Caenorhabditis elegans gene dpy-5, DumPY : shorter than wild-type, encoding nematode cuticle collagen, N-terminal and collagen triple helix repeat precursor family member.
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-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.
Function: 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
Map: 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, NextDB, RNAiDB.
Other names: 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, COL4A2, COL21A1, COL6A3, COL4A5, COL6A2, ADIPOQ, COL2A1, COL4A1, COL9A2, SCARA5, C1QB, MARCO, SPATA13andC1QTNF9, SFTPA1.
The closest mouse genes, according to BlastP, are the AceView genes Col24a1 (e=0.017), Col6a3 (e=0.022), Cthrc1 (e=0.036), Col6a2 (e=0.23)
          Complete gene on genome diagram: back to top
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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-5 5' 3' encoded on minus strand of chromosome I from 5,433,057 to 5,432,151 100bp 0 907 bp exon 907 bp exon Transpliced 5' end, 9 accessions Validated 3' end, 288 accessions 907 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 3' UTR Upstream sequence Transcription
Downstream sequence
a 907 bp 284 aa 49 bp 2kb including Promoter 907 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
1F991 I P 1F995 D C R P 1F999 C R 1G3 C P D C R P coq-1 C R 1F986 D C I R P 1F990 D C I R P atp-3 D C I P dpy-5 C 1G2 C P 1G10 5kb 0 1F991, 33 accessions 1F995, 5 accessions, 2 variants 1F999, 73 accessions, 3 variants 1G3, 9 accessions 1F993, 1 accession 1G18, 7 accessions, 2 variants 1G20, 2 accessions frm-4, 62 accessions, 9 variants coq-1, 29 accessions, 3 variants 1F986, 48 accessions, 4 variants 1F990, 41 accessions, 7 variants atp-3, 110 accessions 4 variants dpy-5, 94 accessions 1G2, 37 accessions, 3 variants 1G10, 0 accession 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 15 articles in PubMed.
In addition we found 91 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA 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 see the mRNA diagram, sequence and annotation, click the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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