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Aliases for TOM1 Gene

Aliases for TOM1 Gene

  • Target Of Myb1 Membrane Trafficking Protein 2 3 5
  • Target Of Myb1 (Chicken) Homolog 2
  • Target Of Myb1 (Chicken) 2

External Ids for TOM1 Gene

Previous GeneCards Identifiers for TOM1 Gene

  • GC22P032391
  • GC22P034020
  • GC22P035695
  • GC22P018656

Summaries for TOM1 Gene

Entrez Gene Summary for TOM1 Gene

  • 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]

GeneCards Summary for TOM1 Gene

TOM1 (Target Of Myb1 Membrane Trafficking Protein) is a Protein Coding gene. Diseases associated with TOM1 include Deafness, Autosomal Recessive 37 and Deafness, Autosomal Dominant 22. Among its related pathways are Innate Immune System and C-MYB transcription factor network. GO annotations related to this gene include clathrin binding. An important paralog of this gene is TOM1L2.

UniProtKB/Swiss-Prot for TOM1 Gene

  • May be involved in intracellular trafficking. Probable association with membranes.

Gene Wiki entry for TOM1 Gene

Additional gene information for TOM1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TOM1 Gene

Genomics for TOM1 Gene

Regulatory Elements for TOM1 Gene

Enhancers for TOM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22H035327 1.9 FANTOM5 Ensembl ENCODE dbSUPER 38.4 +30.2 30210 4 FOXA2 MLX ZFP64 ARID4B DMAP1 YY1 ZNF121 SLC30A9 ATF7 RUNX3 TOM1 MB APOL6 HMOX1 MIR3909 GC22P035300
GH22H035309 1.9 FANTOM5 Ensembl ENCODE dbSUPER 38 +14.0 14034 6 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 SLC30A9 FOS RUNX3 SP5 TOM1 APOL6 HMOX1 GC22P035300 MIR3909
GH22H035305 1.7 FANTOM5 Ensembl ENCODE dbSUPER 26.5 +8.1 8135 3 TBL1XR1 JUN ZMYM3 ZNF2 RELA POLR2A EED ZNF143 ATF7 NFE2 TOM1 APOL6 GC22P035300 MIR3909
GH22H035298 1.4 ENCODE dbSUPER 25.7 +1.8 1769 4 HDGF FOXA2 PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 HMGXB4 TOM1 RBFOX2 MCM5 GC22P035300 MIR3909
GH22H035256 1.1 ENCODE 23.9 -41.4 -41350 2 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 SP3 CEBPZ SP5 ZHX2 HMGXB4 TOM1 LOC105373017 GC22P035250
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TOM1 on UCSC Golden Path with GeneCards custom track

Promoters for TOM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000145662 1125 2001 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SLC30A9

Genomic Location for TOM1 Gene

Chromosome:
22
Start:
35,299,275 bp from pter
End:
35,347,994 bp from pter
Size:
48,720 bases
Orientation:
Plus strand

Genomic View for TOM1 Gene

Genes around TOM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TOM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TOM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TOM1 Gene

Proteins for TOM1 Gene

  • Protein details for TOM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O60784-TOM1_HUMAN
    Recommended name:
    Target of Myb protein 1
    Protein Accession:
    O60784
    Secondary Accessions:
    • B4DEL9
    • B4DNA1
    • Q5TIJ6
    • Q86X74

    Protein attributes for TOM1 Gene

    Size:
    492 amino acids
    Molecular mass:
    53818 Da
    Quaternary structure:
    • Interacts with ZFYVE16; interaction is required to target it to endosomes.

    Three dimensional structures from OCA and Proteopedia for TOM1 Gene

    Alternative splice isoforms for TOM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TOM1 Gene

Post-translational modifications for TOM1 Gene

  • Ubiquitination at Lys106, Lys116, Lys147, posLast=311311, posLast=385385, and posLast=443443
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TOM1 Gene

Domains & Families for TOM1 Gene

Gene Families for TOM1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for TOM1 Gene

Suggested Antigen Peptide Sequences for TOM1 Gene

Graphical View of Domain Structure for InterPro Entry

O60784

UniProtKB/Swiss-Prot:

TOM1_HUMAN :
  • Belongs to the TOM1 family.
Family:
  • Belongs to the TOM1 family.
genes like me logo Genes that share domains with TOM1: view

Function for TOM1 Gene

Molecular function for TOM1 Gene

GENATLAS Biochemistry:
target of mybl (chicken ortholog),ubiquitous with highest expression in skeletal muscle,placenta,heart,liver,involved in the control of vesicular trafficking to lysosome (suppression of cell growth)
UniProtKB/Swiss-Prot Function:
May be involved in intracellular trafficking. Probable association with membranes.

Phenotypes From GWAS Catalog for TOM1 Gene

Gene Ontology (GO) - Molecular Function for TOM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 14563850
GO:0030276 clathrin binding IDA 16412388
genes like me logo Genes that share ontologies with TOM1: view
genes like me logo Genes that share phenotypes with TOM1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for TOM1
  • Applied Biological Materials Clones for TOM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TOM1 Gene

Localization for TOM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TOM1 Gene

Cytoplasm. Membrane; Peripheral membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TOM1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytosol 5
lysosome 5
endosome 5
cytoskeleton 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Microtubule organizing center (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TOM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm IDA,IEA 16412388
GO:0005768 endosome IDA 16412388
GO:0005769 early endosome IDA 14613930
GO:0005829 cytosol IDA 14613930
genes like me logo Genes that share ontologies with TOM1: view

Pathways & Interactions for TOM1 Gene

genes like me logo Genes that share pathways with TOM1: view

Pathways by source for TOM1 Gene

1 BioSystems pathway for TOM1 Gene
3 Reactome pathways for TOM1 Gene

Gene Ontology (GO) - Biological Process for TOM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006886 intracellular protein transport IEA --
GO:0006897 endocytosis NAS 10329004
GO:0015031 protein transport NAS 14613930
GO:0016197 endosomal transport TAS 10329004
genes like me logo Genes that share ontologies with TOM1: view

No data available for SIGNOR curated interactions for TOM1 Gene

Drugs & Compounds for TOM1 Gene

(1) Drugs for TOM1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for TOM1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TOM1: view

Transcripts for TOM1 Gene

Unigene Clusters for TOM1 Gene

Target of myb1 (chicken):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for TOM1
  • Applied Biological Materials Clones for TOM1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for TOM1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b
SP1: - - - - -
SP2: - - - - - - -
SP3: - - - - - - -
SP4: - - -
SP5: - -
SP6:
SP7:
SP8:

Relevant External Links for TOM1 Gene

GeneLoc Exon Structure for
TOM1
ECgene alternative splicing isoforms for
TOM1

Expression for TOM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TOM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TOM1 Gene

This gene is overexpressed in Whole Blood (x5.6) and Muscle - Skeletal (x5.1).

Protein differential expression in normal tissues from HIPED for TOM1 Gene

This gene is overexpressed in Saliva (14.2), Lavage (10.6), and Bone marrow stromal cell (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for TOM1 Gene



Protein tissue co-expression partners for TOM1 Gene

NURSA nuclear receptor signaling pathways regulating expression of TOM1 Gene:

TOM1

SOURCE GeneReport for Unigene cluster for TOM1 Gene:

Hs.474705

mRNA Expression by UniProt/SwissProt for TOM1 Gene:

O60784-TOM1_HUMAN
Tissue specificity: Widely expressed. Highly expressed in skeletal muscle, heart, placenta and liver.

Evidence on tissue expression from TISSUES for TOM1 Gene

  • Nervous system(5)
  • Heart(4.3)
  • Liver(4.3)
  • Blood(2.6)
  • Bone marrow(2.1)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with TOM1: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for TOM1 Gene

Orthologs for TOM1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TOM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TOM1 33 34
  • 99.39 (n)
cow
(Bos Taurus)
Mammalia TOM1 33 34
  • 90.58 (n)
dog
(Canis familiaris)
Mammalia TOM1 33 34
  • 89.21 (n)
mouse
(Mus musculus)
Mammalia Gm5884 34
  • 89 (a)
OneToMany
Tom1 33 16 34
  • 85.91 (n)
rat
(Rattus norvegicus)
Mammalia Tom1 33
  • 85.43 (n)
oppossum
(Monodelphis domestica)
Mammalia TOM1 34
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TOM1 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves TOM1 33 34
  • 75.5 (n)
lizard
(Anolis carolinensis)
Reptilia TOM1 34
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tom1 33
  • 67.56 (n)
Str.15040 33
zebrafish
(Danio rerio)
Actinopterygii tom1 34
  • 46 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9213 33
fruit fly
(Drosophila melanogaster)
Insecta CG3529 35 34
  • 41 (a)
worm
(Caenorhabditis elegans)
Secernentea C07A12.7a 35
  • 48 (a)
C07A12.7b 35
  • 48 (a)
C07A12.7 34
  • 42 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HSE1 34
  • 13 (a)
OneToMany
Species where no ortholog for TOM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TOM1 Gene

ENSEMBL:
Gene Tree for TOM1 (if available)
TreeFam:
Gene Tree for TOM1 (if available)

Paralogs for TOM1 Gene

Paralogs for TOM1 Gene

genes like me logo Genes that share paralogs with TOM1: view

Variants for TOM1 Gene

Sequence variations from dbSNP and Humsavar for TOM1 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1000091351 -- 35,322,691(+) CATCT(C/T)AGATG intron-variant
rs1000095565 -- 35,323,255(+) TCGAG(A/G)CCATC intron-variant
rs1000142057 -- 35,328,522(+) AGCAG(A/G)GCTGC intron-variant
rs1000147599 -- 35,323,408(+) AGGGA(A/G)AGAAT intron-variant
rs1000197920 -- 35,346,803(+) TGGGG(A/G)CGTGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TOM1 Gene

Variant ID Type Subtype PubMed ID
nsv1147614 CNV insertion 26484159
nsv3610 CNV insertion 18451855
nsv953076 CNV deletion 24416366

Variation tolerance for TOM1 Gene

Residual Variation Intolerance Score: 49.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.38; 81.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TOM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TOM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TOM1 Gene

Disorders for TOM1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for TOM1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
deafness, autosomal recessive 37
  • autosomal recessive nonsyndromic deafness 37
deafness, autosomal dominant 22
  • deafness, autosomal dominant 22, with hypertrophic cardiomyopathy
- elite association - COSMIC cancer census association via MalaCards
Search TOM1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for TOM1

Genetic Association Database (GAD)
TOM1
Human Genome Epidemiology (HuGE) Navigator
TOM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TOM1
genes like me logo Genes that share disorders with TOM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TOM1 Gene

Publications for TOM1 Gene

  1. TOM1 genes map to human chromosome 22q13.1 and mouse chromosome 8C1 and encode proteins similar to the endosomal proteins HGS and STAM. (PMID: 10329004) Seroussi E … Dumanski JP (Genomics 1999) 2 3 4 22 60
  2. Endofin recruits TOM1 to endosomes. (PMID: 14613930) Seet LF … Hong W (The Journal of biological chemistry 2004) 3 4 22 60
  3. Structure of the VHS domain of human Tom1 (target of myb 1): insights into interactions with proteins and membranes. (PMID: 10985773) Misra S … Hurley JH (Biochemistry 2000) 3 4 22 60
  4. The emerging role of VHS domain-containing Tom1, Tom1L1 and Tom1L2 in membrane trafficking. (PMID: 20604899) Wang T … Hong W (Traffic (Copenhagen, Denmark) 2010) 2 3 60
  5. miR-126 is downregulated in cystic fibrosis airway epithelial cells and regulates TOM1 expression. (PMID: 20083669) Oglesby IK … Greene CM (Journal of immunology (Baltimore, Md. : 1950) 2010) 3 22 60

Products for TOM1 Gene

  • Addgene plasmids for TOM1

Sources for TOM1 Gene

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