Caenorhabditis elegans gene cpr-6, encoding cysteine PRotease related.
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SUMMARY back to top
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Wormbase predicts 3 models, 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 9 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 12.3 times the average gene in this release, at all stages of development [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 9%, L1 or L2 larvae 15%, L3 to adult 75%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 130 cDNA clones and 32 elements defined by RNA-seq, some from mixed (seen 11 times), l2 (5), embryo (4), l4 (4), l1 (once). We annotate structural defects or features in 5 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 19 distinct introns (18 gt-ag, 1 gc-ag). Transcription produces at least 9 alternatively spliced mRNAs. Variant a is transpliced to SL1. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 6 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 5 cassette exons, overlapping exons with different boundaries.
Function: There are 2 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. This gene is associated to a phenotype. 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).
Protein coding potential: The 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (5 complete, 2 COOH complete, 2 partial), some containing peptidase C1A, papain C-terminal domain [Pfam]; 4 of the 5 complete proteins appear to be secreted.
Isoform cpr-6.i is annotated using as Met a Kozak-compatible a..AGGg start, thereby gaining 62 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 X, links to other databases and other names
Map: This gene cpr-6 maps on chomosome X at position -2.87 (interpolated). In AceView, it covers 2.04 kb, from 6606972 to 6609012 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name XH227, in Wormbase by its cosmid.number name C25B8.3, in NextDB, the Nematode expression pattern database, as CEYK2175.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene CTSB.
The closest mouse gene, according to BlastP, is the AceView gene Ctsb (e=10-81).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT4G01610, AT1G02300, AT1G02305
          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-6 5' 3' encoded on plus strand of chromosome X from 6,607,164 to 6,609,004 a b c d e f g h i 1 2kb 0 240 bp exon 240 bp exon 216 bp uORF 240 bp exon 49 bp [gt-ag] intron 100 GenBank accessions 216 bp uORF 76 bp exon 76 bp exon 47 bp [gt-ag] intron 96 GenBank accessions 95 bp exon 95 bp exon 43 bp [gt-ag] intron 101 GenBank accessions 96 bp exon 96 bp exon 193 bp [gt-ag] intron 97 GenBank accessions 342 bp exon 342 bp exon 54 bp [gt-ag] intron 48 GenBank accessions 273 bp exon 273 bp exon 47 bp [gt-ag] intron 61 GenBank accessions 218 bp exon 218 bp exon 146 bp [gt-ag] intron 72 GenBank accessions 122 bp exon 122 bp exon 133 accessions, some from mixed (seen 8 times) embryo (3), l4 (3), l2 (2) l1 (once) Transpliced 5' end, 5 accessions Validated 3' end, 107 accessions 122 bp exon 48 bp exon 48 bp exon 49 bp [gt-ag] intron 100 GenBank accessions 76 bp exon 47 bp [gt-ag] intron 96 GenBank accessions 95 bp exon 43 bp [gt-ag] intron 101 GenBank accessions 96 bp exon 193 bp [gt-ag] intron 97 GenBank accessions 351 bp exon 45 bp [gt-ag] intron 1 GenBank accession 273 bp exon 47 bp [gt-ag] intron 61 GenBank accessions 218 bp exon 146 bp [gt-ag] intron 72 GenBank accessions 110 bp exon 12 accessions, some from l2 (seen 2 times) mixed (2), embryo (once) l4 (once) capped 5' end, 3 accessions Validated 3' end, 59 accessions 110 bp exon 48 bp exon 48 bp exon 52 bp [gt-ag] intron 2 GenBank accessions 73 bp exon 47 bp [gt-ag] intron 96 GenBank accessions 95 bp exon 43 bp [gt-ag] intron 101 GenBank accessions 96 bp exon 193 bp [gt-ag] intron 97 GenBank accessions 342 bp exon 54 bp [gt-ag] intron 48 GenBank accessions 273 bp exon 47 bp [gt-ag] intron 61 GenBank accessions 218 bp exon 146 bp [gt-ag] intron 72 GenBank accessions 93 bp exon 2 accessions, some from mixed (seen once) capped 5' end, 1 accession 93 bp exon 48 bp exon 48 bp exon 49 bp [gt-ag] intron 100 GenBank accessions 76 bp exon 77 bp [gt-ag] intron 3 GenBank accessions 65 bp exon 43 bp [gt-ag] intron 101 GenBank accessions 96 bp exon 193 bp [gt-ag] intron 97 GenBank accessions 377 bp exon 4 accessions Validated 3' end, 5 accessions 377 bp exon 41 bp exon 41 bp exon 172 bp [gt-ag] intron 1 GenBank accession 95 bp exon 49 bp [gt-ag] intron 1 GenBank accession 90 bp exon 242 bp [gt-ag] intron 1 GenBank accession 290 bp exon 3 accessions 290 bp exon 90 bp exon 58 bp [gt-ag] intron 1 GenBank accession 43 bp exon 82 bp [gt-ag] intron 1 GenBank accession 349 bp exon 2 accessions 349 bp exon 42 bp exon 757 bp [gc-ag] intron 1 GenBank accession 150 bp exon 50 bp [gt-ag] intron 1 GenBank accession 2 accessions 213 bp exon 90 bp exon 90 bp exon 183 bp [gt-ag] intron 1 GenBank accession 1 accession 349 bp exon 43 bp exon 43 bp exon 92 bp [gt-ag] intron 1 GenBank accession 339 bp exon 1 accession 339 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.
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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 uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
a 1462 bp 379 aa 237 bp 85 bp 213 bp 2kb including Promoter 2041 bp 1kb
b 1267 bp 382 aa 45 bp 73 bp 2kb including Promoter 1837 bp 1kb
c 1238 bp 378 aa 45 bp 56 bp 2kb including Promoter 1820 bp 1kb
d 662 bp 200 aa 45 bp 14 bp 2kb probably including promoter 1024 bp 1kb
e 516 bp 155 aa 47 bp 2kb probably including promoter 979 bp 1kb
f 482 bp 144 aa 47 bp 2kb 622 bp 1kb
g 405 bp 135 aa 2kb 1212 bp 1kb
h 439 bp 123 aa 70 bp 2kb possibly including promoter 622 bp 1kb
i 382 bp 97 aa 41 bp 47 bp 2kb possibly including promoter 474 bp 1kb

Gene neighbors and Navigator on chromosome X back to top
XH213 C cpr-6 D C R P C R kqt-1 C R P XH203 XH217 XH218 C ttr-6 C R XH216 D C R P clec-266 C XH246 5kb 0 XH213, 52 accessions, 7 variants cpr-6, 162 accessions 9 variants XH233, 11 accessions, 2 variants kqt-1, 31 accessions, 4 variants XH203, 0 accession XH217, 0 accession XH220, 12 accessions, 7 variants XH218, 0 accession XH192, 5 accessions ttr-6, 87 accessions, 2 variants XH216, 11 accessions, 3 variants clec-266, 350 accessions 8 variants XH246, 11 accessions XH248, 14 accessions, 4 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 2 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, .d, .e, .f, .g, .h, .i 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'.

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