Caenorhabditis elegans gene cpr-5, encoding cysteine PRotease cathepsin B-like.
SUMMARY back to top
[Wormbase] cpr-5 encodes a cysteine protease.
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, 22.3 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 29%, L3 to adult 70%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 185 cDNA clones and 109 elements defined by RNA-seq, some from l2 (seen 14 times), mixed (12), l4 (5), l1 (2), whole worm (once). We annotate structural defects or features in 6 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 3 distinct introns (2 gt-ag, 1 gc-ag). Transcription produces 2 alternatively spliced mRNAs. There are 2 validated alternative polyadenylation sites (see the diagram).
Function: There are 4 articles specifically referring to this gene in PubMed. In addition we point below to 3 abstracts. 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 (extracellular space, mitochondrion). These proteins appear to interact with other proteins (CIF-1, KLP-15, NPP-11).
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), some containing peptidase C1A, papain C-terminal domain [Pfam]; 1 of the 2 complete proteins appears to be secreted.

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 gene cpr-5 maps on chomosome V at position -20.18 (interpolated). In AceView, it covers 1.38 kb, from 1133968 to 1132591 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5B612, in Wormbase by its cosmid.number name W07B8.5, in NextDB, the Nematode expression pattern database, as CEYK1544.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene CTSB (e=4 10-33).
The closest mouse gene, according to BlastP, is the AceView gene Ctsb (e=4 10-34).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT1G02305 (e=9 10-33), AT1G02300 (e=2 10-31), AT4G01610 (e=4 10-31)
          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-5 5' 3' encoded on minus strand of chromosome V from 1,133,968 to 1,132,592 a b 500bp 0 470 bp exon 470 bp exon 186 bp [gt-ag] intron 130 GenBank accessions 242 bp exon 48 bp [gt-ag] intron 81 GenBank accessions 432 bp exon 292 accessions, some from l2 (seen 13 times) mixed (12), l4 (5), l1 (2) whole worm (once) capped 5' end, 13 accessions Validated 3' end, 530 accessions 432 bp exon 231 bp exon 231 bp exon 231 bp exon 56 bp [gc-ag] intron 1 GenBank accession 432 bp exon 432 bp exon 1 accession Validated 3' end, 530 accessions 432 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 1144 bp 344 aa 12 bp 97 bp 2kb including Promoter 1378 bp 1kb
b 663 bp 129 aa 176 bp 97 bp 2kb possibly including promoter 719 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
5B607 C I P 5B617 C cutl-22 C cmd-1 D C I R P 5B587 5B591 C R 5B610 C I R P cpr-5 5kb 0 5B607, 19 accessions, 4 variants 5B617, 10 accessions cutl-22, 10 accessions 2 variants cmd-1, 263 accessions 3 variants 5B587, 0 accession 5B591, 1 accession 5B610, 45 accessions cpr-5, 294 accessions 2 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 4 articles in PubMed.
In addition we found 3 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes CI

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 !