Caenorhabditis elegans gene dpy-21, DumPY : shorter than wild-type.
SUMMARY back to top
[Wormbase] dpy-21 encodes a novel, conserved protein with a proline-rich N terminus; dpy-21 affects RNA levels of X-linked dosage-compensated genes, body length in hermaphrodites, and fertility and male tail development in males; DPY-21 interacts in vivo with DPY-27 and SDC-3, members of the dosage compensation complex, and like members of the dosage compensation complex, is diffusely localized in nuclei of XX embryos containing <40 cells, but then specifically localizes to X chromosomes of XX embryos with >40 cells, remaining on the X throughout development; in XO embryos, DPY-21 is dispersed throughout the nucleus in multiple foci that are not coincident with the X chromosome; in hermaphrodites, localization of DPY-21 to the X chromosome requires activity of SDC-2, SDC-3, DPY-26, DPY-27, and DPY-28; DPY-21 is not, however, required reciprocally for the stability or localization of these other dosage compensation proteins; in addition, unlike SDC-3 and other members of the dosage compensation complex, DPY-21 is not recruited to the autosomal her-1 regulatory region, suggesting that DPY-21 is not part of the gene-specific complex that represses her-1 expression in hermaphrodites.
Wormbase predicts one model from 2 genes, 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 3 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 2.6 times the average gene in this release, at all stages of development [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 22%, L1 or L2 larvae 9%, L3 to adult 69%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 16 cDNA clones and 18 elements defined by RNA-seq, some from mixed (seen 7 times), embryo (5), l2 (once). We annotate structural defects or features in 6 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 12 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. Variant a is transpliced to SL2. There are 2 probable alternative promotors and 2 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of a cassette exon, overlapping exons with different boundaries.
Function: There are 10 articles specifically referring to this gene in PubMed. In addition we point below to 47 abstracts. This gene is associated to a phenotype (DumPY : shorter than wild-type). The gene interacts with 8 other genes (HER-1, LET-2, LIN-14, LIN-15A, LIN-15B, SDC-3, TRA-1, XOL-1).
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (1 complete, 2 partial), some containing a coiled coil stretch [Psort2].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome V, links to other databases and other names
Map: This gene dpy-21 maps on chomosome V at position +13.19 (interpolated). In AceView, it covers 12.89 kb, from 17949149 to 17936256 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5S418, in Wormbase by its cosmid.number name Y59A8B.1, in NextDB, the Nematode expression pattern database, as CEYK3009.
          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-21 5' 3' encoded on minus strand of chromosome V from 17,949,149 to 17,936,256 a b c 1 2kb 0 178 bp exon 178 bp exon 48 bp [gt-ag] intron 3 GenBank accessions 51 bp exon 863 bp [gt-ag] intron 3 GenBank accessions 95 bp exon 167 bp [gt-ag] intron 3 GenBank accessions 150 bp exon 543 bp [gt-ag] intron 3 GenBank accessions 68 bp exon 479 bp [gt-ag] intron 2 GenBank accessions 3412 bp exon 2122 bp [gt-ag] intron 3 GenBank accessions 246 bp exon 1001 bp [gt-ag] intron 2 GenBank accessions 292 bp exon 991 bp [gt-ag] intron 2 GenBank accessions 324 bp exon 672 bp [gt-ag] intron 4 GenBank accessions 72 bp exon 360 bp [gt-ag] intron 4 GenBank accessions 760 bp exon 21 accessions, some from mixed (seen 7 times) embryo (5), l2 (once) Transpliced 5' end, 1 accession Validated 3' end, 4 accessions Validated 3' end, 5 accessions 760 bp exon 23 bp exon 48 bp [gt-ag] intron 3 GenBank accessions 51 bp exon 863 bp [gt-ag] intron 3 GenBank accessions 95 bp exon 167 bp [gt-ag] intron 3 GenBank accessions 150 bp exon 543 bp [gt-ag] intron 3 GenBank accessions 68 bp exon 6013 bp [gt-ag] intron 1 GenBank accession 246 bp exon 246 bp exon 1001 bp [gt-ag] intron 2 GenBank accessions 292 bp exon 991 bp [gt-ag] intron 2 GenBank accessions 324 bp exon 672 bp [gt-ag] intron 4 GenBank accessions 72 bp exon 360 bp [gt-ag] intron 4 GenBank accessions 191 bp exon 1 accession 191 bp exon 785 bp exon 785 bp exon 2215 bp [gt-ag] intron 1 GenBank accession 243 bp exon 1 accession 243 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 uORF Upstream sequence Transcription
Downstream sequence
a 5648 bp 1641 aa 154 bp 568 bp 2kb including Promoter 12894 bp 1kb
b 1512 bp 349 aa 463 bp 132 bp 2kb possibly including promoter 12170 bp 1kb
c 1028 bp 329 aa 39 bp 2kb probably including promoter 3243 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
5S403 C 5S413 D C R P 5S411c R 5S409 5S411 5S411a 5S411b 5S411d 5S433 D C I R P dpy-21 C R P gck-3 5kb 0 5S401, 76 accessions, 10 variants 5S403, 0 accession 5S413, 35 accessions, 4 variants 5S411c, 0 accession 5S409, 0 accession 5S411, 0 accession 5S411a, 0 accession 5S411b, 0 accession 5S411d, 0 accession 5S433, 0 accession dpy-21, 34 accessions 3 variants gck-3, 20 accessions, 5 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 10 articles in PubMed.
In addition we found 47 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c 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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !