Caenorhabditis elegans gene dpy-21, DumPY : shorter than wild-type, encoding round spermatid basic protein 1-like CRA a.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
SUMMARY back to top
Summary
[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, 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 summary
Expression: According to AceView, this gene is well expressed, 1.2 times the average gene in this release, at all stages of development [Kohara cDNAs]. The sequence of this gene is defined by 16 cDNA clones. We annotate structural defects or features in 2 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. The mRNAs appear to differ by by presence or absence of a cassette exon.
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete, 1 COOH complete), some containing a coiled coil stretch [Psort2].
Function: There are 9 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). Proteins are expected to localize in nucleus.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
Map on chromosome CHROMOSOME_V, links to other databases and other names back to top ?
Map: This gene dpy-21 maps on chomosome V at position +13.19 (interpolated). In AceView, it covers 12.89 kb, from 17949149 to 17936262 (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.
Closest AceView homologs in other species back to top ?
The closest human genes, according to BlastP, are the AceView genes RSBN1L (e=9 10^-74), RSBN1 (e=9 10^-74).
The closest mouse genes, according to BlastP, are the AceView genes Rsbn1l (e=3 10^-74), Rsbn1andPhtf1 (e=3 10^-72)
Complete gene on genome diagram:               (in true scale, with colored introns) back to top
Compact gene diagram back to top
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 cDNA clones supporting each intron. Superimposed introns of the same color are identical, of different colors are different.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. 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. Details on tissue of origin for each intron and exon is available from the intron and exons table. Good predicted proteins are in pink, yellow proteins may be partial or unconvincing, green are uORFs. Proteins supported by a single continuous GenBank accession 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.
More legend
Sequences back to top
What is known about the gene and its neighbors on chromosome CHROMOSOME_V back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         (see the Legend)
Annotated mRNA diagrams back to top
Bibliography back to top
? Gene Summary Gene on genome mRNA:.a, .b Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function and related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function and 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 and 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 all variants, their summarized annotations, 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. Merci !