Human Gene TOM1L2 (ENST00000581396.5) Description and Page Index
  Description: Homo sapiens target of myb1 like 2 membrane trafficking protein (TOM1L2), transcript variant 1, mRNA. (from RefSeq NM_001033551)
RefSeq Summary (NM_001033551): This gene belongs to a small gene family whose members have an N-terminal VHS domain followed by a GAT domain; domains which typically participate in vesicular trafficking. The canonical protein encoded by this gene also has a C-terminal clathrin binding motif. This protein has been shown to interact with Tollip, clathrin and ubiquitin and is thought to play a role in endosomal sorting. This gene resides in the 3.7 Mb deletion of chromosome region 17p11.2 that is associated with Smith-Magenis syndrome. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Apr 2017]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR7346977.2324549.1, BC051650.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END##
Gencode Transcript: ENST00000581396.5
Gencode Gene: ENSG00000175662.17
Transcript (Including UTRs)
   Position: hg38 chr17:17,843,511-17,972,410 Size: 128,900 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg38 chr17:17,847,635-17,972,313 Size: 124,679 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:17,843,511-17,972,410)mRNA (may differ from genome)Protein (457 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMGIneXtProtOMIMPubMed
Stanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: TM1L2_HUMAN
DESCRIPTION: RecName: Full=TOM1-like protein 2; AltName: Full=Target of Myb-like protein 2;
FUNCTION: Probable role in protein transport. May regulate growth factor-induced mitogenic signaling.
SUBUNIT: Interacts with clathrin, SRC and TOLLIP.
TISSUE SPECIFICITY: Ubiquitously expressed with higher expression in heart and skeletal muscle.
DOMAIN: The GAT domain mediates interaction with TOLLIP.
SIMILARITY: Belongs to the TOM1 family.
SIMILARITY: Contains 1 GAT domain.
SIMILARITY: Contains 1 VHS domain.
SEQUENCE CAUTION: Sequence=AAL78338.1; Type=Frameshift; Positions=101, 121, 170;

-  MalaCards Disease Associations
  MalaCards Gene Search: TOM1L2
Diseases sorted by gene-association score: smith-magenis syndrome (4)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 43.28 RPKM in Brain - Cortex
Total median expression: 1150.29 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -38.9097-0.401 Picture PostScript Text
3' UTR -1751.904124-0.425 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:
PF03127 - GAT domain
PF00790 - VHS domain

ModBase Predicted Comparative 3D Structure on Q6ZVM7
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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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0019901 protein kinase binding
GO:0030276 clathrin binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0007165 signal transduction
GO:0015031 protein transport
GO:0045839 negative regulation of mitotic nuclear division

Cellular Component:
GO:0005622 intracellular
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF213768 - JP 2014500723-A/21271: Polycomb-Associated Non-Coding RNAs.
MA449345 - JP 2018138019-A/21271: Polycomb-Associated Non-Coding RNAs.
BC051650 - Homo sapiens target of myb1-like 2 (chicken), mRNA (cDNA clone MGC:51035 IMAGE:5298847), complete cds.
AF467441 - Homo sapiens target of myb1-like protein 2 (TOM1L2) mRNA, complete cds.
AK124331 - Homo sapiens cDNA FLJ42340 fis, clone UTERU1000031, moderately similar to G.gallus mRNA for tom-1B protein.
AK301944 - Homo sapiens cDNA FLJ58550 complete cds, highly similar to Homo sapiens target of myb1-like 2 (TOM1L2), transcript variant 2, mRNA.
AK294846 - Homo sapiens cDNA FLJ60511 complete cds, highly similar to Mus musculus target of myb1-like 2 (chicken) (Tom1l2), transcript variant 1, mRNA.
AK295111 - Homo sapiens cDNA FLJ54050 complete cds, highly similar to Homo sapiens target of myb1-like 2 (TOM1L2), transcript variant 2, mRNA.
AK299872 - Homo sapiens cDNA FLJ54058 complete cds, highly similar to Homo sapiens target of myb1-like 2 (TOM1L2), transcript variant 2, mRNA.
KJ895598 - Synthetic construct Homo sapiens clone ccsbBroadEn_04992 TOM1L2 gene, encodes complete protein.
AK303305 - Homo sapiens cDNA FLJ52529 complete cds, highly similar to Homo sapiens target of myb1-like 2 (TOM1L2), transcript variant 1, mRNA.
AL133641 - Homo sapiens mRNA; cDNA DKFZp586E1521 (from clone DKFZp586E1521).
AK055959 - Homo sapiens cDNA FLJ31397 fis, clone NT2NE1000163.
DQ573317 - Homo sapiens piRNA piR-41429, complete sequence.
AF038192 - Homo sapiens clone 23808 mRNA sequence.
AY358769 - Homo sapiens clone DNA128309 SHSS3124 (UNQ3124) mRNA, complete cds.
JD021298 - Sequence 2322 from Patent EP1572962.
JD027736 - Sequence 8760 from Patent EP1572962.
DQ589236 - Homo sapiens piRNA piR-56348, complete sequence.
AK057308 - Homo sapiens cDNA FLJ32746 fis, clone TESTI2001512, moderately similar to TOM1 (target of myb 1).
JD216213 - Sequence 197237 from Patent EP1572962.
JD446103 - Sequence 427127 from Patent EP1572962.
JD139067 - Sequence 120091 from Patent EP1572962.
JD383984 - Sequence 365008 from Patent EP1572962.
JD402864 - Sequence 383888 from Patent EP1572962.
JD100086 - Sequence 81110 from Patent EP1572962.
JD259193 - Sequence 240217 from Patent EP1572962.
JD219760 - Sequence 200784 from Patent EP1572962.
JD228395 - Sequence 209419 from Patent EP1572962.
JD219736 - Sequence 200760 from Patent EP1572962.
JD194552 - Sequence 175576 from Patent EP1572962.
JD233103 - Sequence 214127 from Patent EP1572962.
JD078128 - Sequence 59152 from Patent EP1572962.
JD278063 - Sequence 259087 from Patent EP1572962.
JD113621 - Sequence 94645 from Patent EP1572962.
JD188299 - Sequence 169323 from Patent EP1572962.
JD289907 - Sequence 270931 from Patent EP1572962.
JD393728 - Sequence 374752 from Patent EP1572962.
JD405964 - Sequence 386988 from Patent EP1572962.
JD125166 - Sequence 106190 from Patent EP1572962.
JD444007 - Sequence 425031 from Patent EP1572962.
JD144868 - Sequence 125892 from Patent EP1572962.
JD354936 - Sequence 335960 from Patent EP1572962.
LF209091 - JP 2014500723-A/16594: Polycomb-Associated Non-Coding RNAs.
MA444668 - JP 2018138019-A/16594: Polycomb-Associated Non-Coding RNAs.
AK025154 - Homo sapiens cDNA: FLJ21501 fis, clone COL05642.
DQ574580 - Homo sapiens piRNA piR-42692, complete sequence.
JD079018 - Sequence 60042 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z7F4, NM_001033551, Q6ZVM7, Q86V61, Q8TDE7, Q96M88, TM1L2_HUMAN, uc002gry.1, uc002gry.2, uc002gry.3, uc002gry.4, uc002gry.5
UCSC ID: uc002gry.5
RefSeq Accession: NM_001033551
Protein: Q6ZVM7 (aka TM1L2_HUMAN)
CCDS: CCDS32584.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.