Caenorhabditis elegans essential gene cpr-3, encoding cysteine PRotease cathepsin B-like.
SUMMARY back to top
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 well expressed, 1.4 times the average gene in this release, from L2 larvae to adult [Kohara cDNAs], but not in dauers [SAGE, Jones et al, 2001]. 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 11%, L3 to adult 87%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 13 cDNA clones and 5 elements defined by RNA-seq, some from mixed (seen 3 times), l4 (2), l2 (once).
Alternative mRNA variants and regulation: The gene contains 4 distinct gt-ag introns. Transcription produces 3 alternatively spliced mRNAs. There are 2 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ splicing versus retention of 2 introns.
Function: There are 5 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. This essential gene is associated to a phenotype (Embryonic Lethal, Up-regulated upon pathogen infection). Functionally, the gene has been proposed to participate in a process (proteolysis and peptidolysis). Proteins are expected to have molecular function (cysteine-type peptidase activity) and to localize in various compartments (cytoplasm, extracellular space).
Protein coding potential: The 3 spliced mRNAs putatively encode good proteins, altogether 3 different isoforms (2 complete, 1 COOH complete), some containing peptidase C1A, papain C-terminal domain [Pfam]; 1 of the 2 complete proteins appears to be secreted.
Isoform cpr-3.b1 is annotated using as Met a Kozak-compatible a..ACG. start, thereby gaining 121 amino acids N-terminal to the first AUG.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome V, links to other databases and other names
Map: This essential gene cpr-3 maps on chomosome V at position +7.30 (interpolated). In AceView, it covers 1.86 kb, from 15298652 to 15296791 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5P778, in Wormbase by its cosmid.number name T10H4.12, in NextDB, the Nematode expression pattern database, as CEYK5601.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene CTSB (e=6 10-69).
The closest mouse gene, according to BlastP, is the AceView gene Ctsb (e=2 10-66).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT4G01610 (e=5 10-48), AT1G02300 (e=8 10-46), AT1G02305 (e=10-44)
          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 cpr-3 5' 3' encoded on minus strand of chromosome V from 15,298,652 to 15,296,822 a b c 500bp 0 81 bp exon 81 bp exon 48 bp [gt-ag] intron 6 GenBank accessions 667 bp exon 406 bp [gt-ag] intron 7 GenBank accessions 332 bp exon 44 bp [gt-ag] intron 8 GenBank accessions 284 bp exon 16 accessions, some from mixed (seen 3 times) l2 (once), l4 (once) capped 5' end, 1 accession Validated 3' end, 5 accessions Validated 3' end, 5 accessions 284 bp exon 1405 bp exon 1405 bp exon 44 bp [gt-ag] intron 8 GenBank accessions 231 bp exon 1 accession from l4 Validated 3' end, 5 accessions 231 bp exon 667 bp exon 127 bp [gt-ag] intron 1 GenBank accession 609 bp exon 1 accession 609 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 1364 bp 370 aa 60 bp 191 bp 2kb including Promoter 1862 bp 1kb
b 1636 bp 132 aa 1099 bp 138 bp 2kb possibly including promoter 1680 bp 1kb
c 1276 bp 223 aa 604 bp 2kb 1403 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
srx-51 C 5P793 C nhr-246 C C 5P761 5P794 C C srw-17 D P srw-18 C srw-19 C P cyp-34A1 C P cyp-34A2 C str-96 D C R P cpr-3 C 5P782 C srx-48 C C C srz-10 C srt-22 5kb 0 srx-51, 3 accessions 5P793, 0 accession nhr-246, 10 accessions 3 variants 5P803, 1 accession 5P761, 0 accession 5P794, 0 accession srw-16, 0 accession srw-17, 15 accessions 3 variants srw-18, 0 accession srw-19, 4 accessions cyp-34A1, 23 accessions cyp-34A2, 25 accessions 2 variants str-96, 0 accession cpr-3, 18 accessions, 3 variants 5P782, 9 accessions srx-48, 2 accessions 5P784b, 0 accession 5P784a, 0 accession srz-10, 3 accessions srt-22, 3 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.
In addition we found 2 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 DC

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'.

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