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    Tbc1d5 TBC1 domain family, member 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 501088, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Tbc1d5provided by RGD
    Official Full Name
    TBC1 domain family, member 5provided by RGD
    Primary source
    RGD:1561626
    See related
    EnsemblRapid:ENSRNOG00000010637 AllianceGenome:RGD:1561626
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1561626
    Summary
    Predicted to enable AP-2 adaptor complex binding activity; GTPase activator activity; and retromer complex binding activity. Predicted to be involved in several processes, including macroautophagy; positive regulation of receptor internalization; and retrograde transport, endosome to Golgi. Predicted to be located in autophagosome. Predicted to be part of AP-2 adaptor complex; Atg1/ULK1 kinase complex; and retromer complex. Predicted to be active in Golgi apparatus and endosome membrane. Orthologous to human TBC1D5 (TBC1 domain family member 5). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Spleen (RPKM 110.4), Adrenal (RPKM 93.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tbc1d5 in Genome Data Viewer
    Location:
    9q11
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (3740032..4256971, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (3503328..4017131, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (1144641..1747732)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120094621 Neighboring gene uncharacterized LOC134480316 Neighboring gene phospholipase C-like 2 Neighboring gene uncharacterized LOC134480471 Neighboring gene NADH:ubiquinone oxidoreductase subunit B1, pseudogene 1 Neighboring gene ribosomal protein L10, pseudogene 10 Neighboring gene uncharacterized LOC120094782 Neighboring gene ribosomal protein S20, pseudogene 12 Neighboring gene uncharacterized LOC134480258

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. TBC1D5 and the AP2 complex regulate ATG9 trafficking and initiation of autophagy. Popovic D, et al. EMBO Rep, 2014 Apr. PMID 24603492, Free PMC Article
    2. Membrane recruitment of the cargo-selective retromer subcomplex is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5. Seaman MN, et al. J Cell Sci, 2009 Jul 15. PMID 19531583, Free PMC Article
    3. Parkinson Disease-linked Vps35 R524W Mutation Impairs the Endosomal Association of Retromer and Induces α-Synuclein Aggregation. Follett J, et al. J Biol Chem, 2016 Aug 26. PMID 27385586, Free PMC Article
    4. The cargo-selective retromer complex is a recruiting hub for protein complexes that regulate endosomal tubule dynamics. Harbour ME, et al. J Cell Sci, 2010 Nov 1. PMID 20923837, Free PMC Article
    5. Retromer and sorting nexins in endosomal sorting. Gallon M, et al. Biochem Soc Trans, 2015 Feb. PMID 25619244

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables AP-2 adaptor complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables retromer complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in autophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in macroautophagy ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of receptor internalization ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT involved_in regulation of cilium assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to starvation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of AP-2 adaptor complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of Atg1/ULK1 kinase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in autophagosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of retromer complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of retromer complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    TBC1 domain family member 5

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001134762.1 → NP_001128234.1  TBC1 domain family member 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A0A8I6AMF2, F1M9Q1
      Related
      ENSRNOP00000014171.5, ENSRNOT00000014171.8
      Conserved Domains (1) summary
      smart00164
      Location:79 → 381
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086027.1 Reference GRCr8

      Range
      3740032..4256971 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063267576.1 → XP_063123646.1  TBC1 domain family member 5 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AMF2

    2. XM_039084056.2 → XP_038939984.1  TBC1 domain family member 5 isoform X6

      UniProtKB/TrEMBL
      A0A8I6AMF2
      Conserved Domains (1) summary
      smart00164
      Location:55 → 266
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    3. XM_039084054.2 → XP_038939982.1  TBC1 domain family member 5 isoform X5

      UniProtKB/TrEMBL
      A0A8I6AMF2
      Conserved Domains (1) summary
      smart00164
      Location:56 → 267
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    4. XM_008766768.4 → XP_008764990.1  TBC1 domain family member 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K712, A0A8I6AMF2
      Related
      ENSRNOP00000074017.1, ENSRNOT00000083387.3
      Conserved Domains (1) summary
      smart00164
      Location:79 → 381
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    5. XM_063267575.1 → XP_063123645.1  TBC1 domain family member 5 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AMF2, F1M9Q1

    6. XM_017596593.3 → XP_017452082.1  TBC1 domain family member 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K712, A0A8I6AMF2
      Conserved Domains (1) summary
      smart00164
      Location:79 → 381
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    7. XM_063267572.1 → XP_063123642.1  TBC1 domain family member 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K712, A0A8I6AMF2

    8. XM_063267577.1 → XP_063123647.1  TBC1 domain family member 5 isoform X4

      UniProtKB/TrEMBL
      A0A8I6AMF2

    9. XM_039084053.2 → XP_038939981.1  TBC1 domain family member 5 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AMF2
      Conserved Domains (1) summary
      smart00164
      Location:78 → 380
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    10. XM_063267574.1 → XP_063123644.1  TBC1 domain family member 5 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AMF2, F1M9Q1

    11. XM_039084050.2 → XP_038939978.1  TBC1 domain family member 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K712, A0A8I6AMF2
      Conserved Domains (1) summary
      smart00164
      Location:79 → 381
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    12. XM_017596594.3 → XP_017452083.1  TBC1 domain family member 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K712, A0A8I6AMF2
      Conserved Domains (1) summary
      smart00164
      Location:79 → 381
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    13. XM_063267573.1 → XP_063123643.1  TBC1 domain family member 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K712, A0A8I6AMF2

    14. XM_039084051.1 → XP_038939979.1  TBC1 domain family member 5 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K712, A0A8I6AMF2
      Conserved Domains (1) summary
      smart00164
      Location:79 → 381
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    15. XM_039084057.2 → XP_038939985.1  TBC1 domain family member 5 isoform X7

      Conserved Domains (1) summary
      smart00164
      Location:1 → 208
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    16. XM_039084058.2 → XP_038939986.1  TBC1 domain family member 5 isoform X8

      Conserved Domains (1) summary
      smart00164
      Location:79 → 380
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    RNA

    1. XR_010054624.1 RNA Sequence

    2. XR_005488952.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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