Caenorhabditis elegans gene cyn-9, encoding CYclophiliN, peptidyl-prolyl cis-trans isomerase.
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SUMMARY back to top
Summary
[Wormbase] cyn-9 encodes a peptidyl prolyl cis-trans isomerase most similar to human cyclophilin G (OMIM:606093); CYN-9 likely functions as a catalyst in the folding and modification of cuticle collagens; a cyn-9::lacZ reporter is expressed in the syncytial hypodermis from early larval through adult stages; cyn-9 mRNA is expressed most strongly at the mid-L3 and mid-L4 larval stages, the intermoult period when collagens are synthesized.
Wormbase predicts one model
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AceView synopsis, each blue text links to tables and details
According to AceView, this gene is well expressed, 1.4 times the average gene in this release, in embryos, L3 and L4 larvae, and adult [Kohara cDNAs]. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 6 cDNA clones and 12 elements defined by RNA-seq, some from embryo (seen once), mixed (once).
The gene contains 5 distinct gt-ag introns. Transcription produces one mRNA. Variant a is transpliced to SL2, SL3. There are 2 validated alternative polyadenylation sites (see the diagram).
Function: There are 3 articles specifically referring to this gene in PubMed. In addition we point below to 2 abstracts. Proteins are expected to localize in nucleus. No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
The spliced mRNA putatively encodes a good protein, containing Peptidyl-prolyl cis-trans isomerase, cyclophilin-type domain [Pfam].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome III, links to other databases and other names
Map: This gene cyn-9 maps on chomosome III at position -5.67 (interpolated). In AceView, it covers 1.85 kb, from 3699619 to 3697771 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known cyp-9, in Wormgenes/AceView by its positional name 3E788, in Wormbase by its cosmid.number name T27D1.1, in NextDB, the Nematode expression pattern database, as CEYK6623.
EC number: This gene encodes protein number: EC 5.2.1.8.
Closest AceView homologs in other species ?
The closest human genes, according to BlastP, are the AceView genes PPIG, NKTR, PPID.
The closest mouse genes, according to BlastP, are the AceView genes Ppig (e=10-45), Ppid (e=6 10-43), Nktr (e=3 10-42).
The closest A.thaliana gene, according to BlastP, is the AceView gene SQN
          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-9 5' 3' encoded on minus strand of chromosome III from 3,699,619 to 3,697,799 a 1kb 0 95 bp exon 95 bp exon 51 bp [gt-ag] intron 6 GenBank accessions 128 bp exon 45 bp [gt-ag] intron 6 GenBank accessions 204 bp exon 397 bp [gt-ag] intron 6 GenBank accessions 324 bp exon 265 bp [gt-ag] intron 6 GenBank accessions 138 bp exon 50 bp [gt-ag] intron 6 GenBank accessions 152 bp exon 18 accessions, some from embryo (seen once) mixed (once) Transpliced 5' end, 1 accession Validated 3' end, 7 accessions Validated 3' end, 19 accessions 152 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 Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
a 1041 bp 309 aa 7 bp 104 bp 2kb including Promoter 1849 bp 1kb

Gene neighbors and Navigator on chromosome III back to top
3E791 D C I P 3E793 C I R P 3E795 D C I R P dph-1 C I P 3E801 C R P 3E807 C R 3E810 C npr-15 C P cyn-9 D C I P pdi-1 C I P 3E806 5kb 0 3E791, 65 accessions, 3 variants 3E793, 14 accessions, 3 variants 3E795, 85 accessions, 2 variants dph-1, 23 accessions 3E801, 17 accessions, 3 variants 3E807, 36 accessions, 7 variants 3E772, 17 accessions, 2 variants 3E810, 33 accessions, 5 variants npr-15, 10 accessions 2 variants cyn-9, 18 accessions pdi-1, 211 accessions 3 variants 3E806, 37 accessions, 3 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 3 articles in PubMed.
In addition we found 2 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA Expression Tissue Function, regulation, related genes C

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 see the mRNA diagram, sequence and annotation, click 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 !