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    Tom1 target of myb1 membrane trafficking protein [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361370, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Tom1provided by RGD
    Official Full Name
    target of myb1 membrane trafficking proteinprovided by RGD
    Primary source
    RGD:1308024
    See related
    EnsemblRapid:ENSRNOG00000014093 AllianceGenome:RGD:1308024
    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
    Summary
    Predicted to enable several functions, including clathrin heavy chain binding activity; phosphatidylinositol-5-phosphate binding activity; and ubiquitin binding activity. Predicted to be involved in several processes, including endosomal transport; macroautophagy; and regulation of organelle organization. Predicted to be located in cytosol; early endosome; and endosome membrane. Predicted to be active in endosome and membrane. Human ortholog(s) of this gene implicated in primary immunodeficiency disease. Orthologous to human TOM1 (target of myb1 membrane trafficking protein). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in Heart (RPKM 187.8), Thymus (RPKM 159.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tom1 in Genome Data Viewer
    Location:
    19p11
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (13411227..13446129)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (13405482..13440384)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (14392405..14426482)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein S2, pseudogene 41 Neighboring gene HMG-box containing 4 Neighboring gene uncharacterized LOC102556139 Neighboring gene uncharacterized LOC134483111 Neighboring gene heme oxygenase 1 Neighboring gene minichromosome maintenance complex component 5

    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 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. Endofin recruits TOM1 to endosomes. Seet LF, et al. J Biol Chem, 2004 Feb 6. PMID 14613930
    2. Recruitment of clathrin onto endosomes by the Tom1-Tollip complex. Katoh Y, et al. Biochem Biophys Res Commun, 2006 Mar 3. PMID 16412388
    3. Tollip is a mediator of protein sumoylation. Ciarrocchi A, et al. PLoS One, 2009. PMID 19198660, Free PMC Article
    4. Role of the AP2 beta-appendage hub in recruiting partners for clathrin-coated vesicle assembly. Schmid EM, et al. PLoS Biol, 2006 Sep. PMID 16903783, Free PMC Article
    5. Large-scale proteomics and phosphoproteomics of urinary exosomes. Gonzales PA, et al. J Am Soc Nephrol, 2009 Feb. PMID 19056867, Free PMC Article

    See all (8) 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

    Clone Names

    • MGC95142

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables clathrin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables clathrin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables clathrin heavy chain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables myosin VI binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-5-phosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables polyubiquitin modification-dependent protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ubiquitin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in autophagosome-lysosome fusion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endosomal transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of autophagosome maturation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of endosome organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in substrate localization to autophagosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    target of Myb1 membrane trafficking protein
    Names
    target of Myb protein 1
    target of myb1 homolog

    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_001008365.2 → NP_001008366.1  target of Myb1 membrane trafficking protein

      See identical proteins and their annotated locations for NP_001008366.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      F7EYC4, Q5XI21
      Related
      ENSRNOP00000089787.2, ENSRNOT00000108363.2
      Conserved Domains (2) summary
      cd03565
      Location:12 → 152
      VHS_Tom1; VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of ...
      cd14236
      Location:214 → 308
      GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)

    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_086037.1 Reference GRCr8

      Range
      13411227..13446129
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255145.5 → XP_006255207.1  target of Myb1 membrane trafficking protein isoform X1

      UniProtKB/TrEMBL
      F7EYC4
      Conserved Domains (2) summary
      cd03565
      Location:12 → 146
      VHS_Tom1; VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of ...
      cd14236
      Location:208 → 302
      GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)

    2. XM_017601310.2 → XP_017456799.1  target of Myb1 membrane trafficking protein isoform X2

      UniProtKB/TrEMBL
      A0A8I6ACG3, F7EYC4
      Conserved Domains (2) summary
      cd14236
      Location:181 → 275
      GAT_TOM1; canonical GAT domain found in target of Myb protein 1 (Tom1)
      cl02544
      Location:1 → 115
      VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily

    3. XM_039097811.2 → XP_038953739.1  target of Myb1 membrane trafficking protein isoform X3

      Conserved Domains (1) summary
      cd14236
      Location:62 → 156
      GAT_TOM1; canonical GAT domain found in target of Myb protein 1 (Tom1)
    Nucleotide Protein Strain
    Heading Accession and Version

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