[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.
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 184.108.40.206. 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
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. Read more...
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table.
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink and ] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags to any single letter variant of the main . More explanations are given in the gene help file
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 !