syg-1 Ig-like domain-containing protein;Synaptogenesis protein syg-1 [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: syg-1
Official Full Name: Ig-like domain-containing protein;Synaptogenesis protein syg-1
Primary source: WormBase:WBGene00006365
Locus tag: CELE_K02E10.8
See related: AllianceGenome:WB:WBGene00006365
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: Enables cell adhesion molecule binding activity. Involved in actin filament bundle assembly; cell-cell signaling; and nervous system development. Located in axon and synapse. Is expressed in amphid sheath cell; egg-laying apparatus; head muscle; and neurons. Used to study nephrotic syndrome. Human ortholog(s) of this gene implicated in nephrotic syndrome type 23. Orthologous to several human genes including KIRREL1 (kirre like nephrin family adhesion molecule 1) and KIRREL2 (kirre like nephrin family adhesion molecule 2). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

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See syg-1 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 16

Sequence:: Chromosome: X; NC_003284.9 (2509313..2515324, complement)

Chromosome X - NC_003284.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003284.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Robo functions as an attractive cue for glial migration through SYG-1/Neph.
Title: Robo functions as an attractive cue for glial migration through SYG-1/Neph.
Through a series of biochemical, biophysical, and in vivo functional experiments, study finds that the extracellular affinity, docking geometry, and rigidity of the SYG-1 and SYG-2 ectodomains play crucial roles in specifying a functional synaptic architecture in C. elegans.
Title: Extracellular architecture of the SYG-1/SYG-2 adhesion complex instructs synaptogenesis.
Assembly of the F-actin network requires a direct interaction between the synaptic cell adhesion molecule SYG-1 and a key regulator of actin cytoskeleton, the WVE-1/WAVE regulatory complex.
Title: Local F-actin network links synapse formation and axon branching.
Data show that the nephrin/Neph1 orthologs SYG-2 and SYG-1 form intercellular contacts strictly in trans between epithelial guidepost cells and neurons specifying the localization of synapses.
Title: Functional and spatial analysis of C. elegans SYG-1 and SYG-2, orthologs of the Neph/nephrin cell adhesion module directing selective synaptogenesis.
study found stereotyped developmental elimination of synapses in the motor neuron (HSNL) was mediated by a Skp1-cullin-F-box (SCF) complex composed of SKR-1 & SEL-10; SYG-1 bound to SKR-1 & inhibited assembly of the SCF complex, protecting nearby synapses
Title: Spatial regulation of an E3 ubiquitin ligase directs selective synapse elimination.
SYG-2 binds SYG-1, the receptor on HSNL, and directs SYG-1 accumulation and synapse formation to adjacent regions of HSNL.
Title: Synaptic specificity is generated by the synaptic guidepost protein SYG-2 and its receptor, SYG-1.

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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

K02E10.8 (e-PCR)
- UniSTS:311368

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	IBA Inferred from Biological aspect of Ancestor more info
enables cell adhesion molecule binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in actin filament bundle assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in branching morphogenesis of a nerve	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell-cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collateral sprouting	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nervous system development	IEA Inferred from Electronic Annotation more info
involved_in synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synapse organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic target recognition	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in cell-cell junction	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in synapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Ig-like domain-containing protein;Synaptogenesis protein syg-1

NP_001123159.1

Confirmed by transcript evidence

NP_001360786.1

Confirmed by transcript evidence

NP_508457.3

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_003284.9 Reference assembly

Range

2509313..2515324 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001129687.6 → NP_001123159.1 Synaptogenesis protein syg-1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001123159.1

Status: REVIEWED

UniProtKB/Swiss-Prot

B1Q236, H2L0B4

Conserved Domains (4) summary

smart00410
Location:450 → 535

IG_like; Immunoglobulin like

cd00096
Location:458 → 462

Ig; Ig strand B [structural motif]

pfam13927
Location:358 → 423

Ig_3; Immunoglobulin domain

cl11960
Location:24 → 124

Ig; Immunoglobulin domain
NM_001373246.4 → NP_001360786.1 Ig-like domain-containing protein [Caenorhabditis elegans]

Status: REVIEWED

UniProtKB/TrEMBL

A0A4V0IKN9

Conserved Domains (4) summary

smart00409
Location:450 → 535

IG; Immunoglobulin

smart00410
Location:283 → 353

IG_like; Immunoglobulin like

pfam13927
Location:361 → 423

Ig_3; Immunoglobulin domain

cl11960
Location:24 → 124

Ig; Immunoglobulin domain
NM_076056.8 → NP_508457.3 Synaptogenesis protein syg-1 [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_508457.3

Status: REVIEWED

UniProtKB/Swiss-Prot

B1Q236

Conserved Domains (4) summary

smart00410
Location:450 → 535

IG_like; Immunoglobulin like

pfam07679
Location:24 → 124

I-set; Immunoglobulin I-set domain

pfam13895
Location:368 → 438

Ig_2; Immunoglobulin domain

cl11960
Location:440 → 528

Ig; Immunoglobulin domain