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    TOM1 target of myb1 membrane trafficking protein [ Homo sapiens (human) ]

    Gene ID: 10043, updated on 9-Dec-2024

    Summary

    Official Symbol
    TOM1provided by HGNC
    Official Full Name
    target of myb1 membrane trafficking proteinprovided by HGNC
    Primary source
    HGNC:HGNC:11982
    See related
    Ensembl:ENSG00000100284 MIM:604700; AllianceGenome:HGNC:11982
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    IMD85
    Summary
    This gene was identified as a target of the v-myb oncogene. The encoded protein shares its N-terminal domain in common with proteins associated with vesicular trafficking at the endosome. It is recruited to the endosomes by its interaction with endofin. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
    Expression
    Ubiquitous expression in bone marrow (RPKM 24.4), esophagus (RPKM 24.1) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TOM1 in Genome Data Viewer
    Location:
    22q12.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (35299275..35347973)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (35757154..35805980)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (35695268..35743966)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1399 Neighboring gene COX7B pseudogene 1 Neighboring gene uncharacterized LOC105373017 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35652780-35653280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13652 Neighboring gene RNA, U7 small nuclear 167 pseudogene Neighboring gene HMG-box containing 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35695462-35695984 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35695985-35696507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35697031-35697552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35713551-35714052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35714053-35714552 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35714588-35715088 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35715089-35715589 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:35718923-35720122 Neighboring gene Sharpr-MPRA regulatory region 10159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35726353-35726853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35732808-35733717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35745310-35745842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35745843-35746375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35746966-35747474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35748292-35749167 Neighboring gene microRNA 3909 Neighboring gene microRNA 6069 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:35772530-35773729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18906 Neighboring gene heme oxygenase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:35821835-35822340 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:35822341-35822848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:35822849-35823354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:35831135-35831636 Neighboring gene minichromosome maintenance complex component 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18909 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:35844065-35845031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:35845032-35845997

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Immunodeficiency 85 and autoimmunity
    MedGen: C5561976 OMIM: 619510 GeneReviews: Not available
    not available

    EBI GWAS Catalog

    Description
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of target of myb1 (TOM1) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ33404

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables clathrin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables clathrin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables clathrin heavy chain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables myosin VI binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylinositol-5-phosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in autophagosome-lysosome fusion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endocytosis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in endosomal transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in endosomal transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in endosomal transport TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of endosome organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in substrate localization to autophagosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in azurophil granule membrane TAS
    Traceable Author Statement
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in specific granule membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    target of Myb1 membrane trafficking protein
    Names
    target of Myb protein 1
    target of myb 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001135729.2NP_001129201.1  target of Myb1 membrane trafficking protein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains a different 5' terminal exon and uses an alternate donor splice site at the penultimate exon compared to transcript variant 1. This results in translation initiation from a downstream AUG and an isoform (3) with a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AJ006973, AK097066, AK293694
      Consensus CDS
      CCDS46698.1
      UniProtKB/TrEMBL
      B4DKQ5
      Related
      ENSP00000398876.1, ENST00000447733.5
      Conserved Domains (2) summary
      cd14236
      Location:181275
      GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)
      cl02544
      Location:1119
      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_001135730.2NP_001129202.1  target of Myb1 membrane trafficking protein isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) is missing an in-frame coding exon compared to transcript variant 1, resulting in a shorter isoform (4) lacking an internal 45 aa segment compared to isoform 1.
      Source sequence(s)
      AJ006973, AK097066, DC297234
      Consensus CDS
      CCDS46697.1
      UniProtKB/TrEMBL
      B4DKQ5
      Related
      ENSP00000394924.1, ENST00000425375.5
      Conserved Domains (2) summary
      cd14236
      Location:169263
      GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)
      cl02544
      Location:12123
      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 ...
    3. NM_001135732.2NP_001129204.1  target of Myb1 membrane trafficking protein isoform 2

      See identical proteins and their annotated locations for NP_001129204.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate donor splice site at the penultimate exon compared to transcript variant 1, resulting in an isoform (2) with one extra aa compared to isoform 1.
      Source sequence(s)
      BC046151, DC297234
      Consensus CDS
      CCDS46696.1
      UniProtKB/TrEMBL
      B4DKQ5
      Related
      ENSP00000413697.1, ENST00000411850.5
      Conserved Domains (2) summary
      cd03565
      Location:12152
      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:214308
      GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)
    4. NM_005488.3NP_005479.1  target of Myb1 membrane trafficking protein isoform 1

      See identical proteins and their annotated locations for NP_005479.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the most predominant transcript and encodes isoform 1.
      Source sequence(s)
      AJ006973, AK097066, DC297234
      Consensus CDS
      CCDS13913.1
      UniProtKB/Swiss-Prot
      B4DEL9, B4DNA1, O60784, Q5TIJ6, Q86X74
      UniProtKB/TrEMBL
      B4DKQ5
      Related
      ENSP00000394466.2, ENST00000449058.7
      Conserved Domains (2) summary
      cd03565
      Location:12152
      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:214308
      GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)

    RNA

    1. NR_024194.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate acceptor splice site at one of the coding exons compared to transcript variant 1. This results in a frame-shift and premature translation termination, rendering the transcript susceptible to nonsense mediated mRNA decay (NMD). This variant is sufficiently abundant to represent as a RefSeq record, however, the predicted protein is not represented because it is significantly truncated.
      Source sequence(s)
      AK097066, AK296670, DC297234
      Related
      ENST00000424387.5
    2. NR_024195.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) is missing an internal coding exon and uses an alternate acceptor splice site at another coding exon compared to transcript variant 1. This results in a frame-shift and premature translation termination, rendering the transcript susceptible to nonsense mediated mRNA decay (NMD). This variant is sufficiently abundant to represent as a RefSeq record, however, the predicted protein is not represented because it is significantly truncated.
      Source sequence(s)
      AJ006973, AK097066, AK295918, DC297234
    3. NR_156428.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) is missing an internal coding exon compared to transcript variant 1. This results in a frame-shift and premature translation termination, rendering the transcript susceptible to nonsense mediated mRNA decay (NMD). This variant is sufficiently abundant to represent as a RefSeq record, however, the predicted protein is not represented because it is significantly truncated.
      Source sequence(s)
      AL008635, Z82244

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      35299275..35347973
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441068.1XP_047297024.1  target of Myb1 membrane trafficking protein isoform X1

      UniProtKB/TrEMBL
      B4DKQ5
    2. XM_047441069.1XP_047297025.1  target of Myb1 membrane trafficking protein isoform X2

      UniProtKB/TrEMBL
      B4DKQ5
    3. XM_011529820.3XP_011528122.1  target of Myb1 membrane trafficking protein isoform X4

      Conserved Domains (1) summary
      cd14236
      Location:62156
      GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)
    4. XM_011529818.3XP_011528120.1  target of Myb1 membrane trafficking protein isoform X3

      UniProtKB/TrEMBL
      B4DJ44
      Conserved Domains (2) summary
      cd14236
      Location:147241
      GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)
      cl02544
      Location:185
      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 ...
    5. XM_047441070.1XP_047297026.1  target of Myb1 membrane trafficking protein isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      35757154..35805980
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324975.1XP_054180950.1  target of Myb1 membrane trafficking protein isoform X1

      UniProtKB/TrEMBL
      B4DKQ5
    2. XM_054324976.1XP_054180951.1  target of Myb1 membrane trafficking protein isoform X2

      UniProtKB/TrEMBL
      B4DKQ5
    3. XM_054324978.1XP_054180953.1  target of Myb1 membrane trafficking protein isoform X4

    4. XM_054324977.1XP_054180952.1  target of Myb1 membrane trafficking protein isoform X3

      UniProtKB/TrEMBL
      B4DJ44
    5. XM_054324979.1XP_054180954.1  target of Myb1 membrane trafficking protein isoform X5