Caenorhabditis elegans essential gene dpy-27, encoding chromosome condensation protein, required for dosage compensation; part of a complex including SDC-3/Zinc finger protein and MIX-1 which represses the expression of X chromosomes genes in XX hermaphrodites (but not XO males), by localizing specifically to sites of transcription initiation, DumPY : shorter than wild-type.
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SUMMARY back to top
Summary
[Wormbase] dpy-27 encodes an ATP-binding protein that is a homolog of the SMC4 subunit of mitotic condensin; DPY-27, in combination with other proteins including MIX-1, act as a unit to repress X-linked gene expression during hermaphrodite dosage compensation; in XX oocytes and early embryos, DPY-27 exhibits diffuse nuclear localization, but by the 30-cell stage of embryogenesis, DPY-27 specifically localizes to X chromosomes; in XO animals at all stages, DPY-27 remains diffusely nuclear; the sex-specific localization of DPY-27 to X chromosomes is dependent upon wild-type activity of xol-1, as DPY-27 mislocalizes to the X chromosome of XO embryos in a xol-1 mutant background.
Wormbase predicts one model, 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 very high level, 4.1 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 19%, L1 or L2 larvae 14%, L3 to adult (including dauer) 67%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 26 cDNA clones and 28 elements defined by RNA-seq, some from mixed (seen 10 times), embryo (7), l1 (4), dauer (once), l4 (once). We annotate structural defects or features in 3 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 13 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. Variant a is transpliced to SL1. There are 2 probable alternative promotors and 7 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, overlapping exons with different boundaries.
Function: There are 16 articles specifically referring to this gene in PubMed. In addition we point below to 49 abstracts. This essential gene is associated to a phenotype (DumPY : shorter than wild-type, EGg Laying defective, embryonic lethal, partial, Larval arrest, Sterile adult, UNCoordinated locomotion, X chromosome dosage compensation defect, affects axonal growth or guidance). Proteins are expected to have molecular functions (ATP binding activity, protein binding activity) and to localize in chromosome. These proteins appear to interact with other proteins (DPY-28, MIX-1). The gene interacts with 6 other genes (DPY-26, LIN-14, MIX-1, SDC-1, SDC-3, XOL-1).
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (1 complete, 2 partial), some containing domains SMCs flexible hinge, RecF/RecN/SMC protein, N-terminal [Pfam], a second peroximal domain, 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-27 maps on chomosome III at position -5.12 (interpolated). In AceView, it covers 6.91 kb, from 3819658 to 3812751 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 3E904, in Wormbase by its cosmid.number name R13G10.1, in NextDB, the Nematode expression pattern database, as CEYK342.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene SMC4.
The closest mouse gene, according to BlastP, is the AceView gene Smc4 (e=4 10-82).
The closest A.thaliana gene, according to BlastP, is the AceView gene ATSMC3
          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-27 5' 3' encoded on minus strand of chromosome III from 3,819,658 to 3,812,751 a b c 1 2kb 0 428 bp exon 428 bp exon 49 bp [gt-ag] intron 3 GenBank accessions 102 bp exon 82 bp [gt-ag] intron 2 GenBank accessions 359 bp exon 184 bp [gt-ag] intron 1 GenBank accession 756 bp exon 63 bp [gt-ag] intron 6 GenBank accessions 238 bp exon 206 bp [gt-ag] intron 6 GenBank accessions 209 bp exon 48 bp [gt-ag] intron 4 GenBank accessions 451 bp exon 131 bp [gt-ag] intron 4 GenBank accessions 438 bp exon 319 bp [gt-ag] intron 5 GenBank accessions 278 bp exon 67 bp [gt-ag] intron 5 GenBank accessions 349 bp exon 104 bp [gt-ag] intron 5 GenBank accessions 541 bp exon 106 bp [gt-ag] intron 13 GenBank accessions 1400 bp exon 52 accessions, some from mixed (seen 10 times) embryo (7), l1 (4), dauer (once) l4 (once) Transpliced 5' end, 2 accessions Validated 3' end, 11 accessions Validated 3' end, 11 accessions Validated 3' end, 1 accession Validated 3' end, 13 accessions Validated 3' end, 1 accession Validated 3' end, 5 accessions Validated 3' end, 13 accessions 1400 bp exon 100 bp exon 119 bp [gt-ag] intron 1 GenBank accession 1 accession 320 bp exon 32 bp exon 32 bp exon 126 bp [gt-ag] intron 1 GenBank accession 1 accession 201 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.
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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
unit
pre-mRNA		 Downstream sequence
a 5549 bp 1469 aa 1137 bp 2kb including Promoter 6908 bp 1kb
b 420 bp 140 aa 2kb 539 bp 1kb
c 233 bp 70 aa 23 bp 2kb possibly including promoter 359 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
amx-1 C P cyp-25A1 C P cyp-25A2 C P C R P mtm-3 C I P xbx-5 C P toh-1 D C I R P dpy-27 C 3E916 I P 3E918 P C P cyp-25A3 5kb 0 amx-1, 45 accessions, 2 variants cyp-25A1, 19 accessions cyp-25A2, 38 accessions 3 variants 3E890, 1 accession mtm-3, 118 accessions 13 variants xbx-5, 6 accessions toh-1, 19 accessions dpy-27, 54 accessions 3 variants 3E916, 23 accessions 3E918, 0 accession 3E920, 19 accessions, 3 variants cyp-25A3, 30 accessions 3 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 16 articles in PubMed.
In addition we found 49 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'.

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