Aliases for TOM1L1 Gene

Aliases for TOM1L1 Gene

  • Target Of Myb1 Like 1 Membrane Trafficking Protein 2 3 5
  • SRCASM 2 3 4
  • Src-Activating And Signaling Molecule Protein 3 4
  • Target Of Myb-Like Protein 1 3 4
  • TOM1-Like Protein 1 3 4
  • Target Of Myb1 (Chicken) Homolog-Like 1 2
  • Target Of Myb1 (Chicken)-Like 1 2
  • TOM1L1 5

External Ids for TOM1L1 Gene

Previous GeneCards Identifiers for TOM1L1 Gene

  • GC17P052708
  • GC17P055459
  • GC17P053320
  • GC17P053452
  • GC17P050333
  • GC17P052978
  • GC17P048336

Summaries for TOM1L1 Gene

GeneCards Summary for TOM1L1 Gene

TOM1L1 (Target Of Myb1 Like 1 Membrane Trafficking Protein) is a Protein Coding gene. Diseases associated with TOM1L1 include Nodular Basal Cell Carcinoma. Gene Ontology (GO) annotations related to this gene include protein kinase binding and ubiquitin binding. An important paralog of this gene is TOM1L2.

UniProtKB/Swiss-Prot Summary for TOM1L1 Gene

  • Probable adapter protein involved in signaling pathways. Interacts with the SH2 and SH3 domains of various signaling proteins when it is phosphorylated. May promote FYN activation, possibly by disrupting intramolecular SH3-dependent interactions (By similarity).

Gene Wiki entry for TOM1L1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TOM1L1 Gene

Genomics for TOM1L1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TOM1L1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J054898 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +1.9 1941 5.2 IKZF1 ZNF600 ATF2 KLF9 CEBPA ZNF10 NFIC POLR2A ZIC2 YY1 HSALNG0117472 TOM1L1 lnc-STXBP4-8 STXBP4 COX11
GH17J054920 Enhancer 0.2 Ensembl 11.8 +20.3 20314 0.2 COX11 STXBP4 TOM1L1 RF00017-2205 HSALNG0117472
GH17J054932 Enhancer 0.2 ENCODE 11.3 +34.6 34615 3.9 RF00017-2205 COX11 STXBP4 TOM1L1 HSALNG0117472
GH17J054939 Enhancer 0.2 FANTOM5 2.8 +40.7 40710 0.2 HSALNG0117487 TOM1L1 HSALNG0117489 STXBP4
GH17J054891 Enhancer 0.8 Ensembl ENCODE 0.4 -8.2 -8172 0.4 ZNF654 JUND REST CTCF RAD21 SMC3 FOSL2 MEIS2 PKNOX1 ATF3 STXBP4 TOM1L1 HSALNG0117472 LOC112268185
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TOM1L1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TOM1L1

Top Transcription factor binding sites by QIAGEN in the TOM1L1 gene promoter:
  • AP-4
  • AREB6
  • c-Myb
  • FAC1
  • FOXO1
  • FOXO1a
  • GR
  • GR-alpha
  • STAT1
  • STAT1alpha

Genomic Locations for TOM1L1 Gene

Latest Assembly
chr17:54,899,387-54,961,967
(GRCh38/hg38)
Size:
62,581 bases
Orientation:
Plus strand

Previous Assembly
chr17:52,978,213-53,039,317
(GRCh37/hg19 by Entrez Gene)
Size:
61,105 bases
Orientation:
Plus strand

chr17:52,976,748-53,039,310
(GRCh37/hg19 by Ensembl)
Size:
62,563 bases
Orientation:
Plus strand

Genomic View for TOM1L1 Gene

Genes around TOM1L1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TOM1L1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TOM1L1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TOM1L1 Gene

Proteins for TOM1L1 Gene

  • Protein details for TOM1L1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75674-TM1L1_HUMAN
    Recommended name:
    TOM1-like protein 1
    Protein Accession:
    O75674
    Secondary Accessions:
    • B7Z9E2
    • Q53G06
    • Q8N749

    Protein attributes for TOM1L1 Gene

    Size:
    476 amino acids
    Molecular mass:
    52989 Da
    Quaternary structure:
    • Interacts with FYN, GRB2 and PIK3R1 when phosphorylated. Interacts with LYN.

    Three dimensional structures from OCA and Proteopedia for TOM1L1 Gene

    Alternative splice isoforms for TOM1L1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TOM1L1 Gene

Post-translational modifications for TOM1L1 Gene

  • Phosphorylated on tyrosines by FYN and LYN.
  • Ubiquitination at Lys5, Lys148, and Lys191
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TOM1L1 Gene

Domains & Families for TOM1L1 Gene

Gene Families for TOM1L1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for TOM1L1 Gene

InterPro:
Blocks:
  • VHS
  • GAT domain

Suggested Antigen Peptide Sequences for TOM1L1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52768, highly similar to TOM1-like 1 protein (B4DUW5_HUMAN)
  • cDNA, FLJ78806, highly similar to TOM1-like 1 protein (B7Z9E2_HUMAN)
  • Target of myb1-like 1 (Chicken), isoform CRA_a (Q8N749_HUMAN)
  • Target of Myb-like protein 1 (TM1L1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75674

UniProtKB/Swiss-Prot:

TM1L1_HUMAN :
  • Belongs to the TOM1 family.
Family:
  • Belongs to the TOM1 family.
genes like me logo Genes that share domains with TOM1L1: view

Function for TOM1L1 Gene

Molecular function for TOM1L1 Gene

UniProtKB/Swiss-Prot Function:
Probable adapter protein involved in signaling pathways. Interacts with the SH2 and SH3 domains of various signaling proteins when it is phosphorylated. May promote FYN activation, possibly by disrupting intramolecular SH3-dependent interactions (By similarity).

Phenotypes From GWAS Catalog for TOM1L1 Gene

Gene Ontology (GO) - Molecular Function for TOM1L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15611048
GO:0017124 SH3 domain binding IEA --
GO:0019901 protein kinase binding IPI 16479011
GO:0030276 clathrin binding IBA,IDA 16412388
GO:0030295 protein kinase activator activity IEA --
genes like me logo Genes that share ontologies with TOM1L1: view
genes like me logo Genes that share phenotypes with TOM1L1: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TOM1L1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TOM1L1 Gene

Localization for TOM1L1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TOM1L1 Gene

Golgi apparatus, Golgi stack. Endosome membrane. Cytoplasm. Membrane. Peripheral membrane protein. Cytoplasmic side. Note=A small proportion is membrane-associated. {ECO:0000250}.

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 TOM1L1 gene
Compartment Confidence
endosome 5
cytosol 5
extracellular 4
lysosome 4
golgi apparatus 3
nucleus 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for TOM1L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 16412388
GO:0005764 lysosome TAS 10329004
GO:0005768 endosome IBA,IDA 15611048
GO:0005794 Golgi apparatus IEA --
GO:0005795 Golgi stack IEA --
genes like me logo Genes that share ontologies with TOM1L1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TOM1L1 Gene

Pathways & Interactions for TOM1L1 Gene

PathCards logo

SuperPathways for TOM1L1 Gene

No Data Available

SIGNOR curated interactions for TOM1L1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for TOM1L1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0007165 signal transduction IBA,IDA 16479011
GO:0015031 protein transport IEA --
GO:0031954 positive regulation of protein autophosphorylation IDA 16479011
GO:0032147 activation of protein kinase activity IEA,IDA 16479011
genes like me logo Genes that share ontologies with TOM1L1: view

No data available for Pathways by source for TOM1L1 Gene

Drugs & Compounds for TOM1L1 Gene

(1) Drugs for TOM1L1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for TOM1L1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TOM1L1: view

Transcripts for TOM1L1 Gene

mRNA/cDNA for TOM1L1 Gene

5 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
23 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TOM1L1

Alternative Splicing Database (ASD) splice patterns (SP) for TOM1L1 Gene

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

Relevant External Links for TOM1L1 Gene

GeneLoc Exon Structure for
TOM1L1

Expression for TOM1L1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TOM1L1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TOM1L1 Gene

This gene is overexpressed in Pancreas (9.3), Islet of Langerhans (8.7), Liver (8.7), Skin (8.4), Tonsil (6.4), and Kidney (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TOM1L1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TOM1L1

SOURCE GeneReport for Unigene cluster for TOM1L1 Gene:

Hs.153504

Evidence on tissue expression from TISSUES for TOM1L1 Gene

  • Kidney(4.4)
  • Liver(4.4)
  • Adrenal gland(4.2)
  • Nervous system(2.4)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with TOM1L1: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TOM1L1 Gene

Orthologs for TOM1L1 Gene

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

Orthologs for TOM1L1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TOM1L1 29 30
  • 99.58 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TOM1L1 29 30
  • 88.34 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TOM1L1 29 30
  • 88.21 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tom1l1 29
  • 83.33 (n)
Mouse
(Mus musculus)
Mammalia Tom1l1 29 16 30
  • 82.99 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TOM1L1 30
  • 67 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TOM1L1 30
  • 57 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TOM1L1 29 30
  • 63.51 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TOM1L1 30
  • 68 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tom1l1 29
  • 57.21 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC52738 29
Zebrafish
(Danio rerio)
Actinopterygii tom1l2 30
  • 30 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea stam-1 30
  • 14 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes HSE1 30
  • 11 (a)
OneToMany
Species where no ortholog for TOM1L1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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 TOM1L1 Gene

ENSEMBL:
Gene Tree for TOM1L1 (if available)
TreeFam:
Gene Tree for TOM1L1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TOM1L1: view image
Alliance of Genome Resources:
Additional Orthologs for TOM1L1

Paralogs for TOM1L1 Gene

Paralogs for TOM1L1 Gene

(5) SIMAP similar genes for TOM1L1 Gene using alignment to 17 proteins:

  • TM1L1_HUMAN
  • B4DUW5_HUMAN
  • B7Z9E2_HUMAN
  • I3L0N2_HUMAN
  • I3L1G1_HUMAN
  • I3L1Q1_HUMAN
  • I3L1T2_HUMAN
  • I3L367_HUMAN
  • I3L3M3_HUMAN
  • I3L3T4_HUMAN
  • I3L4G0_HUMAN
  • I3L4I4_HUMAN
  • I3L4N3_HUMAN
  • I3NI44_HUMAN
  • J3KQU4_HUMAN
  • K7EP47_HUMAN
  • Q8N749_HUMAN
genes like me logo Genes that share paralogs with TOM1L1: view

Variants for TOM1L1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TOM1L1 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs16955377 -- p.Arg108Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TOM1L1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TOM1L1 Gene

Variant ID Type Subtype PubMed ID
dgv3266n100 CNV loss 25217958
esv2471400 CNV deletion 19546169
esv3640828 CNV gain 21293372
esv3640830 CNV gain 21293372
esv3640831 CNV loss 21293372
esv8118 CNV gain 19470904
nsv111920 CNV deletion 16902084
nsv457853 CNV loss 19166990
nsv575661 CNV loss 21841781
nsv962343 CNV duplication 23825009

Variation tolerance for TOM1L1 Gene

Residual Variation Intolerance Score: 18.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.23; 40.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TOM1L1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TOM1L1
Leiden Open Variation Database (LOVD)
TOM1L1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TOM1L1 Gene

Disorders for TOM1L1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TOM1L1 Gene - From: COP

Disorder Aliases PubMed IDs
nodular basal cell carcinoma
  • basal cell carcinoma, nodular
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TOM1L1

genes like me logo Genes that share disorders with TOM1L1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TOM1L1 Gene

Publications for TOM1L1 Gene

  1. Interactions of TOM1L1 with the multivesicular body sorting machinery. (PMID: 15611048) Puertollano R (The Journal of biological chemistry 2005) 2 3 22
  2. 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
  3. Decreased Srcasm expression in hyperproliferative cutaneous lesions. (PMID: 19220627) Meulener MC … Seykora JT (Journal of cutaneous pathology 2009) 3 22
  4. TOM1L1 is a Lyn substrate involved in FcepsilonRI signaling in mast cells. (PMID: 17977829) Zhang J … Siraganian RP (The Journal of biological chemistry 2007) 2 3
  5. Recruitment of clathrin onto endosomes by the Tom1-Tollip complex. (PMID: 16412388) Katoh Y … Nakayama K (Biochemical and biophysical research communications 2006) 3 22

Products for TOM1L1 Gene

Sources for TOM1L1 Gene