Summary
[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, 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 summary
Expression: According to AceView, this gene is
expressed at high level, 1.7 times the average gene in this release, mostly in embryos, and some at all stages of development [Kohara cDNAs]. The
sequence of this gene is defined by
22 cDNA clones. 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
3 alternatively spliced mRNAs. There are 3 validated
alternative polyadenylation sites (see the
diagram).
Protein coding potential: The 3 spliced mRNAs putatively encode
the same good protein, some containing
domains Peptidyl-prolyl cis-trans isomerase, cyclophilin-type, RNA recognition motif, RNP-1 [Pfam].
Function: There are
3 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). No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Please quote:
AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
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 5.2.1.8.
The closest human gene, according to BlastP, is the AceView gene
PPIE (e=2 10^-94).
The closest mouse gene, according to BlastP, is the AceView gene
Ppie (e=2 10^-94).
The closest A.thaliana genes, according to BlastP, are the AceView genes
ROC3 (e=3 10^-52),
AT2G21130 (e=4 10^-50),
ROC1 (e=5 10^-50),
ROC2 (e=2 10^-48),
ROC5 (e=7 10^-47),
ROC4 (e=6 10^-46),
CYP5 (e=2 10^-45),
ROC7 (e=4 10^-45)
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 cDNA clones supporting each intron. Superimposed introns of the same color are identical, of different colors are different.
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. 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. Details on tissue of origin for each intron and exon is available from the
intron and exons table. Good predicted proteins are in pink, yellow proteins may be partial or unconvincing, green are uORFs. Proteins supported by a single continuous GenBank accession 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.
More legend
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
