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 are thought to form trimers or higher order polymers. They can be grouped into subfamilies according to homology (Johnstone, 2000). 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. During cuticle synthesis, the genes are expressed in a distinct temporal series, reiterated at each molt, and the temporal groups contribute distinct discrete substructure of the extracellular matrix: The early group of cuticle collagen genes is required for the formation of annuli, it includes DPY-2, 3, 7, 8 and 10, and peaks in mRNA abundance about 4 h before the new cuticle is secreted; these 5 proteins localise in the annuli of the outermost layer of cuticle, right above the actin bundles in the epidermal cell. The intermediate group includes DPY-5 and DPY-13, peaks about 2 hours later, and these collagens go below and in between the annuli (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 the DPY genes above, loss of function causes a change in body shape (dumpy, squat or long), or leads to animals that roll when moving (alae helically twisted), or to male ray morphology defects. Some collagens that participate in the inner basement membranes are essential for viability, or play a critical role in synaptogenesis, 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: Iain Johnstone and Jim Kramer; Don Riddle, Ann Rose, Bob Horvitz, Sidney Brenner][Wormbase] dpy-5 encodes a Group I cuticle procollagen; dpy-5 activity is required for wild-type body length, cuticle structure (width of the annuli), postembryonic growth rates, and reproduction; dpy-5 is described as an intermediate collagen gene, as its mRNA, which is present in all larval stages, adults, and dauer larvae, increases in abudance two hours prior to the secretion of each new cuticle; a dpy-5::gfp fusion gene is expressed in hypodermal cells from mid-to-late L1 larval stages to adulthood, with notably variable expression in the V lineage-derived seam cells; dpy-5 mutations suppress mutations in bli-4, which encodes a proprotein convertase that may process DPY-5 for normal cuticle production; in addition, dpy-5 is required for normal expression patterns of the COL-19, DPY-7, and DPY-13 cuticle collagens.
Wormbase predicts one model from 2 genes
AceView synopsis, each blue text links to tables and details
According to AceView, this gene is expressed at very high level
, 7.1 times the average gene in this release, mostly from L2 larvae to adult [Kohara cDNAs], in the intermediate group, peaking about 2 hours before cuticle secretion [McMahon et al, 2003]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: L1 or L2 larvae 41%, L3 to adult 58%. See the in situ hybridization pattern in Kohara NextDB
. The sequence
of this gene is defined by 19 cDNA clones
and 75 elements defined by RNA-seq, some from l2 (seen 7 times), l4 (2), mixed (2). We annotate structural defects or features
in one cDNA clone. Variant a is transpliced to SL1.
There are 15 articles
specifically referring to this gene in PubMed. In addition we point below
to 91 abstracts. This gene is associated to a phenotype
(DumPY : shorter than wild-type). Proteins are expected to have molecular function
(structural constituent of cuticle) and to localize
in extracellular space. The gene interacts
with 6 other genes (DPY-2, DPY-3, DPY-7, DPY-8, DPY-10, DPY-13). This gene contains domains
collagen triple helix repeat, nematode cuticle collagen, N-terminal [Pfam]; the complete protein appears to be secreted
Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
Map on chromosome I, links to other databases and other names
This gene dpy-5 maps on chomosome I at position +0.00 (interpolated). In AceView, it covers 0.91 kb
, from 5433057 to 5432151 (WS190), on the reverse strand.
Links to: WormBase
The gene is also known in Wormgenes/AceView by its positional name 1G0, in Wormbase by its cosmid.number name F27C1.8, in NextDB, the Nematode expression pattern database, as CEYK1557.
Closest AceView homologs in other species
The closest human genes
, according to BlastP, are the AceView genes CTHRC1
The closest mouse genes
, according to BlastP, are the AceView genes Col24a1
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.
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.
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.
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