Caenorhabditis elegans gene cps-6, CED-3 Protease Suppressor, encoding similar to endonuclease G.
SUMMARY back to top
[Wormbase] cps-6 encodes an ortholog of human mitochondrial endonuclease G (EndoG) that promotes apoptosis, and is required to degrade nicked (TUNEL-positive) DNA in apoptotic cells; transgenic CPS-6 is localized to mitochondria, but transgenic CPS-6 lacking a mitochondrial localization sequence is found in nuclei, and nuclei may be the in vivo target of CPS-6 after its activation by CED-3; CPS-6 has magnesium-dependent nuclease activity in vitro; cps-6(sm116) and cps-6(RNAi) animals have delayed CED-3-induced apoptosis, and cps-6(sm116) suppresses a constitutively active ced-3 transgene; cps-6(sm116) can be transgenically rescued by mouse EndoG; CPS-6 binds WAH-1 (an apoptosis-inducing factor ortholog) in vitro, WAH-1 binding enhances CPS-6's endonuclease activity, and constitutive transgenic coexpression of cps-6 with wah-1 induces cell death not seen with constitutive expression of either cps-6 or wah-1 alone; CPS-6 binds CRN-1 (a flap endonuclease ortholog) in vitro, and may form a large complex in vivo with CRN-1, CRN-4, CRN-5, CYP-13, and WAH-1; CRN-1 enhances CPS-6's endonuclease activity in vitro, CPS-6 enhances CRN-1's gap-dependent endonuclease and 5'-3' exonuclease activities, and cps-6 is required for excess cell deaths induced by a crn-1 transgene.
Wormbase predicts one model

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is well expressed, 1.3 times the average gene in this release, 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 58%, L3 to adult 39%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 7 cDNA clones and 10 elements defined by RNA-seq, some from l1 (seen 2 times), l2 (2), l4 (once). We annotate structural defects or features in 4 cDNA clones.
The gene contains 4 distinct gt-ag introns. Transcription produces one mRNA. Variant a is transpliced to SL1, SL2, SL3, SL4, SL5, SL6. 347 bp of this gene are antisense to spliced gene eif-3.H, raising the possibility of regulated alternate expression.
Function: There are 6 articles specifically referring to this gene in PubMed. In addition we point below to 3 abstracts. This gene is associated to a phenotype (CED-3 Protease Suppressor). Functionally, the gene has been proposed to participate in a process (DNA degradation in apoptosis). Proteins are expected to have molecular functions (endonuclease activity, nucleic acid binding activity) and to localize in cytoplasm. This protein appears to interact with another protein (WAH-1). The gene interacts with 6 other genes (2K881+CRN-3, CED-3, CED-4, CED-8, CRN-1, CRN-2).
The spliced mRNA putatively encodes a good protein, containing DNA/RNA non-specific endonuclease domain [Pfam], a vacuolar 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 gene cps-6 maps on chomosome I at position -1.30 (interpolated). In AceView, it covers 1.88 kb, from 4448462 to 4446586 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 1F14, in Wormbase by its cosmid.number name C41D11.8, in NextDB, the Nematode expression pattern database, as CEYK9485.
          Complete gene on genome diagram: back to top
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This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene cps-6 5' 3' encoded on minus strand of chromosome I from 4,448,462 to 4,446,586 a 1kb 0 127 bp exon 127 bp exon 46 bp [gt-ag] intron 7 GenBank accessions 177 bp exon 509 bp [gt-ag] intron 6 GenBank accessions 123 bp exon 56 bp [gt-ag] intron 7 GenBank accessions 155 bp exon 255 bp [gt-ag] intron 7 GenBank accessions 429 bp exon 17 accessions, some from l1 (seen 2 times) l2 (2), l4 (once) Transpliced 5' end, 5 accessions Validated 3' end, 22 accessions 429 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 1011 bp 308 aa 7 bp 77 bp 2kb including Promoter 1877 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
eif-3.H D C P eri-6 D C R P 1F27 1F28 C 1E998 D C I P cps-6 C P 1F16 C P 1F18 D C R P eri-7 5kb 0 1E995, 37 accessions, 3 variants eif-3.H, 20 accessions 2 variants eri-6, 45 accessions, 11 variants 1F27, 1 accession 1F28, 0 accession 1E998, 29 accessions, 6 variants cps-6, 17 accessions 1F16, 14 accessions, 2 variants 1F18, 14 accessions, 2 variants eri-7, 22 accessions, 6 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 6 articles in PubMed.
In addition we found 3 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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