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    tom1 target of myb1 membrane trafficking protein [ Danio rerio (zebrafish) ]

    Gene ID: 553244, updated on 9-Dec-2024

    Summary

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    Official Symbol
    tom1provided by ZNC
    Official Full Name
    target of myb1 membrane trafficking proteinprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-060721-1
    See related
    Ensembl:ENSDARG00000104581 AllianceGenome:ZFIN:ZDB-GENE-060721-1
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    Tom1l2
    Summary
    Predicted to enable clathrin binding activity. Predicted to be involved in signal transduction. 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, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See tom1 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (25907266..25939259)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (25776704..25808386)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene zgc:171844 Neighboring gene major facilitator superfamily domain containing 6-like Neighboring gene uncharacterized LOC110439128 Neighboring gene uncharacterized LOC101885347

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Identification of Novel Transcribed Regions in Zebrafish (Danio rerio) Using RNA-Sequencing. Wang J, et al. PLoS One, 2016. PMID 27462902, Free PMC Article
    2. Convergent extension movements and ciliary function are mediated by ofd1, a zebrafish orthologue of the human oral-facial-digital type 1 syndrome gene. Ferrante MI, et al. Hum Mol Genet, 2009 Jan 15. PMID 18971206, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    5. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables clathrin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ubiquitin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    target of Myb1 membrane trafficking protein

    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_001351651.1 → NP_001338580.1  target of Myb1 membrane trafficking protein isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC078346, CU683826, EH551587, EH589099
      UniProtKB/TrEMBL
      A0A0R4IY33, A0A8M1P9P8
      Related
      ENSDARP00000141619.2, ENSDART00000170324.2
      Conserved Domains (2) summary
      cd14233
      Location:203 → 289
      GAT_TOM1_like; GAT domain found in target of myb protein 1 (Tom1) protein family
      cl02544
      Location:12 → 152
      VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal ...

    2. NM_001351652.1 → NP_001338581.1  target of Myb1 membrane trafficking protein isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2) has the same N- and C-termini, but is shorter than isoform 1.
      Source sequence(s)
      BC078346, CU683826, EH551587, EH589099
      UniProtKB/TrEMBL
      A0A2R8QER9, A0A8M1P5P3
      Related
      ENSDARP00000151444.1, ENSDART00000192633.1
      Conserved Domains (2) summary
      cd14233
      Location:203 → 289
      GAT_TOM1_like; GAT domain found in target of myb protein 1 (Tom1) protein family
      cl02544
      Location:12 → 152
      VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal ...

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007114.7 Reference GRCz11 Primary Assembly

      Range
      25907266..25939259
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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