Tom1 target of myb1 trafficking protein [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Tom1provided by MGI
Official Full Name: target of myb1 trafficking proteinprovided by MGI
Primary source: MGI:MGI:1338026
See related: Ensembl:ENSMUSG00000042870 AllianceGenome:MGI:1338026
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Predicted to enable clathrin binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within protein transport. Predicted to be located in cytosol and early endosome. Predicted to be active in endosome and membrane. Is expressed in several structures, including brain and intestine. Human ortholog(s) of this gene implicated in primary immunodeficiency disease. Orthologous to human TOM1 (target of myb1 membrane trafficking protein). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis adult (RPKM 30.9), heart adult (RPKM 26.6) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 8; 8 C1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	8	NC_000074.7 (75760270..75796749)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	8	NC_000074.6 (75033642..75070121)

Chromosome 8 - NC_000074.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study shows that TOM1 regulates neuronal accumulation of amyloid-beta oligomers by FcgammaRIIb2 variant in Alzheimer's Disease (AD). Study provides a molecular mechanism responsible for neuronal uptake of pathogenic Abeta found in AD.
Title: TOM1 Regulates Neuronal Accumulation of Amyloid-β Oligomers by FcγRIIb2 Variant in Alzheimer's Disease.
a Tom1-Tollip complex functions as a factor that links polyubiquitinated proteins to clathrin
Title: Tom1, a VHS domain-containing protein, interacts with tollip, ubiquitin, and clathrin.
These results indicate that, in conjunction with Tollip, Tom1 family proteins play an important role in recruiting clathrin onto endosomes and suggest that they modulate endosomal functions.
Title: Recruitment of clathrin onto endosomes by the Tom1-Tollip complex.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH136490 (e-PCR)
- UniSTS:210474

NoName (e-PCR)
- UniSTS:235931

Homology

Homologs of the Tom1 gene: The Tom1 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, and frog.
Orthologs from Annotation Pipeline: 481 organisms have orthologs with human gene Tom1
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables clathrin binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables clathrin binding	ISO Inferred from Sequence Orthology more info
enables clathrin heavy chain binding	ISO Inferred from Sequence Orthology more info
enables myosin VI binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylinositol binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol-5-phosphate binding	ISO Inferred from Sequence Orthology more info
enables polyubiquitin modification-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in autophagosome-lysosome fusion	ISO Inferred from Sequence Orthology more info
involved_in endosomal transport	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of autophagosome maturation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of endosome organization	ISO Inferred from Sequence Orthology more info
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in substrate localization to autophagosome	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in early endosome	ISO Inferred from Sequence Orthology more info
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in endosome membrane	ISO Inferred from Sequence Orthology more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: target of Myb1 membrane trafficking protein; target of Myb protein 1

Names: target of myb1 homolog

NCBI Reference Sequences (RefSeq)

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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)

NM_001136259.1 → NP_001129731.1 target of Myb1 membrane trafficking protein isoform 2

See identical proteins and their annotated locations for NP_001129731.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) represents the longer transcript and encodes the longer protein (isoform 2).

Source sequence(s)

AL603864

Consensus CDS

CCDS52600.1

UniProtKB/TrEMBL

Q3UDC3

Related

ENSMUSP00000077891.6, ENSMUST00000078847.13

Conserved Domains (2) summary

cd03565
Location:12 → 152

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:214 → 308

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)
NM_011622.3 → NP_035752.1 target of Myb1 membrane trafficking protein isoform 1

See identical proteins and their annotated locations for NP_035752.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) lacks an alternate in-frame exon in the coding region compared to variant 2. The resulting protein (isoform 1) is shorter but has the same N- and C-termini compared to isoform 2.

Source sequence(s)

AL603864

Consensus CDS

CCDS52601.1

UniProtKB/Swiss-Prot

O88746, Q9D120

UniProtKB/TrEMBL

Q561M4

Related

ENSMUSP00000130854.2, ENSMUST00000165630.3

Conserved Domains (2) summary

cd03565
Location:12 → 152

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:214 → 308

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000074.7 Reference GRCm39 C57BL/6J

Range

75760270..75796749

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017312661.2 → XP_017168150.1 target of Myb protein 1 isoform X1

Conserved Domains (2) summary

cd14236
Location:181 → 275

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)

cl02544
Location:1 → 115

VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily
XM_036153878.1 → XP_036009771.1 target of Myb protein 1 isoform X2

Conserved Domains (1) summary

cd14236
Location:62 → 156

GAT_TOM1; canonical GAT domain found in target of Myb protein 1 (Tom1)
XM_006530843.4 → XP_006530906.1 target of Myb protein 1 isoform X2

See identical proteins and their annotated locations for XP_006530906.1

Conserved Domains (1) summary

cd14236
Location:62 → 156

GAT_TOM1; canonical GAT domain found in target of Myb protein 1 (Tom1)
XM_006530844.4 → XP_006530907.1 target of Myb protein 1 isoform X2

See identical proteins and their annotated locations for XP_006530907.1

Conserved Domains (1) summary

cd14236
Location:62 → 156

GAT_TOM1; canonical GAT domain found in target of Myb protein 1 (Tom1)
XM_036153876.1 → XP_036009769.1 target of Myb protein 1 isoform X2

Conserved Domains (1) summary

cd14236
Location:62 → 156

GAT_TOM1; canonical GAT domain found in target of Myb protein 1 (Tom1)