Caenorhabditis elegans gene dpy-13, DumPY : shorter than wild-type, encoding collagen 3.
SUMMARY back to top
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-13 encodes a member of the collagen superfamily containing 20 copies of the collagen triple helix repeat; transcipt levels oscillate, peaking once during each larval stage.
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 2 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 40.9 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 [Johnstone et al, 1996]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: L1 or L2 larvae 28%, L3 to adult 71%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 41 cDNA clones and 497 elements defined by RNA-seq, some from l2 (seen 14 times), l4 (11), mixed (5). We annotate structural defects or features in 17 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 3 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. There are 3 validated alternative polyadenylation sites (see the diagram).
Function: There are 13 articles specifically referring to this gene in PubMed. In addition we point below to 49 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 nucleus. The gene interacts with 4 other genes (DPY-2, DPY-5, DPY-7, DPY-10).
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 COOH complete), some containing domains collagen triple helix repeat, nematode cuticle collagen, N-terminal [Pfam], a vacuolar domain [Psort2].

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 dpy-13 maps on chomosome IV at position +0.00 (interpolated). In AceView, it covers 1.13 kb, from 4235614 to 4236742 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known dpy-16, in Wormgenes/AceView by its positional name 4F1, in Wormbase by its cosmid.number name F30B5.1, in NextDB, the Nematode expression pattern database, as CEYK1902.
          Complete gene on genome diagram: back to top
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.
Compact gene diagram back to top
Gene dpy-13 5' 3' encoded on plus strand of chromosome IV from 4,235,614 to 4,236,742 a b 500bp 0 91 bp exon 91 bp exon 58 bp [gt-ag] intron 22 GenBank accessions 655 bp exon 50 bp [gt-ag] intron 31 GenBank accessions 240 bp exon 37 accessions, some from l2 (seen 13 times) l4 (10), mixed (5) capped 5' end, 14 accessions Validated 3' end, 13894 accessions 240 bp exon 58 bp exon 58 bp exon 149 bp [gt-ag] intron 2 GenBank accessions 176 bp exon 499 accessions Validated 3' end, 27 accessions Validated 3' end, 8 accessions 176 bp exon 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.
Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
Downstream sequence
a 986 bp 302 aa 10 bp 67 bp 2kb including Promoter 1094 bp 1kb
b 234 bp 71 aa 16 bp 2kb 383 bp 1kb

Gene neighbors and Navigator on chromosome IV back to top
dpy-13 D C I P ttr-20 C ama-1 D C I R P 4F3 4F10 C 4E982 C C srbc-70 C 4E994 P D C P col-34 5kb 0 4E981, 24 accessions, 4 variants dpy-13, 538 accessions 2 variants ttr-20, 13 accessions ama-1, 54 accessions, 5 variants 4F3, 0 accession srbc-72, 0 accession 4F2, 2 accessions 4F4, 1 accession 4F10, 0 accession 4E982, 6 accessions srbc-71, 4 accessions 2 variants srbc-70, 0 accession 4E994, 31 accessions, 4 variants 4F6, 3 accessions col-34, 113 accessions 4 variants ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography back to top
Please see these 13 articles in PubMed.
In addition we found 49 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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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