emb-9 Collagen alpha-1(IV) chain [Caenorhabditis elegans] - Gene

Summary

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Gene symbol: emb-9
Gene description: Collagen alpha-1(IV) chain
Locus tag: CELE_K04H4.1
See related: AllianceGenome:WB:WBGene00001263
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: Predicted to be an extracellular matrix structural constituent. Involved in several processes, including nematode larval development; positive regulation of axon regeneration; and positive regulation of protein secretion. Located in basement membrane. Is expressed in several structures, including GLR; head; head mesodermal cell; muscle cell; and reproductive system. Human ortholog(s) of this gene implicated in Alport syndrome (multiple); artery disease (multiple); benign familial hematuria; brain small vessel disease 1; and end stage renal disease. Orthologous to several human genes including COL4A5 (collagen type IV alpha 5 chain). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See emb-9 in Genome Data Viewer

Location:: chromosome: III

Exon count:: 12

Sequence:: Chromosome: III; NC_003281.10 (9336881..9344447, complement)

Chromosome III - NC_003281.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003281.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A dominant mutation in the EMB-9/type IV collagen alpha1 subunit can compensate for loss of FBL-1 activity in gonadogenesis.
Title: Tissue architecture in the Caenorhabditis elegans gonad depends on interactions among fibulin-1, type IV collagen and the ADAMTS extracellular protease.

Submit: New GeneRIF Correction

Pathways from PubChem

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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

K04H4.1 (e-PCR)
- UniSTS:321560

Homology

Orthologs from OrthoDB

Gene Ontology Provided by WormBase

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	IEA Inferred from Electronic Annotation more info
enables extracellular matrix structural constituent	TAS Traceable Author Statement more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in anatomical structure development	IEA Inferred from Electronic Annotation more info
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 extracellular matrix organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle organ development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nematode larval development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of axon regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to serotonin	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
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 cellular anatomical entity	IEA Inferred from Electronic Annotation more info
part_of collagen trimer	IEA Inferred from Electronic Annotation 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-1(IV) chain

NP_001022662.2

Confirmed by transcript evidence

NP_001022663.1

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_003281.10 Reference assembly

Range

9336881..9344447 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001027491.7 → NP_001022662.2 Collagen alpha-1(IV) chain [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022662.2

Status: REVIEWED

UniProtKB/Swiss-Prot

P17139, Q6LAD0

Conserved Domains (3) summary

smart00111
Location:1645 → 1758

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

pfam01391
Location:1379 → 1437

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1536 → 1642

C4; C-terminal tandem repeated domain in type 4 procollagen
NM_001027492.6 → NP_001022663.1 Collagen alpha-1(IV) chain [Caenorhabditis elegans]

See identical proteins and their annotated locations for NP_001022663.1

Status: REVIEWED

UniProtKB/Swiss-Prot

P17139

Conserved Domains (3) summary

smart00111
Location:1388 → 1501

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

pfam01391
Location:1122 → 1180

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1279 → 1385

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