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

TBC1D25 Gene

protein-coding   GIFtS: 47
GCID: GC0XP048397

TBC1 Domain Family, Member 25

(Previous name: ornithine aminotransferase-like 1)
(Previous symbol: OATL1)
  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)
About This Section

Aliases
TBC1 Domain Family, Member 251 2
OATL11 2 3 5
Ornithine Aminotransferase-Like 11 2
5SN3 SnoRNA2
MG812
TBC1 Domain Family Member 252

External Ids:    HGNC: 80921   Entrez Gene: 49432   Ensembl: ENSG000000683547   OMIM: 3112405   UniProtKB: Q3MII63   

Export aliases for TBC1D25 gene to outside databases

Previous GC identifers: GC0XP048283 GC0XP046061


(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 TBC1D25 Gene:
This gene encodes a protein with a TBC domain and may function as a Rab GTPase activating protein. This gene was
previously known as ornithine aminotransferase-like 1, but has no similarity to ornithine aminotransferase.
(provided by RefSeq, Jul 2008)

GeneCards Summary for TBC1D25 Gene: 
TBC1D25 (TBC1 domain family, member 25) is a protein-coding gene. Diseases associated with TBC1D25 include papillary renal cell carcinoma, and synovial sarcoma. GO annotations related to this gene include protein binding and Rab GTPase activator activity. An important paralog of this gene is SGSM1.

UniProtKB/Swiss-Prot: TBC25_HUMAN, Q3MII6
Function: Acts as a GTPase-activating protein specific for RAB33B. Involved in the regulation of autophagosome
maturation, the process in which autophagosomes fuse with endosomes and lysosomes




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.2  NT_079573.4  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TBC1D25 gene promoter:
         HFH-3   AML1a   C/EBPalpha   FOXI1   PPAR-alpha   CREB   GATA-6   deltaCREB   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTBC1D25 promoter sequence
   Search SABiosciences Chromatin IP Primers for TBC1D25

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TBC1D25


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

Entrez Gene cytogenetic band: Xp11.23   Ensembl cytogenetic band:  Xp11.23   HGNC cytogenetic band: Xp11.23

TBC1D25 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TBC1D25 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP048397:  view genomic region     (about GC identifiers)

Start:
48,397,845 bp from pter      End:
48,420,997 bp from pter
Size:
23,153 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: TBC25_HUMAN, Q3MII6 (See protein sequence)
Recommended Name: TBC1 domain family member 25  
Size: 688 amino acids; 76327 Da
Subunit: Interacts (via N-terminus) with MAP1LC3B, GABARAP and GABARAPL2
Subcellular location: Cytoplasm. Cytoplasmic vesicle, autophagosome. Note=It is dispersed in the cytoplasm under
nutrient-rich conditions. Localizes at autophagosomes under cell starving conditions
Secondary accessions: Q08AN9 Q3MII4 Q8TAR9
Alternative splicing: 2 isoforms:  Q3MII6-1   Q3MII6-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TBC1D25: NX_Q3MII6

Explore proteomics data for TBC1D25 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q3MII6

  • TBC1D25 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    TBC1D25 Protein Expression
    REFSEQ proteins: NP_002527.1  
    ENSEMBL proteins: 
     ENSP00000365962   ENSP00000402268   ENSP00000387764   ENSP00000444091  

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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005776autophagic vacuole IDA--
    GO:0031410cytoplasmic vesicle IEA--

    TBC1D25 for ontologies           About GeneDecksing



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

    Graphical View of Domain Structure for InterPro Entry Q3MII6

    ProtoNet protein and cluster: Q3MII6

    1 Blocks protein domain: IPB000195 RabGAP/TBC domain

    UniProtKB/Swiss-Prot: TBC25_HUMAN, Q3MII6
    Similarity: Contains 1 Rab-GAP TBC domain


    TBC1D25 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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TBC25_HUMAN, Q3MII6
    Function: Acts as a GTPase-activating protein specific for RAB33B. Involved in the regulation of autophagosome
    maturation, the process in which autophagosomes fuse with endosomes and lysosomes

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005097Rab GTPase activator activity IDA--
    GO:0005515protein binding IPI--
    GO:0008483transaminase activity ----
         
    TBC1D25 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for TBC1D25:
     Decreased viability 

    Animal Models:
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TBC1D25

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    5/7 Interacting proteins for TBC1D25 (Q3MII63 ENSP000003659624) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FEZ1Q996893, ENSP000002789194I2D: score=2 STRING: ENSP00000278919
    FEZ2Q9UHY83, ENSP000003685474I2D: score=1 STRING: ENSP00000368547
    GABARAPENSP000003068664STRING: ENSP00000306866
    GABARAPL2ENSP000000372434STRING: ENSP00000037243
    MAP1LC3BENSP000002686074STRING: ENSP00000268607
    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:0006914autophagy IEA--
    GO:0032313regulation of Rab GTPase activity ----
    GO:0032851positive regulation of Rab GTPase activity IDA--
    GO:1901096regulation of autophagic vacuole maturation IMP--

    TBC1D25 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 TBC1D25 (TBC25)

    Search CenterWatch for drugs/clinical trials and news about TBC1D25 / TBC25

    (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,
    RNAi Products from EMD Millipore,
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    About This Section

    REFSEQ mRNAs for TBC1D25 gene (2 alternative transcripts): 
    NM_001006113.1  NM_002536.2  

    Unigene Cluster for TBC1D25:

    TBC1 domain family, member 25
    Hs.694353  [show with all ESTs]
    Unigene Representative Sequence: NM_002536
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000376771(uc004dka.1 uc011mly.1 uc004dkb.1 uc011mlz.1 uc011mma.1 uc004dkc.1 uc011mmb.1 uc011mmc.1 uc011mmd.1)
    ENST00000481090 ENST00000494495 ENST00000476141 ENST00000418627 ENST00000427713
    ENST00000537536
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    SwitchGear 3'UTR luciferase reporter plasmidTBC1D25 3' UTR sequence
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    Additional mRNA sequence: 

    AB449912.1 AJ508600.1 AK293521.1 AK293875.1 AK294776.1 AK297924.1 AK298884.1 AK299561.1 
    AK316199.1 BC026050.1 BC036942.1 BC041614.1 BC052609.1 BC064334.1 BC082255.1 BC101817.1 
    BC101819.1 BC125088.1 BC125089.1 BC143395.1 L08240.1 

    8 DOTS entries:

    DT.100779009  DT.97858635  DT.108929  DT.100779000  DT.121315750  DT.121315760  DT.86858749  DT.92434493 

    24/155 AceView cDNA sequences (see all 155):

    BQ651229 CK299092 CA447032 AA476223 BQ646486 BU737793 AI247867 BQ669144 
    BQ673865 CR592577 BQ643383 BC082255 CD519271 BC052609 BX280004 AI057414 
    BQ673117 BU726929 CB155002 AW269150 BC041614 C01849 BC064334 BE671227 

    GeneLoc Exon Structure

    5/11 Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D25 (see all 11)    About this scheme

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


    ECgene alternative splicing isoforms for TBC1D25

    (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

    TBC1D25 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGACCCCACC
    TBC1D25 Expression
    About this image


    See TBC1D25 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TBC1D25

    SOURCE GeneReport for Unigene cluster: Hs.694353
        SABiosciences Custom PCR Arrays for TBC1D25
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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 and fungi.

    Orthologs for TBC1D25 gene from 6/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Tbc1d251 , 5 TBC1 domain family, member 251, 5 87.16(n)1
    94.04(a)1
      X (3.69 cM)5
    2098151  NM_001166437.11  NP_001159909.11 
     81544725 
    chicken
    (Gallus gallus)
    Aves TBC1D256
    TBC1 domain family, member 25
    54(a)
    1 ↔ 1
    JH375710.1(21-1417)
    lizard
    (Anolis carolinensis)
    Reptilia TBC1D256
    TBC1 domain family, member 25
    66(a)
    1 ↔ 1
    2(69358195-69369500)
    zebrafish
    (Danio rerio)
    Actinopterygii tbc1d251 TBC1 domain family, member 25 63.99(n)
    70.02(a)
      556338  NM_001128236.1  NP_001121708.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG81551 CG8155 56.26(n)
    50.89(a)
      36698  NM_137185.3  NP_611029.3 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GYP76
    GTPase-activating protein for yeast Rab family mem...
    14(a)
    1 → many
    IV(34237-36477)


    ENSEMBL Gene Tree for TBC1D25 (if available)
    TreeFam Gene Tree for TBC1D25 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TBC1D25 gene
    SGSM12  TBC1D172  TBC1D162  SGSM22  TBC1D152  
    3 SIMAP similar genes for TBC1D25 using alignment to 4 protein entries:     TBC25_HUMAN (see all proteins):
    OATL1    DKFZp761D0223    TBC1D16

    TBC1D25 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for TBC1D25
    PGOHUM00000237278


    (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) 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

    10/312 SNPs in TBC1D25 are shown (see all 312)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs585792381,2
    C--48396502(+) TGGCCA/CCTTCT 1 -- us2k10--------
    rs734857341,2
    C,F--48396957(+) TTCATG/ACAGGA 1 -- us2k11Minor allele frequency- A:0.50WA 2
    rs1812818291,2
    --48397056(+) GGTATA/CAATTA 1 -- us2k10--------
    rs726190211,2
    C--48397094(+) TCTGTA/GGTGCA 1 -- us2k10--------
    rs556519281,2
    C--48397165(+) CTGCCA/GCTTCA 1 -- us2k10--------
    rs1867635201,2
    --48397201(+) GTGTGC/TGCCAC 1 -- us2k10--------
    rs1915540831,2
    --48397242(+) AGAGAC/TGGGGT 1 -- us2k10--------
    rs736323841,2
    C,F--48397838(+) TGGCGG/AACGAG 1 -- us2k11Minor allele frequency- A:0.00WA 2
    rs1838087191,2
    --48398021(+) GGCGAC/TCTCCA 1 -- us2k10--------
    rs1871176421,2
    --48398054(+) GGTGGC/GGGGTA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TBC1D25 (48397845 - 48420997 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for TBC1D25:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv528292CNV Gain19592680
    esv32909CNV Gain+Loss17666407

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    (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.)
    About This Section
    OMIM gene information: 311240    OMIM disorders: --

    6 diseases for TBC1D25:    About MalaCards
    papillary renal cell carcinoma    synovial sarcoma    mood disorder    wiskott-aldrich syndrome
    renal cell carcinoma    sarcoma


    TBC1D25 for disorders           About GeneDecksing


    Export disorders for TBC1D25 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 TBC1D25 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with TBC1D25)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. OATL1, a novel autophagosome-resident Rab33B-GAP, reg ulates autophagosomal maturation. (PubMed id 21383079)1, 2, 3 Itoh T....Fukuda M. (2011)
    2. Rab GTPase-activating proteins in autophagy: regulatio n of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. (PubMed id 22354992)1 Popovic D....Dikic I. (2012)
    3. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
    4. Association of polyaminergic loci with anxiety, mood disorders, and attempted suicide. (PubMed id 21152090)1 Fiori L.M....Turecki G. (2010)
    5. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (2009)
    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. (2009)
    7. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
    8. Screening for target Rabs of TBC (Tre-2/Bub2/Cdc16) domain-containing proteins based on their Rab-binding activity. (PubMed id 16923123)1 Itoh T.... Fukuda M. (2006)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    10. FEZ1 dimerization and interaction with transcription regulatory proteins involves its coiled-coil region. (PubMed id 16484223)1 Assmann E.M.... Kobarg J. (2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
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      Query String
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    OMIM
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      (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)
    About This Section
    Entrez Gene: 4943 HGNC: 8092 AceView: OATL1 Ensembl:ENSG00000068354 euGenes: HUgn4943
    ECgene: TBC1D25 H-InvDB: TBC1D25

    (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 TBC1D25 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 TBC1D25 gene:
    Search GeneIP for patents involving TBC1D25

    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: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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