Caenorhabditis elegans essential gene ptc-1, encoding patched family member, functions in cytokinesis in the germline.
SUMMARY back to top
[Wormbase] ptc-1 encodes an ortholog of Drosophila PATCHED (PTC) and human PTCH (OMIM:601309, mutated in basal cell nevus syndrome), which defines one of seven paralogous families of sterol sensing domain (SSD) proteins; PTC-1 is required for cytokinesis in the germline, but not in somatic cells (the converse of PTR-2's function, and a role conserved in C. briggsae); PTC-1 is also required to isolate meiotic germline nuclei from one another so that their nuclear divisions are asynchronous; PTC-1 is (very weakly) required for normal molting; PTC-1 protein is found in the membranes of all germline cells except sperm; ptc-1 transcripts are present in germline, very early (2- and 4-cell) embryos, and in the germline precursor P4; ptc-1 null mutants have normal somatic tissues, but are sterile with multinucleate oocytes; murine PTCH is found in midbodies by mass tandem spectroscopy, indicating that PTC-1's function in cytokinesis may be conserved among metazoa; since PTC-1 has an SSD, PTC-1's core function may be to transport proteins, lipids, or sterols.
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 5 spliced variants

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at very high level, 4.0 times the average gene in this release, only in embryos, L1, L2 and L3 larvae [Kohara cDNAs], limited to the germline [Kuwabara et al, 2000]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 31%, L1 or L2 larvae 69%, L3 to adult 0%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 15 cDNA clones and 38 elements defined by RNA-seq, some from l1 (seen 8 times), embryo (3), whole worm (once). We annotate structural defects or features in 9 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 12 distinct gt-ag introns. Transcription produces at least 5 alternatively spliced mRNAs. Variant a is transpliced to SL1, d to SL3. There are 2 probable alternative promotors, 4 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 3' end, overlapping exons with different boundaries.
Function: There are 3 articles specifically referring to this gene in PubMed. In addition we point below to 5 abstracts. This essential gene is associated to a phenotype (Sterile adult, CYtoKinesis defect). Proteins are expected to have molecular function (patched receptor activity) and to localize in various compartments (membrane, plasma membrane).
Protein coding potential: 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 partial), some containing patched domain [Pfam], some transmembrane domains, a coiled coil stretch [Psort2]. The remaining 3 mRNA variants (3 spliced; 1 partial) appear not to encode good proteins.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome II, links to other databases and other names
Map: This essential gene ptc-1 maps on chomosome II at position +0.50 (interpolated). In AceView, it covers 16.05 kb, from 7884398 to 7900452 (WS190), on the direct strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2I189, in Wormbase by its cosmid.number name ZK675.1, in NextDB, the Nematode expression pattern database, as CEYK7574.
          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 ptc-1 5' 3' encoded on plus strand of chromosome II from 7,884,398 to 7,900,452 a e b c d 1 2kb 0 127 bp exon 127 bp exon 46 bp [gt-ag] intron 2 GenBank accessions 86 bp exon 42 bp [gt-ag] intron 2 GenBank accessions 132 bp exon 1889 bp [gt-ag] intron 3 GenBank accessions 431 bp exon 49 bp [gt-ag] intron 2 GenBank accessions 722 bp exon 46 bp [gt-ag] intron 3 GenBank accessions 1396 bp exon 48 bp [gt-ag] intron 3 GenBank accessions 1044 bp exon 47 bp [gt-ag] intron 7 GenBank accessions 112 bp exon 50 bp [gt-ag] intron 7 GenBank accessions 1026 bp exon 47 accessions, some from l1 (seen 8 times) embryo (3), whole worm (once) Transpliced 5' end, 2 accessions Validated 3' end, 55 accessions Validated 3' end, 4 accessions Validated 3' end, 56 accessions 1026 bp exon 191 bp exon 191 bp exon 191 bp exon 2104 bp [gt-ag] intron 1 GenBank accession 1 accession 54 bp exon 86 bp exon 86 bp exon 51 bp [gt-ag] intron 1 GenBank accession 1 accession 120 bp exon 90 bp exon 90 bp exon 47 bp [gt-ag] intron 1 GenBank accession 120 bp exon 1 accession 120 bp exon 194 bp exon 194 bp exon 51 bp uORF 194 bp exon 194 bp exon 8568 bp [gt-ag] intron 1 GenBank accession 120 bp exon 120 bp exon 3 accessions Transpliced 5' end, 1 accession 120 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 uORF Upstream sequence Transcription
Downstream sequence
a 5076 bp 1408 aa 36 bp 813 bp 2kb including Promoter 7293 bp 1kb
b 206 bp 68 aa 2kb probably including promoter 257 bp 1kb
c 210 bp 42 aa 79 bp 2kb probably including promoter 257 bp 1kb
d 314 bp 21 aa 151 bp 97 bp 48 bp 2kb including Promoter 8882 bp 1kb
e 245 bp 16 aa 46 bp 148 bp 2kb probably including promoter 2349 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
2I173 D C P ptc-1 D C R P rev-1 D C I P 2I201 C 2I169 C R 2I162 C 2I166 D C I R P vha-4 C R 2I196 5kb 0 2I173, 16 accessions ptc-1, 53 accessions, 5 variants rev-1, 22 accessions, 3 variants 2I201, 4 accessions 2I169, 6 accessions, 2 variants 2I188, 0 accession ztf-17, 56 accessions 3 variants 2I162, 44 accessions, 5 variants 2I166, 49 accessions, 7 variants vha-4, 82 accessions, 2 variants 2I196, 39 accessions, 5 variants 2I202, 42 accessions, 10 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 5 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e 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'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !