Tom1 target of myb1 membrane trafficking protein [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tom1provided by RGD
Official Full Name: target of myb1 membrane trafficking proteinprovided by RGD
Primary source: RGD:1308024
See related: EnsemblRapid:ENSRNOG00000014093 AllianceGenome:RGD:1308024
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including clathrin heavy chain binding activity; phosphatidylinositol-5-phosphate binding activity; and ubiquitin binding activity. Predicted to be involved in several processes, including endosomal transport; macroautophagy; and regulation of organelle organization. Predicted to be located in cytosol; early endosome; and endosome membrane. Predicted to be active in endosome and membrane. 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, Nov 2024]
Expression: Biased expression in Heart (RPKM 187.8), Thymus (RPKM 159.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19p11

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (13411227..13446129)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (13405482..13440384)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (14392405..14426482)

Chromosome 19 - NC_086037.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables clathrin binding	IBA Inferred from Biological aspect of Ancestor more info
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-5-phosphate binding	ISO Inferred from Sequence Orthology more info
enables polyubiquitin modification-dependent protein binding	ISO Inferred from Sequence Orthology more info
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
involved_in 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
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
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
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

Names: target of Myb protein 1; 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_001008365.2 → NP_001008366.1 target of Myb1 membrane trafficking protein

See identical proteins and their annotated locations for NP_001008366.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000019

UniProtKB/TrEMBL

F7EYC4, Q5XI21

Related

ENSRNOP00000089787.2, ENSRNOT00000108363.2

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: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086037.1 Reference GRCr8

Range

13411227..13446129

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255145.5 → XP_006255207.1 target of Myb1 membrane trafficking protein isoform X1

UniProtKB/TrEMBL

F7EYC4

Conserved Domains (2) summary

cd03565
Location:12 → 146

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:208 → 302

GAT_TOM1; GAT domain found in target of Myb protein 1 (Tom1)
XM_017601310.2 → XP_017456799.1 target of Myb1 membrane trafficking protein isoform X2

UniProtKB/TrEMBL

A0A8I6ACG3, F7EYC4

Conserved Domains (2) summary

cd14236
Location:181 → 275

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

cl02544
Location:1 → 115

VHS_ENTH_ANTH; VHS, ENTH and ANTH domain superfamily
XM_039097811.2 → XP_038953739.1 target of Myb1 membrane trafficking protein isoform X3

Conserved Domains (1) summary

cd14236
Location:62 → 156

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