Summary
Cuticle and basement membrane collagens are extracellular matrix components encoded by a family of about 160 genes known to be expressed to which this gene belongs. Collagens have short interrupted blocks of Gly-X-Y sequence flanked by conserved cysteine residues, akin to vertebrate fibril-associated collagens with interrupted triple helix, and form trimers or higher order polymers. They have been grouped into five main subfamilies. The Caenorhabditis elegans cuticle is a complex multilayered extracellular matrix, consisting predominantly of cuticle collagens and synthesised by the underlying epidermal cell layer (called hypodermis). It is secreted five times during development, in embryos and before each molt, and is slightly different from stage to stage. During cuticle synthesis, the genes are expressed in a distinct temporal series, and the temporal groups contribute distinct discrete substructure of the extracellular matrix (McMahon et al, 2003). For a small number of collagen genes, with no distinctive sequence feature, but certainly critical to assembly or function of the extracellular matrix, such as dpy-2, 3, 7, 8, 10, 5 or 13, sqt-3, lon-3, bli-1, bli-2 or ram-4, loss of function causes a change in body shape (dumpy, squat, long, blistered), or leads to animals that roll when moving (helically twisted), or to male ray morphology defects. Some collagens that participate in the inner basement membranes such as let-2, emb-9, cle-1, mec-5 or unc-122 are essential for viability, or play critical roles in synaptogenesis or synaptic transmission, muscle attachment, cell migration and process guidance. But most other collagens probably have a redundant role, since loss of their function is apparently wild type, and alleles with visible effects in these genes are gain of function mutations. [Main specialists: Jim Kramer and Iain Johnstone][Wormbase] col-34 encodes a cuticle collagen protein and is a critical component of male tail cuticle organization affecting ray morphology.
Wormbase predicts one model, but Caenorhabditis elegans cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 4 spliced variants.
AceView synopsis, each blue text links to tables and details Expression: According to AceView, this gene is expressed at very high level, 8.6 times the average gene in this release, in L3, L4 larvae and in adult [Kohara and Riddle cDNAs]. The sequence of this gene is defined by 3 cDNA clones and 110 elements defined by RNA-seq, some from mixed (seen once). We annotate structural defects or features in 3 cDNA clones. Alternative mRNA variants and regulation: The gene contains 5 distinct gt-ag introns. Transcription produces 4 alternatively spliced mRNAs. The mRNAs appear to differ by presence or absence of 2 cassette exons, overlapping exons with different boundaries, splicing versus retention of 3 introns. 369 bp of this gene are antisense to spliced gene anticol-34artefact, raising the possibility of regulated alternate expression. Function: There are 4 articles specifically referring to this gene in PubMed. In addition we point below to 7 abstracts. This gene is associated to a phenotype (abnormal RAy Morphology). Proteins are expected to have molecular function (structural constituent of cuticle). Protein coding potential: The 4 spliced mRNAs putatively encode good proteins, altogether 4 different isoforms (1 COOH complete, 3 partial), some containing domains collagen triple helix repeat, nematode cuticle collagen, N-terminal [Pfam].
Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12. Map on chromosome IV, links to other databases and other names Map: This gene col-34 maps on chomosome IV at position +0.03 (interpolated). In AceView, it covers 1.07 kb, from 4244603 to 4243537 (WS190), on the reverse strand. Links to:WormBase, RNAiDB.
as Other names: The gene is also known ram-4, in Wormgenes/AceView by its positional name 4F8, in Wormbase by its cosmid.number name F36A4.10.
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript. Read more...
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table.
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink and ] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags to any single letter variant of the main . More explanations are given in the gene help file
The mRNAs diagrams with the aligned cDNA sequence accessions and their mismatches are available in the mRNA pages accessible from the tab at the top of the page, or here:
In Flash: .a, .b, .c, .d.
or in GIF: .a, .b, .c, .d
To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.
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