904889 AI634959 BX358379 BQ646177 BU631891 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D17 (see all 13)    About this scheme

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

    ExUns: 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19
    SP1:                                                      
    SP2:                                                      
    SP3:                                                      
    SP4:                                                      
    SP5:                                                      


    ECgene alternative splicing isoforms for TBC1D17

    (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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    TBC1D17 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGTCCGGCT
    TBC1D17 Expression
    About this image


    TBC1D17 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Eye (Sensory Organs)
             Retina
    TBC1D17 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TBC1D17 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.631587
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TBC1D17

    (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 and fungi.

    Orthologs for TBC1D17 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tbc1d171 , 5 TBC1 domain family, member 171, 5 84.94(n)1
    89.88(a)1
      7 (28.93 cM)5
    2332041  NM_001042655.11  NP_001036120.11 
     448409015 
    lizard
    (Anolis carolinensis)
    Reptilia TBC1D176
    TBC1 domain family, member 17
    64(a)
    1 ↔ 1
    GL343287.1(133654-158173)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia tbc1d171 TBC1 domain family, member 17 62.25(n)
    64.59(a)
      780364  NM_001079434.1  NP_001072902.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufc56c022 wufc56c02 73.14(n)   325133  BQ261770.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG114906
    --
    29(a)
    1 → many
    2L(207179-210725)
    worm
    (Caenorhabditis elegans)
    Secernentea tbc-156
    Protein TBC-15 (tbc-15) mRNA, complete cds
    46(a)
    1 → many
    II(13437598-13441406) WBGene00013016
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GYP76
    GTPase-activating protein for yeast Rab family mem...
    23(a)
    1 → many
    IV(34237-36477) YDL234C


    ENSEMBL Gene Tree for TBC1D17 (if available)
    TreeFam Gene Tree for TBC1D17 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for TBC1D17 gene
    SGSM12  TBC1D162  SGSM22  TBC1D152  TBC1D252  
    3 SIMAP similar genes for TBC1D17 using alignment to 5 protein entries:     TBC17_HUMAN (see all proteins):
    DKFZp761D0223    TBC1D15    TBC1D16

    Find genes that share paralogs with TBC1D17           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 TBC1D17 (see all 428)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs354136141,2
    C--50383107(+) TTTTC-/T/TT  
      TTTTTT
    TTTTT
    1 -- us2k11NA 2
    rs1458712091,2
    C--50555668(+) GGGAGA/GAAACT 2 -- us2k10--------
    rs1894977181,2
    --50555670(+) GAGGAA/CACTGA 2 -- us2k10--------
    rs1813568421,2
    --50555772(+) ACATGC/TGGAGA 2 -- us2k10--------
    rs1386103961,2
    --50555867(+) TGAAAC/TAGGGT 2 -- us2k10--------
    rs760057351,2
    C,F--50555873(+) AGGGTG/AAGTGA 2 -- us2k11Minor allele frequency- A:0.02EA 120
    rs1857858981,2
    --50555898(+) CCCAAA/CTCAGG 2 -- us2k10--------
    rs38102671,2
    C,F,H--50555939(+) CACAGA/GCCTCT 2 -- us2k124Minor allele frequency- G:0.49EA NS NA WA CSA 3662
    rs1427051651,2
    --50555987(+) CAGGAC/GAGTAG 2 -- us2k10--------
    rs38102681,2
    C,F,A--50556079(+) ACCCGC/TCCCGA 2 -- us2k112Minor allele frequency- T:0.28EA NA WA CSA 1473

    HapMap Linkage Disequilibrium report for TBC1D17 (50380682 - 50392007 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for TBC1D17:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv912269CNV Loss21882294
    dgv54n68CNV Loss17160897
    dgv53n68CNV Loss17160897
    dgv3974n71CNV Loss21882294
    nsv524068CNV Loss19592680
    nsv2519CNV Loss18451855
    nsv526372CNV Loss19592680
    nsv9739CNV Gain+Loss18304495

    Site Specific Mutation Identification with 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.)
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    (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 TBC1D17 gene, integrated from 10 sources (see all 17):
    (articles sorted by number of sources associating them with TBC1D17)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Optineurin mediates a negative regulation of Rab8 by the GTPase-activating protein TBC1D17. (PubMed id 22854040)1, 3 Vaibhava V....Swarup G. (J. Cell. Sci. 2012)
    2. 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. (Genome Res. 2004)
    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. Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. (PubMed id 22354992)1 Popovic D....Dikic I. (Mol. Cell. Biol. 2012)
    5. A high-throughput approach for measuring temporal changes in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (Nat. Methods 2012)
    6. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    7. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    8. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    9. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)
    10. 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)

    (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)
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    Entrez Gene: 79735 HGNC: 25699 AceView: TBC1D17 Ensembl:ENSG00000104946 euGenes: HUgn79735
    ECgene: TBC1D17 H-InvDB: TBC1D17

    (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 TBC1D17 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 TBC1D17 gene:
    Search GeneIP for patents involving TBC1D17

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



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