tom-1 Lethal giant larvae homologue 2 domain-containing protein;V-SNARE coiled-coil homology domain-containing protein [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: tom-1
Official Full Name: Lethal giant larvae homologue 2 domain-containing protein;V-SNARE coiled-coil homology domain-containing protein
Primary source: WormBase:WBGene00006594
Locus tag: CELE_M01A10.2
See related: AllianceGenome:WB:WBGene00006594
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Caenorhabditis elegans (strain: Bristol N2)
Lineage: Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
Summary: Involved in several processes, including regulation of presynaptic dense core granule exocytosis; regulation of synaptic vesicle docking; and synaptic vesicle priming. Located in GABA-ergic synapse; cholinergic synapse; and neuromuscular junction. Is extrinsic component of neuronal dense core vesicle membrane. Part of SNARE complex. Is expressed in head neurons; tail neurons; and ventral cord neurons. Orthologous to several human genes including STXBP5 (syntaxin binding protein 5). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See tom-1 in Genome Data Viewer

Location:: chromosome: I

Exon count:: 27

Sequence:: Chromosome: I; NC_003279.8 (5546118..5561689)

Chromosome I - NC_003279.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003279.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TOM-1/tomosyn acts with the UNC-6/netrin receptor UNC-5 to inhibit growth cone protrusion in Caenorhabditis elegans.
Title: TOM-1/tomosyn acts with the UNC-6/netrin receptor UNC-5 to inhibit growth cone protrusion in Caenorhabditis elegans.
Thus, our study provides novel mechanistic insights into how Munc18/UNC-18 primes synaptic vesicle release and how this protein interacts functionally with Munc13/UNC-13 and Tomosyn/TOM-1.
Title: UNC-18 and Tomosyn Antagonistically Control Synaptic Vesicle Priming Downstream of UNC-13 in Caenorhabditis elegans.
tomosyn negatively regulates transmitter and neuropeptide release in vesicle exocytosis
Title: Tomosyn negatively regulates both synaptic transmitter and neuropeptide release at the C. elegans neuromuscular junction.
Overexpression of tomosyn leads to an accumulation of dense-core vesicles at the presynapse.
Title: Tomosyn negatively regulates CAPS-dependent peptide release at Caenorhabditis elegans synapses.
These data indicate that in the intact nervous system, TOM-1 negatively regulates synaptic vesicle priming.
Title: Tomosyn inhibits synaptic vesicle priming in Caenorhabditis elegans.
Synaptic vesicle priming is modulated by the balance between Tomosyn and UNC-13, perhaps by regulating the availability of open-syntaxin.
Title: Antagonistic regulation of synaptic vesicle priming by Tomosyn and UNC-13.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

M01A10.2 (e-PCR)
- UniSTS:317511

M01A10.3 (e-PCR)
- UniSTS:311943

M01A10.4 (e-PCR)
- UniSTS:306364

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables GTPase activator activity	IBA Inferred from Biological aspect of Ancestor more info
enables myosin II binding	IBA Inferred from Biological aspect of Ancestor more info
enables syntaxin binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in Golgi to plasma membrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to salt	IGI Inferred from Genetic Interaction more info	PubMed
involved_in cellular response to salt	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in exocytosis	IEA Inferred from Electronic Annotation more info
involved_in regulation of presynaptic dense core granule exocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of presynaptic dense core granule exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synaptic vesicle docking	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synaptic vesicle docking	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synaptic vesicle priming	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synaptic vesicle priming	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic vesicle priming	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in GABA-ergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in GABA-ergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
part_of SNARE complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SNARE complex	IPI Inferred from Physical Interaction more info	PubMed
located_in cholinergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in cholinergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in extrinsic component of neuronal dense core vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in neuromuscular junction	IDA Inferred from Direct Assay more info	PubMed
located_in neuromuscular junction	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in presynapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Lethal giant larvae homologue 2 domain-containing protein;V-SNARE coiled-coil homology domain-containing protein

NP_001122494.1

Partially confirmed by transcript evidence

NP_001122495.1

Partially confirmed by transcript evidence

NP_001300427.1

Partially confirmed by transcript evidence

NP_001300428.1

Partially confirmed by transcript evidence

NP_001300429.1

Partially confirmed by transcript evidence

NP_491623.3

Confirmed by transcript evidence

NP_491626.2

Partially confirmed by transcript evidence

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_003279.8 Reference assembly

Range

5546118..5561689

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001129023.2 → NP_001122495.1 Lethal giant larvae homologue 2 domain-containing protein [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001122495.1

Status: REVIEWED

UniProtKB/TrEMBL

G5EE26

Conserved Domains (4) summary

cd15873
Location:1066 → 1126

R-SNARE_STXBP5_6; SNARE domain of STXBP5, STXBP6 and related proteins

sd00039
Location:51 → 84

7WD40; WD40 repeat [structural motif]

pfam08366
Location:264 → 364

LLGL; LLGL2

cl29593
Location:50 → 256

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_059222.8 → NP_491623.3 Lethal giant larvae homologue 2 domain-containing protein [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_491623.3

Status: REVIEWED

UniProtKB/TrEMBL

Q49HI3

Conserved Domains (4) summary

cd15873
Location:1057 → 1117

R-SNARE_STXBP5_6; SNARE domain of STXBP5, STXBP6 and related proteins

sd00039
Location:51 → 84

7WD40; WD40 repeat [structural motif]

pfam08366
Location:264 → 364

LLGL; LLGL2

cl29593
Location:50 → 256

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001313499.3 → NP_001300428.1 Lethal giant larvae homologue 2 domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AR90, Q49HI2

Conserved Domains (4) summary

cd15873
Location:1179 → 1239

R-SNARE_STXBP5_6; SNARE domain of STXBP5, STXBP6 and related proteins

sd00039
Location:51 → 84

7WD40; WD40 repeat [structural motif]

pfam08366
Location:264 → 364

LLGL; LLGL2

cl29593
Location:50 → 256

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001313498.3 → NP_001300427.1 Lethal giant larvae homologue 2 domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3AWL6, Q49HI2

Conserved Domains (4) summary

cd15873
Location:1183 → 1243

R-SNARE_STXBP5_6; SNARE domain of STXBP5, STXBP6 and related proteins

sd00039
Location:51 → 84

7WD40; WD40 repeat [structural motif]

pfam08366
Location:264 → 364

LLGL; LLGL2

cl29593
Location:50 → 256

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001129022.5 → NP_001122494.1 Lethal giant larvae homologue 2 domain-containing protein [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001122494.1

Status: REVIEWED

UniProtKB/TrEMBL

Q14DX2

Conserved Domains (4) summary

cd15873
Location:1061 → 1121

R-SNARE_STXBP5_6; SNARE domain of STXBP5, STXBP6 and related proteins

sd00039
Location:51 → 84

7WD40; WD40 repeat [structural motif]

pfam08366
Location:264 → 364

LLGL; LLGL2

cl29593
Location:50 → 256

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001313500.3 → NP_001300429.1 Lethal giant larvae homologue 2 domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A0K3ATN9, Q49HI2

Conserved Domains (4) summary

cd15873
Location:1188 → 1248

R-SNARE_STXBP5_6; SNARE domain of STXBP5, STXBP6 and related proteins

sd00039
Location:51 → 84

7WD40; WD40 repeat [structural motif]

pfam08366
Location:264 → 364

LLGL; LLGL2

cl29593
Location:50 → 256

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_059225.5 → NP_491626.2 V-SNARE coiled-coil homology domain-containing protein [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_491626.2

Status: REVIEWED

UniProtKB/TrEMBL

A8WFN4

Conserved Domains (1) summary

cd15873
Location:126 → 186

R-SNARE_STXBP5_6; SNARE domain of STXBP5, STXBP6 and related proteins