Caenorhabditis elegans essential gene cpl-1, encoding CathePsin L, essential for embryogenesis, plays multiple roles including processing of yolk protein; also associates to chromatin in oocytes and spermatocytes, and binds cohesin in 2-hybrid.
SUMMARY back to top
[Wormbase] cpl-1 encodes a member of the cathepsin L-like cysteine protease family required for embryonic viability and normal growth; expressed in eggshells and throughout early embryos, accumulates in intestinal cells during late embryogenesis, and expressed in the cuticle, gonad, and pharynx later in development.
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 4 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 5.5 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 23%, L1 or L2 larvae 27%, L3 to adult 51%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 61 cDNA clones and 11 elements defined by RNA-seq, some from embryo (seen 9 times), mixed (9), l1 (7), l2 (3), whole animal (2). We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 7 distinct gt-ag introns. Transcription produces at least 5 different mRNAs, 4 alternatively spliced variants and 1 unspliced form. Variant a is transpliced to SL1. There are 2 non overlapping alternative last exons and 4 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 3' end, presence or absence of 2 cassette exons, overlapping exons with different boundaries.
Function: There are 9 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, partial, SLow growth, shared oogenic and spermatogenic protein copurified with chromatin). 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). These proteins appear to interact with other proteins (1O778, COH-2, RPN-2).
Protein coding potential: The 4 spliced and the unspliced mRNAs putatively encode good proteins, altogether 5 different isoforms (2 complete, 3 COOH complete), some containing domains Proteinase inhibitor I29, cathepsin propeptide, peptidase C1A, papain C-terminal [Pfam], a coiled coil stretch [Psort2]; 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 essential gene cpl-1 maps on chomosome V at position +9.40 (interpolated). In AceView, it covers 2.78 kb, from 16595318 to 16592537 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 5R74, in Wormbase by its cosmid.number name T03E6.7, in NextDB, the Nematode expression pattern database, as CEYK2090.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes CTSL1, CTSL2, CTSS, CTSK.
The closest mouse genes, according to BlastP, are the AceView genes Ctsl (e=8 10-87), Ctss (e=10-78), 2310051M13Rik (e=10-78), BC051665 (e=5 10-77), Ctsk (e=3 10-76), 4930486L24Rik (e=5 10-76).
The closest A.thaliana genes, according to BlastP, are the AceView genes AT5G43060, AT3G19390, RD21, AT3G48340, AALP, CP1, XBCP3, AT3G48350, SAG12, AT5G50260, AT3G19400, XCP2, AT3G45310
          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 cpl-1 5' 3' encoded on minus strand of chromosome V from 16,595,318 to 16,592,537 a b c d e 500bp 0 259 bp exon 259 bp exon 476 bp [gt-ag] intron 35 GenBank accessions 99 bp exon 541 bp [gt-ag] intron 38 GenBank accessions 448 bp exon 568 bp [gt-ag] intron 41 GenBank accessions 391 bp exon 65 accessions, some from mixed (seen 9 times) embryo (8), l1 (7), l2 (3) whole animal (2) Transpliced 5' end, 13 accessions Validated 3' end, 160 accessions 391 bp exon 257 bp exon 511 bp [gt-ag] intron 1 GenBank accession 64 bp exon 548 bp [gt-ag] intron 2 GenBank accessions 441 bp exon 441 bp exon 568 bp [gt-ag] intron 41 GenBank accessions 372 bp exon 3 accessions, some from embryo (seen once) 372 bp exon 257 bp exon 257 bp exon 52 bp [gt-ag] intron 1 GenBank accession 517 bp exon 2 accessions Validated 3' end, 3 accessions 517 bp exon 641 bp exon 641 bp exon 1 accession Validated 3' end, 3 accessions 641 bp exon 64 bp exon 64 bp exon 1557 bp [gt-ag] intron 1 GenBank accession 377 bp exon 1 accession 377 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 1197 bp 337 aa 182 bp 2kb including Promoter 2782 bp 1kb
b 1134 bp 198 aa 374 bp 163 bp 2kb probably including promoter 2761 bp 1kb
c 774 bp 130 aa 388 bp 2kb probably including promoter 826 bp 1kb
d 641 bp 104 aa 333 bp 2kb probably including promoter 641 bp 1kb
e 441 bp 96 aa 149 bp 2kb 1998 bp 1kb

Gene neighbors and Navigator on chromosome V back to top
str-149 C str-151 C str-150 C srw-54 C 5R87 5R68 C P C nhr-271 C 5R60 C srw-73 C srh-269 D C I P cpl-1 C C R 5R82 C 5R94 5kb 0 str-149, 0 accession str-151, 6 accessions str-150, 2 accessions srw-54, 0 accession 5R87, 10 accessions 5R68, 0 accession nhr-233, 1 accession nhr-271, 4 accessions 5R60, 0 accession srw-73, 0 accession srh-269, 3 accessions cpl-1, 72 accessions, 5 variants 5R80, 0 accession 5R82, 61 accessions, 16 variants 5R94, 17 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 9 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 Alternative mRNAs features, proteins, introns, exons, sequences 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 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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