Caenorhabditis elegans gene cyn-13, encoding CYclophiliN, peptidyl-prolyl cis-trans isomerase.
SUMMARY back to top
[Wormbase] cyn-13 encodes a predicted cyclophilin that can function as a nuclease in vitro; functions to regulate DNA degradation and cell death in a genetic pathway with wah-1, cps-6, crn-1, crn-4, crn-5 and these proteins are believed to form a complex in vivo.
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 expressed at high level, 2.4 times the average gene in this release, mostly in embryos, and some 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 68%, L1 or L2 larvae 17%, L3 to adult 15%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 22 cDNA clones and 10 elements defined by RNA-seq, some from embryo (seen 13 times), l2 (2), l1 (once), mixed (once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 2 distinct gt-ag introns. Transcription produces 4 different mRNAs, 3 alternatively spliced variants and 1 unspliced form. Variant b is transpliced to SL1, SL2, SL3, SL4, SL5, SL7, c to SL1, SL2, SL3, SL4, SL5, SL8, d to SL1. There are 4 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 one abstract. Proteins are expected to have molecular function (nucleic acid binding activity) and to localize in cytoplasm. These proteins appear to interact with another protein (1E447).
Protein coding potential: The 3 spliced and the unspliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), some containing domains Peptidyl-prolyl cis-trans isomerase, cyclophilin-type, RNA recognition motif, RNP-1 [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 gene cyn-13 maps on chomosome IV at position +16.16 (interpolated). In AceView, it covers 5.59 kb, from 17116628 to 17111037 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known cyp-13, in Wormgenes/AceView by its positional name 4S56, in Wormbase by its cosmid.number name Y116A8C.34, in NextDB, the Nematode expression pattern database, as CEYK3667.
EC number: This gene encodes protein number: EC
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene PPIE (e=3 10-94).
The closest mouse gene, according to BlastP, is the AceView gene Ppie (e=3 10-94).
The closest A.thaliana genes, according to BlastP, are the AceView genes ROC3, AT2G21130, ROC1, ROC2, ROC5, ROC4, CYP5, ROC7
          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 cyn-13 5' 3' encoded on minus strand of chromosome IV from 17,116,628 to 17,111,037 a b c d 500bp 0 263 bp exon 263 bp exon 360 bp [gt-ag] intron 19 GenBank accessions 424 bp exon 4164 bp [gt-ag] intron 19 GenBank accessions 371 bp exon 5 accessions, some from embryo (seen 2 times) 371 bp exon 257 bp exon 257 bp exon 360 bp [gt-ag] intron 19 GenBank accessions 424 bp exon 4164 bp [gt-ag] intron 19 GenBank accessions 379 bp exon 11 accessions, some from embryo (seen 3 times) l1 (once) Transpliced 5' end, 2 accessions Validated 3' end, 19 accessions 379 bp exon 248 bp exon 360 bp [gt-ag] intron 19 GenBank accessions 424 bp exon 4164 bp [gt-ag] intron 19 GenBank accessions 381 bp exon 15 accessions, some from embryo (seen 8 times) l2 (2), mixed (once) Transpliced 5' end, 3 accessions Validated 3' end, 28 accessions 381 bp exon 377 bp exon 377 bp exon 1 accession Transpliced 5' end, 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 1058 bp 331 aa 15 bp 47 bp 2kb probably including promoter 5582 bp 1kb
b 1060 bp 331 aa 9 bp 55 bp 2kb including Promoter 5584 bp 1kb
c 1053 bp 331 aa 57 bp 2kb including Promoter 5577 bp 1kb
d 377 bp 103 aa 12 bp 53 bp 2kb including Promoter 377 bp 1kb

Gene neighbors and Navigator on chromosome IV back to top
4S57 C itsn-1 D C I R P 4S77 C 4S39 4S69 C R P 4S36 C R 4S40 C P 4S44 D C P sfa-1 C I P cyn-13 D C I P uaf-2 C 4S74 5kb 0 snr-1, 316 accessions 3 variants 4S57, 21 accessions itsn-1, 59 accessions 5 variants 4S77, 14 accessions 4S35, 0 accession 4S39, 15 accessions, 3 variants 4S69, 0 accession 4S83, 4 accessions, 2 variants 4S36, 61 accessions, 12 variants 4S40, 0 accession 4S44, 0 accession sfa-1, 27 accessions, 4 variants cyn-13, 32 accessions 4 variants uaf-2, 150 accessions 2 variants 4S74, 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 4 articles in PubMed.
In addition we found 1 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d 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'.

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