nid-1 Nidogen [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: nid-1
Official Full Name: Nidogen
Primary source: WormBase:WBGene00003738
Locus tag: CELE_F54F3.1
See related: AllianceGenome:WB:WBGene00003738
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: An extracellular matrix structural constituent. Involved in several processes, including cholinergic synaptic transmission; nervous system development; and positive regulation of anterior/posterior axon guidance. Located in basal part of cell and basement membrane. Is expressed in several structures, including CEP; egg-laying apparatus; enteric muscle; gonad; and touch receptor neurons. Orthologous to several human genes including NID1 (nidogen 1). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See nid-1 in Genome Data Viewer

Location:: chromosome: V

Exon count:: 16

Sequence:: Chromosome: V; NC_003283.11 (12910107..12917221)

Chromosome V - NC_003283.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003283.11

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

wrk-1 and rig-5 control pioneer and follower axon navigation in the ventral nerve cord of Caenorhabditis elegans in a nid-1 mutant background.
Title: wrk-1 and rig-5 control pioneer and follower axon navigation in the ventral nerve cord of Caenorhabditis elegans in a nid-1 mutant background.
Genetic experiments show that unc-52, nid-1 and genes of the netrin axon guidance signaling cassette share a common pathway to establish the correct number of somatosensory dendrites.
Title: Four specific immunoglobulin domains in UNC-52/Perlecan function with NID-1/Nidogen during dendrite morphogenesis in Caenorhabditis elegans.
FBL-1C and LET-2 act downstream of MIG-17-dependent proteolysis to recruit NID-1 and that LET-2 also activates a NID-1-independent pathway, thereby inducing the remodeling of the BM required for directional control of leader cell migration.
Title: MIG-17/ADAMTS controls cell migration by recruiting nidogen to the basement membrane in C. elegans.

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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

F54F3.1 (e-PCR)
- UniSTS:311791

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell-matrix adhesion	IEA Inferred from Electronic Annotation more info
involved_in interneuron axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of anterior/posterior axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of anterior/posterior axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to synapse	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synapse organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic transmission, cholinergic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ventral cord development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in ventral cord development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in basal part of cell	IDA Inferred from Direct Assay more info	PubMed
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basement membrane	IEA Inferred from Electronic Annotation more info
located_in basement membrane	IMP Inferred from Mutant Phenotype more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Nidogen

NP_001256465.1

Confirmed by transcript evidence

NP_001256466.1

Confirmed by transcript evidence

NP_001256467.1

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_003283.11 Reference assembly

Range

12910107..12917221

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001269538.3 → NP_001256467.1 Nidogen [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001256467.1

Status: REVIEWED

UniProtKB/TrEMBL

C7FZU4

Conserved Domains (6) summary

smart00539
Location:93 → 232

NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins

smart00682
Location:398 → 629

G2F; G2 nidogen domain and fibulin

cd05819
Location:983 → 1018

NHL; NHL repeat [structural motif]

pfam12947
Location:712 → 747

EGF_3; EGF domain

pfam14670
Location:1217 → 1244

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl18310
Location:983 → 1177

NHL; NHL repeat unit of beta-propeller proteins
NM_001269537.4 → NP_001256466.1 Nidogen [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001256466.1

Status: REVIEWED

UniProtKB/TrEMBL

C7FZU3

Conserved Domains (6) summary

smart00539
Location:93 → 232

NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins

smart00682
Location:398 → 629

G2F; G2 nidogen domain and fibulin

cd05819
Location:1262 → 1297

NHL; NHL repeat [structural motif]

pfam12947
Location:712 → 747

EGF_3; EGF domain

pfam14670
Location:1496 → 1523

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl18310
Location:1262 → 1456

NHL; NHL repeat unit of beta-propeller proteins
NM_001269536.4 → NP_001256465.1 Nidogen [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001256465.1

Status: REVIEWED

UniProtKB/TrEMBL

Q93791

Conserved Domains (7) summary

smart00539
Location:93 → 232

NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins

smart00682
Location:398 → 629

G2F; G2 nidogen domain and fibulin

cd05819
Location:1319 → 1354

NHL; NHL repeat [structural motif]

pfam12947
Location:712 → 747

EGF_3; EGF domain

pfam14670
Location:1553 → 1580

FXa_inhibition; Coagulation Factor Xa inhibitory site

cl18310
Location:1319 → 1513

NHL; NHL repeat unit of beta-propeller proteins

cl21504
Location:1205 → 1236

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...