Caenorhabditis elegans gene sig-7, silencing In Germline defective, encoding CYclophiliN, peptidyl-prolyl cis-trans isomerase.
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SUMMARY back to top
Summary
[Wormbase] sig-7 encodes a predicted cyclophilin; loss of sig-7 activity via large-scale RNAi screens results in embryonic and larval lethality as well as reduced brood sizes, suggesting that SIG-7 plays an essential role during C. elegans development.
Wormbase predicts 2 models
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AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 6.3 times the average gene in this release, mostly from L3 larvae to adult [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 1%, L1 or L2 larvae 8%, L3 to adult (including dauer) 91%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 13 cDNA clones and 70 elements defined by RNA-seq, some from mixed (seen 8 times), l1 (once). We annotate structural defects or features in one cDNA clone.
Alternative mRNA variants and regulation: The gene contains 8 distinct introns (7 gt-ag, 1 gc-ag). Transcription produces 2 alternatively spliced mRNAs. Variant a is transpliced to SL3, SL2, SL5, SL4, b to SL3. There are 2 probable alternative promotors and 3 validated alternative polyadenylation sites (see the diagram).
Function:. This gene is associated to a phenotype (Silencing In Germline defective) Proteins are expected to have molecular function (nucleic acid binding activity) and to localize in nucleus.
Protein coding potential: The 2 spliced 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], a coiled coil stretch [Psort2].

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome I, links to other databases and other names
Map: This gene sig-7 maps on chomosome I at position +2.96 (interpolated). In AceView, it covers 5.40 kb, from 8646444 to 8651844 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
as Other names: The gene is also known cyn-14, cyp-14, in Wormgenes/AceView by its positional name 1J227, in Wormbase by its cosmid.number name F39H2.2, in NextDB, the Nematode expression pattern database, as CEYK8616.
EC number: This gene encodes protein number: EC 5.2.1.8.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene PPIL4andZC3H12D (e= 10-102).
The closest mouse gene, according to BlastP, is the AceView gene Ppil4 (e= 10-102).
The closest A.thaliana gene, according to BlastP, is the AceView gene ATCYP59\/CYP59
          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 sig-7 5' 3' encoded on plus strand of chromosome I from 8,646,444 to 8,651,775 a b 1 2kb 0 203 bp exon 3107 bp [gt-ag] intron 10 GenBank accessions 261 bp exon 513 bp [gt-ag] intron 13 GenBank accessions 100 bp exon 50 bp [gt-ag] intron 13 GenBank accessions 117 bp exon 43 bp [gt-ag] intron 11 GenBank accessions 132 bp exon 48 bp [gt-ag] intron 10 GenBank accessions 172 bp exon 45 bp [gt-ag] intron 9 GenBank accessions 163 bp exon 49 bp [gt-ag] intron 9 GenBank accessions 398 bp exon 80 accessions, some from mixed (seen 7 times) l1 (once) Transpliced 5' end, 9 accessions Validated 3' end, 428 accessions Validated 3' end, 9 accessions 398 bp exon 56 bp exon 838 bp [gc-ag] intron 2 GenBank accessions 261 bp exon 261 bp exon 513 bp [gt-ag] intron 13 GenBank accessions 100 bp exon 50 bp [gt-ag] intron 13 GenBank accessions 117 bp exon 43 bp [gt-ag] intron 11 GenBank accessions 132 bp exon 48 bp [gt-ag] intron 10 GenBank accessions 172 bp exon 45 bp [gt-ag] intron 9 GenBank accessions 163 bp exon 49 bp [gt-ag] intron 9 GenBank accessions 213 bp exon 3 accessions, some from mixed (seen once) Transpliced 5' end, 1 accession 213 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 1546 bp 427 aa 262 bp 2kb including Promoter 5401 bp 1kb
b 1214 bp 358 aa 60 bp 77 bp 2kb including Promoter 2800 bp 1kb

Gene neighbors and Navigator on chromosome I back to top
ces-1 D C I P 1J219 D C R P 1J221 C I P sig-7 D C R flp-22 D C P 1J239 C R P 1J241 C P 1J245 C R D C R P fer-1 D C R P cpn-1 D C P mfap-1 D C I R P syp-3 5kb 0 ces-1, 7 accessions 1J219, 29 accessions, 4 variants 1J221, 23 accessions, 3 variants sig-7, 83 accessions, 2 variants flp-22, 11 accessions 2 variants 1J239, 15 accessions, 3 variants 1J241, 38 accessions, 3 variants 1J245, 32 accessions, 2 variants 1J215, 1 accession 1J246, 9 accessions, 4 variants fer-1, 29 accessions, 2 variants cpn-1, 152 accessions 8 variants mfap-1, 0 accession syp-3, 12 accessions, 4 variants ZOOM OUT                 D:disease, C:conserved, I:interactions, R:regulation, P:publications         Read more...
Annotated mRNA diagrams back to top
? Gene Summary Gene on genome mRNA:.a, .b Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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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