Caenorhabditis elegans essential gene ptc-3, encoding patched family member.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
SUMMARY back to top
Summary
[Wormbase] ptc-3 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-3 is strongly required for normal molting from L1 to L3 larval stages; PTC-3 is also required for normal growth to full size and for viability.
Wormbase predicts 3 models, 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 7 spliced variants
.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.6 times the average gene in this release, at all stages of development [Kohara cDNAs]. The expression profile for the gene, derived from the proportion of animals at each stage in each Kohara library is: embryos 23%, L1 or L2 larvae 35%, L3 to adult 42%. See the in situ hybridization pattern in Kohara NextDB. The sequence of this gene is defined by 27 cDNA clones and 20 elements defined by RNA-seq, some from embryo (seen 5 times), l1 (5), l2 (3), mixed (3), whole worm (2), l4 (once). We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 18 distinct gt-ag introns. Transcription produces at least 7 alternatively spliced mRNAs. Variant b is transpliced to SL1. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of a cassette exon, overlapping exons with different boundaries, splicing versus retention of one intron. 337 bp of this gene are antisense to spliced gene 2D131, raising the possibility of regulated alternate expression.
Function: There are 4 articles specifically referring to this gene in PubMed. In addition we point below to 4 abstracts. This essential gene is associated to a phenotype (Larval arrest, Paralysed, UNCoordinated locomotion, MoLT defect, Up-regulated upon pathogen infection). Proteins are expected to have molecular function (patched receptor activity) and to localize in various compartments (membrane, plasma membrane).
Protein coding potential: The 7 spliced mRNAs putatively encode good proteins, altogether 7 different isoforms (1 complete, 2 COOH complete, 4 partial), some containing patched domain [Pfam], some transmembrane domains [Psort2].

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-3 maps on chomosome II at position -8.26 (interpolated). In AceView, it covers 9.15 kb, from 2854509 to 2845362 (WS190), on the reverse strand.
Links to: WormBase, NextDB, RNAiDB.
Other names: The gene is also known in Wormgenes/AceView by its positional name 2D136, in Wormbase by its cosmid.number name Y110A2AL.8, in NextDB, the Nematode expression pattern database, as CEYK2139.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene PTCH2 (e= 10-102).
The closest mouse gene, according to BlastP, is the AceView gene Ptch2 (e= 10-100).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT4G38350 (e=7 10-24)
          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-3 5' 3' encoded on minus strand of chromosome II from 2,854,509 to 2,845,362 a b f c d g e 1 2kb 0 86 bp exon 86 bp exon 338 bp [gt-ag] intron 3 GenBank accessions 123 bp exon 66 bp [gt-ag] intron 7 GenBank accessions 113 bp exon 523 bp [gt-ag] intron 8 GenBank accessions 271 bp exon 60 bp [gt-ag] intron 6 GenBank accessions 116 bp exon 88 bp [gt-ag] intron 6 GenBank accessions 180 bp exon 47 bp [gt-ag] intron 2 GenBank accessions 280 bp exon 190 bp [gt-ag] intron 3 GenBank accessions 1299 bp exon 50 bp [gt-ag] intron 6 GenBank accessions 132 bp exon 449 bp [gt-ag] intron 9 GenBank accessions 726 bp exon 501 bp [gt-ag] intron 1 GenBank accession 98 bp exon 47 bp [gt-ag] intron 7 GenBank accessions 598 bp exon 50 bp [gt-ag] intron 18 GenBank accessions 83 bp exon 3 accessions 83 bp exon 138 bp exon 138 bp exon 749 bp [gt-ag] intron 5 GenBank accessions 123 bp exon 66 bp [gt-ag] intron 7 GenBank accessions 113 bp exon 523 bp [gt-ag] intron 8 GenBank accessions 271 bp exon 60 bp [gt-ag] intron 6 GenBank accessions 116 bp exon 88 bp [gt-ag] intron 6 GenBank accessions 180 bp exon 47 bp [gt-ag] intron 2 GenBank accessions 280 bp exon 190 bp [gt-ag] intron 3 GenBank accessions 1299 bp exon 50 bp [gt-ag] intron 6 GenBank accessions 132 bp exon 449 bp [gt-ag] intron 9 GenBank accessions 726 bp exon 501 bp [gt-ag] intron 1 GenBank accession 98 bp exon 47 bp [gt-ag] intron 7 GenBank accessions 598 bp exon 50 bp [gt-ag] intron 18 GenBank accessions 337 bp exon 32 accessions, some from embryo (seen 5 times) l1 (4), l2 (3), mixed (3) l4 (once) Transpliced 5' end, 3 accessions Validated 3' end, 14 accessions Validated 3' end, 5 accessions 337 bp exon 117 bp exon 73 bp [gt-ag] intron 1 GenBank accession 99 bp exon 1 accession 99 bp exon 468 bp exon 41 bp [gt-ag] intron 2 GenBank accessions 141 bp exon 449 bp [gt-ag] intron 9 GenBank accessions 726 bp exon 501 bp [gt-ag] intron 1 GenBank accession 98 bp exon 47 bp [gt-ag] intron 7 GenBank accessions 598 bp exon 50 bp [gt-ag] intron 18 GenBank accessions 285 bp exon 5 accessions, some from l1 (seen once) 285 bp exon 36 bp exon 1881 bp [gt-ag] intron 1 GenBank accession 138 bp exon 138 bp exon 749 bp [gt-ag] intron 5 GenBank accessions 123 bp exon 66 bp [gt-ag] intron 7 GenBank accessions 113 bp exon 523 bp [gt-ag] intron 8 GenBank accessions 271 bp exon 60 bp [gt-ag] intron 6 GenBank accessions 116 bp exon 88 bp [gt-ag] intron 6 GenBank accessions 180 bp exon 47 bp [gt-ag] intron 2 GenBank accessions 280 bp exon 190 bp [gt-ag] intron 3 GenBank accessions 4 accessions, some from whole worm (seen once) 633 bp exon 82 bp exon 135 bp [gt-ag] intron 1 GenBank accession 52 bp exon 1 accession 52 bp exon 132 bp exon 1676 bp [gt-ag] intron 1 GenBank accession 91 bp exon 1 accession 91 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.
Read more...
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 4105 bp 1367 aa 2kb 6514 bp 1kb
b 4411 bp 1358 aa 81 bp 253 bp 2kb including Promoter 7231 bp 1kb
c 2316 bp 704 aa 201 bp 2kb 3404 bp 1kb
d 1890 bp 591 aa 117 bp 2kb possibly including promoter 5494 bp 1kb
e 223 bp 74 aa 2kb 1899 bp 1kb
f 216 bp 59 aa 36 bp 2kb 289 bp 1kb
g 134 bp 49 aa 2kb 269 bp 1kb

Gene neighbors and Navigator on chromosome II back to top
2D131 D C P 2D155 C 2D157 C R 2D159 C 2D119 2D151 2D152 2D160 C R 2D120 C I P 2D126 C 2D132 D C P 2D134 D C R P ptc-3 C 2D156 5kb 0 2D115, 68 accessions 2D131, 23 accessions, 6 variants 2D155, 2 accessions 2D157, 8 accessions, 2 variants 2D159, 8 accessions, 2 variants 2D117, 1 accession 2D119, 3 accessions 2D151, 0 accession 2D118, 2 accessions 2D152, 0 accession 2D160, 0 accession 2D120, 87 accessions, 4 variants 2D126, 22 accessions 2D132, 7 accessions 2D134, 33 accessions ptc-3, 47 accessions, 7 variants 2D156, 7 accessions 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 4 articles in PubMed.
In addition we found 4 papers for which we do not have a PubMed identifier
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g 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 !