let-2 Collagen alpha-2(IV) chain [Caenorhabditis elegans] - Gene

Summary

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Official Symbol: let-2
Official Full Name: Collagen alpha-2(IV) chain
Primary source: WormBase:WBGene00002280
Locus tag: CELE_F01G12.5
See related: AllianceGenome:WB:WBGene00002280
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 conferring tensile strength. Involved in several processes, including embryo development; gonad morphogenesis; and regulation of distal tip cell migration. Located in basement membrane. Part of collagen type IV trimer. Is expressed in several structures, including anal depressor muscle; head mesodermal cell; nervous system; rectal muscle; and reproductive system. Human ortholog(s) of this gene implicated in Alport syndrome (multiple); X-linked deafness 6; artery disease (multiple); brain small vessel disease 1; and uterine fibroid. Orthologous to human COL4A1 (collagen type IV alpha 1 chain); COL4A5 (collagen type IV alpha 5 chain); and COL4A6 (collagen type IV alpha 6 chain). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See let-2 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 19

Sequence:: Chromosome: X; NC_003284.9 (16380597..16389340, 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?

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

F01G12.5a (e-PCR)
- UniSTS:320032

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	IDA Inferred from Direct Assay more info	PubMed
enables extracellular matrix structural constituent	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular component organization	NAS Non-traceable Author Statement more info	PubMed
involved_in embryo development ending in birth or egg hatching	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in gonad morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of distal tip cell migration	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basement membrane	IEA Inferred from Electronic Annotation more info
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
part_of collagen type IV trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IV trimer	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: Collagen alpha-2(IV) chain

NP_510663.1

Confirmed by transcript evidence

NP_510664.1

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_003284.9 Reference assembly

Range

16380597..16389340 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_078263.5 → NP_510664.1 Collagen alpha-2(IV) chain [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_510664.1

Status: REVIEWED

UniProtKB/Swiss-Prot

P17140

Conserved Domains (2) summary

pfam01391
Location:820 → 878

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1640 → 1750

C4; C-terminal tandem repeated domain in type 4 procollagen
NM_078262.7 → NP_510663.1 Collagen alpha-2(IV) chain [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_510663.1

Status: REVIEWED

UniProtKB/Swiss-Prot

P17140

Conserved Domains (2) summary

pfam01391
Location:821 → 879

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1641 → 1751

C4; C-terminal tandem repeated domain in type 4 procollagen