Caenorhabditis elegans essential gene dpy-28, encoding mutant dosage compensation protein DPY-28, similar to XCAP-D2, DumPY : shorter than wild-type.
SUMMARY back to top
[Wormbase] dpy-28 encodes a non-SMC condensin subunit homolog, similar to XCAP-D2 in Xenopus, Cnd1 in S. pombe, and Ycs4p in S. cerevisiae, that is required for negative, chromosome-wide regulation of X-chromosomal genes in XX but not XO animals (dosage compensation), and for some undetermined aspect of body morphogenesis; DPY-28 is part of a multiprotein 'dosage compensation' complex with DPY-26, DPY-27 and MIX-1.
Wormbase predicts one model

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is expressed at high level, 3.7 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 30%, L1 or L2 larvae 10%, L3 to adult 59%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 24 cDNA clones and 25 elements defined by RNA-seq, some from embryo (seen 9 times), mixed (8), l1 (2). We annotate structural defects or features in 9 cDNA clones.
The gene contains 15 distinct gt-ag introns. Transcription produces one mRNA. Variant a is transpliced to SL2, SL3, SL4. There are 3 validated alternative polyadenylation sites (see the diagram).
Function: There are 11 articles specifically referring to this gene in PubMed. In addition we point below to 48 abstracts. This essential gene is associated to a phenotype (DumPY : shorter than wild-type, Embryonic Lethal, UNCoordinated locomotion, oogenic protein copurified with chromatin). This protein appears to interact with other proteins (DPY-26, DPY-27, MIX-1). The gene interacts with 3 other genes (LIN-14, SDC-3, XOL-1).
The spliced mRNA putatively encodes a good protein, 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 III, links to other databases and other names
Map: This essential gene dpy-28 maps on chomosome III at position +4.13 (interpolated). In AceView, it covers 14.24 kb, from 10763013 to 10777248 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3L865, in Wormbase by its cosmid.number name Y39A1B.3, in NextDB, the Nematode expression pattern database, as CEYK1117.
          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-28 5' 3' encoded on plus strand of chromosome III from 10,763,011 to 10,777,232 a 1 2kb 0 144 bp exon 144 bp exon 668 bp [gt-ag] intron 2 GenBank accessions 218 bp exon 854 bp [gt-ag] intron 3 GenBank accessions 275 bp exon 652 bp [gt-ag] intron 4 GenBank accessions 370 bp exon 782 bp [gt-ag] intron 4 GenBank accessions 524 bp exon 824 bp [gt-ag] intron 5 GenBank accessions 191 bp exon 48 bp [gt-ag] intron 7 GenBank accessions 90 bp exon 280 bp [gt-ag] intron 7 GenBank accessions 160 bp exon 46 bp [gt-ag] intron 9 GenBank accessions 850 bp exon 769 bp [gt-ag] intron 5 GenBank accessions 661 bp exon 773 bp [gt-ag] intron 4 GenBank accessions 156 bp exon 319 bp [gt-ag] intron 4 GenBank accessions 273 bp exon 1183 bp [gt-ag] intron 3 GenBank accessions 87 bp exon 47 bp [gt-ag] intron 4 GenBank accessions 79 bp exon 565 bp [gt-ag] intron 4 GenBank accessions 207 bp exon 1471 bp [gt-ag] intron 4 GenBank accessions 670 bp exon 49 accessions, some from embryo (seen 9 times) mixed (8), l1 (2) Transpliced 5' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 28 accessions Validated 3' end, 7 accessions 670 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 4955 bp 1499 aa 16 bp 439 bp 2kb including Promoter 14236 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
3L839 D C I R P 3L841 C R 3L851 C R dpy-28 D C I R P ptr-19 D C R P clec-163 D C I R P ran-1 D C I R P hpl-2 D C I P rnf-113 D C P 3L848 5kb 0 rib-2, 38 accessions, 4 variants 3L839, 49 accessions, 2 variants 3L841, 11 accessions 3L851, 33 accessions, 4 variants dpy-28, 49 accessions ptr-19, 31 accessions 3 variants ran-1, 311 accessions 2 variants hpl-2, 49 accessions, 7 variants rnf-113, 69 accessions 5 variants 3L848, 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 11 articles in PubMed.
In addition we found 48 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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