Caenorhabditis elegans essential gene ced-3, encoding cell death protein, Caspase, ICE-like apoptotic protease, CEll Death abnormality.
SUMMARY back to top
[Wormbase] The ced-3 gene encodes a protease required for apoptosis.
Wormbase predicts one model

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is expressed at high level, 1.7 times the average gene in this release, in embryos [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 100%, L3 to adult 0%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 13 cDNA clones and 9 elements defined by RNA-seq, some from embryo (seen 4 times).
The gene contains 7 distinct gt-ag introns. Transcription produces one mRNA. Variant a is transpliced to SL1. There are 4 validated alternative polyadenylation sites (see the diagram).
Function: There are 181 articles specifically referring to this gene in PubMed. In addition we point below to 166 abstracts. This essential gene is associated to a phenotype (CEll Death abnormality, Sterile adult). Functionally, the gene has been proposed to participate in processes (proteolysis and peptidolysis, regulation of apoptosis). Proteins are expected to have molecular functions (cysteine-type endopeptidase activity, protein binding activity) and to localize in intracellular. This protein appears to interact with other proteins (CED-4, CED-9, CED-12, DCT-1, FEM-1, MAC-1). The gene interacts with 35 other genes (ABL-1, BEC-1, BMK-1, CAR-1, CDL-1, CED-1, CED-2, CED-5, CED-7, CED-8, CED-9, CED-11, CED-13, CES-1, CES-2, CPB-3, CPS-6, CRN-1, CRN-2, CRN-4, CUP-5, DRP-1, EGL-1, EGL-47, GLD-1, HAM-1, MEV-1, NUC-1, PMK-3, SEL-10, SEL-12, SET-21, TRA-1, URI-1, WAH-1).
The spliced mRNA putatively encodes a good protein, containing domains Caspase Recruitment, Peptidase C14, caspase catalytic [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome IV, links to other databases and other names
Map: This essential gene ced-3 maps on chomosome IV at position +8.46 (interpolated). In AceView, it covers 5.86 kb, from 13204099 to 13198245 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 4N964, in Wormbase by its cosmid.number name C48D1.2, in NextDB, the Nematode expression pattern database, as CEYK4316.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes CASP3 (e=7 10-33), CASP7 (e=8 10-33), TMEM139andCASP2 (e=10-30), PLA2G12AandCASP6 (e=4 10-30).
The closest mouse genes, according to BlastP, are the AceView genes Casp7 (e=10-33), Casp2 (e=2 10-30), Casp3 (e=2 10-30), Casp6 (e=2 10-28)
          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 ced-3 5' 3' encoded on minus strand of chromosome IV from 13,204,099 to 13,198,245 a 1 2kb 0 200 bp exon 200 bp exon 63 bp [gt-ag] intron 8 GenBank accessions 146 bp exon 278 bp [gt-ag] intron 8 GenBank accessions 254 bp exon 1188 bp [gt-ag] intron 7 GenBank accessions 332 bp exon 912 bp [gt-ag] intron 2 GenBank accessions 214 bp exon 54 bp [gt-ag] intron 3 GenBank accessions 128 bp exon 354 bp [gt-ag] intron 4 GenBank accessions 240 bp exon 476 bp [gt-ag] intron 5 GenBank accessions 1016 bp exon 22 accessions, some from embryo (seen 4 times) Transpliced 5' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 3 accessions Validated 3' end, 3 accessions 1016 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 2530 bp 503 aa 65 bp 953 bp 2kb including Promoter 5855 bp 1kb

Gene neighbors and Navigator on chromosome IV back to top
4N951 C 4N955 C P C C 4N958 D C I R P ced-3 P 4N970 C R P cho-1 C 5kb 0 4N951, 7 accessions 4N955, 11 accessions 4N995, 18 accessions, 2 variants 4N989, 0 accession 4N946, 2 accessions, 2 variants 4N952, 23 accessions 4N972, 0 accession lev-1, 15 accessions, 3 variants 4N958, 25 accessions, 5 variants ced-3, 22 accessions 4N970, 3 accessions, 2 variants cho-1, 46 accessions, 5 variants 4N990, 4 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 181 articles in PubMed.
In addition we found 166 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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !