Human Gene TOM1L1 (ENST00000575882.6_9) from GENCODE V47lift37
  Description: target of myb1 like 1 membrane trafficking protein, transcript variant 1 (from RefSeq NM_005486.3)
Gencode Transcript: ENST00000575882.6_9
Gencode Gene: ENSG00000141198.16_15
Transcript (Including UTRs)
   Position: hg19 chr17:52,978,213-53,039,317 Size: 61,105 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr17:52,978,227-53,037,987 Size: 59,761 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:52,978,213-53,039,317)mRNA (may differ from genome)Protein (476 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TM1L1_HUMAN
DESCRIPTION: RecName: Full=TOM1-like protein 1; AltName: Full=Src-activating and signaling molecule protein; AltName: Full=Target of Myb-like protein 1;
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).
SUBUNIT: Interacts with FYN, GRB2 and PIK3R1 when phosphorylated (By similarity). Interacts with LYN (By similarity).
INTERACTION: Q9H0E2:TOLLIP; NbExp=3; IntAct=EBI-712991, EBI-74615; P52735:VAV2; NbExp=2; IntAct=EBI-712991, EBI-297549;
SUBCELLULAR LOCATION: Golgi apparatus, Golgi stack. Endosome membrane (Potential). Cytoplasm (By similarity). Membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Note=A small proportion is membrane-associated (By similarity).
PTM: Phosphorylated on tyrosines by FYN and LYN (By similarity). Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the TOM1 family.
SIMILARITY: Contains 1 GAT domain.
SIMILARITY: Contains 1 VHS domain.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.00 RPKM in Kidney - Cortex
Total median expression: 119.11 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -149.70723-0.207 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008942 - ENTH_VHS
IPR004152 - GAT
IPR014645 - TOM1
IPR002014 - VHS
IPR018205 - VHS_subgr

Pfam Domains:
PF00790 - VHS domain
PF03127 - GAT domain

SCOP Domains:
48464 - ENTH/VHS domain
89009 - GAT-like domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3RRU - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O75674
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0017124 SH3 domain binding
GO:0019901 protein kinase binding
GO:0030276 clathrin binding
GO:0030295 protein kinase activator activity
GO:0043130 ubiquitin binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0007165 signal transduction
GO:0015031 protein transport
GO:0031954 positive regulation of protein autophosphorylation
GO:0032147 activation of protein kinase activity
GO:0043162 ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
GO:0045839 negative regulation of mitotic nuclear division
GO:2000278 regulation of DNA biosynthetic process

Cellular Component:
GO:0005622 intracellular
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK001893 - Homo sapiens cDNA FLJ11031 fis, clone PLACE1004183, highly similar to Homo sapiens for TOM1-like protein.
AK309164 - Homo sapiens cDNA, FLJ99205.
AK225351 - Homo sapiens mRNA for TOM1L1 protein variant, clone: HEP14901.
AJ010071 - Homo sapiens for TOM1-like protein.
AK303912 - Homo sapiens cDNA FLJ54992 complete cds, highly similar to TOM1-like 1 protein.
AK315039 - Homo sapiens cDNA, FLJ95985, highly similar to Homo sapiens target of myb1-like 1 (chicken) (TOM1L1), mRNA.
AK303913 - Homo sapiens cDNA FLJ58664 complete cds, highly similar to TOM1-like 1 protein.
AK315907 - Homo sapiens cDNA, FLJ78806 complete cds, highly similar to TOM1-like 1 protein.
AK300823 - Homo sapiens cDNA FLJ52768 complete cds, highly similar to TOM1-like 1 protein.
BC029396 - Homo sapiens target of myb1 (chicken)-like 1, mRNA (cDNA clone MGC:32609 IMAGE:4612157), complete cds.
AK223125 - Homo sapiens mRNA for target of myb1-like 1 variant, clone: KDN00573.
AB590855 - Synthetic construct DNA, clone: pFN21AE1937, Homo sapiens TOM1L1 gene for target of myb1 (chicken)-like 1, without stop codon, in Flexi system.
KJ904641 - Synthetic construct Homo sapiens clone ccsbBroadEn_14035 TOM1L1-like gene, encodes complete protein.
JD304145 - Sequence 285169 from Patent EP1572962.
JD274747 - Sequence 255771 from Patent EP1572962.
JD327407 - Sequence 308431 from Patent EP1572962.
JD305756 - Sequence 286780 from Patent EP1572962.
JD235435 - Sequence 216459 from Patent EP1572962.
JD491754 - Sequence 472778 from Patent EP1572962.
JD527355 - Sequence 508379 from Patent EP1572962.
JD260000 - Sequence 241024 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z9E2, ENST00000575882.1, ENST00000575882.2, ENST00000575882.3, ENST00000575882.4, ENST00000575882.5, NM_005486, O75674, Q53G06, Q8N749, SRCASM, TM1L1_HUMAN, uc326ecn.1, uc326ecn.2
UCSC ID: ENST00000575882.6_9
RefSeq Accession: NM_005486.3
Protein: O75674 (aka TM1L1_HUMAN or T1L1_HUMAN)

-  Gene Model Information
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-  Methods, Credits, and Use Restrictions
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