Summary
[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.
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.
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. Read more...
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table.
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. Proteins supported by a single continuous cDNA sequence 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.
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink and ] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags to any single letter variant of the main . More explanations are given in the gene help file
The mRNAs diagrams with the aligned cDNA sequence accessions and their mismatches are available in the mRNA pages accessible from the tab at the top of the page, or here:
In Flash: .a.
or in GIF: .a
Please see these 11 articles in PubMed.
In addition we found 48 papers for which we do not have a PubMed identifier
pm19123269
GB:AF177199_1 DPY-28 Is Required for Dosage Compensation and Chromosome Segregation at Meiosis Unpublished
GB:AF177199_2 Submitted (11-AUG-1999) Howard Hughes Medical Institute and Dept. of Molecular and Cell Biology, UC Berkeley, 401 Barker Hall, Berkeley, CA 94720, USA
[wbg8.3p40] mutations exhibiting differential expression in XO and XX animals.
[wbg9.1p75] further steps towards a genetic understanding of dosage compensation.
[wbg9.1p78] egl-16: a gene which unites the sex determination and dosage compensation pathways.
[wbg9.2p92] a maternal-effect mutation that results in XO-specific lethality.
[wbg9.3p47] y9: an XO-specific lethal mutation that suppresses the known XX-specific lethal mutations.
[wbg9.2p91] effects of duplicating X-linked genes on the general expression of the Xchromosome.
[wbg10.1p131] xol-1: a gene essential for male viability is involved in both sex determination and dosage compensation.
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'.
If you know more about this gene, or found errors, please share your knowledge. Thank you !
