Caenorhabditis elegans essential gene csn-2, encoding constitutive photomorphogenic COP9 SigNalosome subunit.
SUMMARY back to top
[Wormbase] csn-2 encodes a homolog of COP9 signalosome complex subunit 2 that affects embryonic viability and growth rate.
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 2 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 6.8 times the average gene in this release, mostly from L1 larvae to adult [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 1%, L1 or L2 larvae 27%, L3 to adult (including dauer) 72%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 76 cDNA clones and 13 elements defined by RNA-seq, some from mixed (seen 26 times), l2 (16), l1 (13), l4 (9). We annotate structural defects or features in 8 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 5 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. Variant a is transpliced to SL7, SL1, SL6, b to SL1, SL2, SL3, SL4, SL7, SL8, SL6, SL5. There are 2 validated alternative polyadenylation sites (see the diagram). 260 bp of this gene are antisense to spliced gene 1G600, raising the possibility of regulated alternate expression.
Function: There are 5 articles specifically referring to this gene in PubMed. This essential gene is associated to a phenotype (Embryonic Lethal, SLow growth, CYtoKinesis defect, excessive blebbing in early embryo, ectopic cytokinetic furrow). Functionally, the gene has been proposed to participate in a process (cytokinesis). Proteins are expected to localize in nucleus. These proteins appear to interact with another protein (CSN-1).
Protein coding potential: The 2 spliced mRNAs putatively encode the same good protein, some containing proteasome component region PCI domain [Pfam], a second peroximal domain [Psort2].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome I, links to other databases and other names
Map: This essential gene csn-2 maps on chomosome I at position +0.65 (interpolated). In AceView, it covers 4.23 kb, from 6022662 to 6026891 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1G601, in Wormbase by its cosmid.number name B0025.2, in NextDB, the Nematode expression pattern database, as CEYK5977.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene COPS2.
The closest mouse gene, according to BlastP, is the AceView gene Cops2 (e= 10-150).
The closest A.thaliana gene, according to BlastP, is the AceView gene FUS12
          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 csn-2 5' 3' encoded on plus strand of chromosome I from 6,022,662 to 6,026,891 a b 1kb 0 65 bp exon 65 bp exon 260 bp [gt-ag] intron 62 GenBank accessions 256 bp exon 364 bp [gt-ag] intron 60 GenBank accessions 417 bp exon 1195 bp [gt-ag] intron 33 GenBank accessions 286 bp exon 296 bp [gt-ag] intron 62 GenBank accessions 301 bp exon 471 bp [gt-ag] intron 65 GenBank accessions 315 bp exon 39 accessions, some from mixed (seen 8 times) l1 (4), l2 (3) Transpliced 5' end, 3 accessions Validated 3' end, 22 accessions 315 bp exon 58 bp exon 58 bp exon 260 bp [gt-ag] intron 62 GenBank accessions 256 bp exon 364 bp [gt-ag] intron 60 GenBank accessions 417 bp exon 1195 bp [gt-ag] intron 33 GenBank accessions 286 bp exon 296 bp [gt-ag] intron 62 GenBank accessions 301 bp exon 471 bp [gt-ag] intron 65 GenBank accessions 307 bp exon 50 accessions, some from mixed (seen 18 times) l2 (13), l1 (9), l4 (9) Transpliced 5' end, 50 accessions Validated 3' end, 53 accessions 307 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 1640 bp 495 aa 23 bp 129 bp 2kb including Promoter 4226 bp 1kb
b 1625 bp 495 aa 16 bp 121 bp 2kb including Promoter 4211 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
1G583 C P 1G597 D C P csn-2 D C I P 1G605 C let-512 D C I R P 1G615 C 1G621 C I R P 1G613 C R P 1G584 C I P rnf-1 P D C R P ceh-2 5kb 0 1G583, 6 accessions 1G597, 31 accessions, 4 variants csn-2, 89 accessions, 2 variants 1G605, 22 accessions, 2 variants let-512, 53 accessions 4 variants 1G615, 15 accessions, 2 variants 1G621, 28 accessions, 2 variants 1G613, 6 accessions 1G580, 0 accession unc-94, 67 accessions 9 variants 1G584, 24 accessions, 3 variants rnf-1, 118 accessions 2 variants 1G600, 3 accessions ceh-2, 18 accessions 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 5 articles in PubMed.
? Gene Summary Gene on genome mRNA:.a, .b 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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