Mus musculus gene Ptch1, encoding patched homolog 1.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), but Mus musculus 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 9 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 2.6 times the average gene in this release. The sequence of this gene is defined by 282 GenBank accessions from 240 cDNA clones, some from brain (seen 35 times), whole brain (25), upper head (15), embryonic stem cell (13), taste buds (10), tongue (10), eye (9) and 60 other tissues. We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 30 distinct introns (29 gt-ag, 1 gc-ag). Transcription produces 13 different mRNAs, 9 alternatively spliced variants and 4 unspliced forms. There are 7 probable alternative promotors, 3 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 2 introns.
Note that mRNA .bSep07 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Function: There are 373 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (cardiovascular system phenotype; cellular phenotype; craniofacial phenotype; digestive/alimentary phenotype; embryogenesis phenotype; endocrine/exocrine gland phenotype; growth/size phenotype; lethality-embryonic/perinatal; life span-post-weaning/aging and 8 others), proposed to participate in pathways (Basal cell carcinoma, Hedgehog signaling pathway) and processes (dorsal/ventral pattern formation, embryonic limb morphogenesis, mammary gland development, negative regulation of body size, neural tube formation, organ morphogenesis, protein processing, regulation of smoothened activity, signal transduction, smoothened signaling pathway). Proteins are expected to have molecular functions (cholesterol binding, hedgehog receptor activity, heparin binding, patched binding, protein binding, zinc ion binding) and to localize in various compartments (extracellular region, integral to membrane, integral to plasma membrane).
Please see the Jackson Laboratory Mouse Genome Database/Informatics site MGI_105373 for in depth functional annotation of this gene.
Protein coding potential: 7 spliced and 3 unspliced mRNAs putatively encode good proteins, altogether 11 different isoforms (3 complete, 4 COOH complete, 4 partial), some containing patched domain [Pfam], some transmembrane domains [Psort2]. The remaining 3 mRNA variants (2 spliced, 1 unspliced; 2 partial) appear not to encode good proteins.
2 isoforms are annotated using as Met a Kozak-compatible non-AUG start, thereby gaining a minimum of 84 amino acids N-terminal to the first AUG.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 13, links to other databases and other names
Map: This gene Ptch1 maps on chromosome 13, at 13 B3|13 36.0 cM according to Entrez Gene. In AceView, it covers 65.32 kb, from 63674768 to 63609453 (NCBI 37a, Aug 2007), on the reverse strand.
Links to: manual annotations from MGI_105373, KEGG_04340, KEGG_05217, the SNP view, gene overviews from Entrez Gene 19206, expression data from UniGene, molecular and other annotations from UCSC.
Other names: The gene is also known as Ptch1, Ptc, mes, Ptc1, PTCH or A230106A15Rik, LOC19206.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene PTCH1 (e=9 10-18).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes ptc-3 (e=8 10-06), ptc-1 (e=10-04), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene AT4G38350 (e=4 10-29), which may contain interesting functional annotation
          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 Ptch1 5' 3' encoded on minus strand of chromosome 13 from 63,674,768 to 63,609,453 a [NM] b c f-u j-u d l k-u m e g h i-u 5kb 0 374 bp exon 374 bp exon 1546 bp [gt-ag] intron 6 GenBank accessions 193 bp exon 15437 bp [gt-ag] intron 14 GenBank accessions 190 bp exon 2689 bp [gt-ag] intron 27 GenBank accessions 70 bp exon 109 bp [gt-ag] intron 33 GenBank accessions 92 bp exon 1347 bp [gt-ag] intron 16 GenBank accessions 199 bp exon 284 bp [gt-ag] intron 14 GenBank accessions 122 bp exon 771 bp [gt-ag] intron 12 GenBank accessions 148 bp exon 876 bp [gt-ag] intron 19 GenBank accessions 132 bp exon 319 bp [gt-ag] intron 18 GenBank accessions 156 bp exon 769 bp [gt-ag] intron 18 GenBank accessions 99 bp exon 455 bp [gt-ag] intron 17 GenBank accessions 126 bp exon 4824 bp [gt-ag] intron 11 GenBank accessions 119 bp exon 623 bp [gt-ag] intron 9 GenBank accessions 403 bp exon 417 bp [gt-ag] intron 10 GenBank accessions 310 bp exon 5247 bp [gt-ag] intron 19 GenBank accessions 143 bp exon 2018 bp [gt-ag] intron 25 GenBank accessions 184 bp exon 1664 bp [gt-ag] intron 24 GenBank accessions 281 bp exon 2593 bp [gt-ag] intron 28 GenBank accessions 138 bp exon 2014 bp [gt-ag] intron 23 GenBank accessions 143 bp exon 3770 bp [gt-ag] intron 19 GenBank accessions 100 bp exon 426 bp [gt-ag] intron 20 GenBank accessions 255 bp exon 1485 bp [gt-ag] intron 16 GenBank accessions 544 bp exon 544 bp exon 419 bp [gt-ag] intron 9 GenBank accessions 31 accessions, NM_008957 some from mammary (seen 3 times) upper head (3), cerebellum (2) embryonic stem cell (2) eye (2) Validated 3' end, 2 accessions 2965 bp exon 369 bp exon 369 bp exon 369 bp exon 9276 bp [gt-ag] intron 9 GenBank accessions 193 bp exon 193 bp exon 15437 bp [gt-ag] intron 14 GenBank accessions 190 bp exon 190 bp exon 2689 bp [gt-ag] intron 27 GenBank accessions 70 bp exon 70 bp exon 109 bp [gt-ag] intron 33 GenBank accessions 92 bp exon 92 bp exon 1347 bp [gt-ag] intron 16 GenBank accessions 199 bp exon 199 bp exon 284 bp [gt-ag] intron 14 GenBank accessions 122 bp exon 122 bp exon 771 bp [gt-ag] intron 12 GenBank accessions 148 bp exon 148 bp exon 876 bp [gt-ag] intron 19 GenBank accessions 132 bp exon 132 bp exon 319 bp [gt-ag] intron 18 GenBank accessions 156 bp exon 156 bp exon 769 bp [gt-ag] intron 18 GenBank accessions 99 bp exon 99 bp exon 455 bp [gt-ag] intron 17 GenBank accessions 126 bp exon 126 bp exon 4824 bp [gt-ag] intron 11 GenBank accessions 119 bp exon 119 bp exon 623 bp [gt-ag] intron 9 GenBank accessions 37 bp exon 37 bp exon 304 bp exon 304 bp exon 304 bp exon 304 bp exon 417 bp [gt-ag] intron 10 GenBank accessions 310 bp exon 310 bp exon 5247 bp [gt-ag] intron 19 GenBank accessions 143 bp exon 143 bp exon 2018 bp [gt-ag] intron 25 GenBank accessions 184 bp exon 184 bp exon 1664 bp [gt-ag] intron 24 GenBank accessions 281 bp exon 281 bp exon 2593 bp [gt-ag] intron 28 GenBank accessions 138 bp exon 138 bp exon 2014 bp [gt-ag] intron 23 GenBank accessions 143 bp exon 143 bp exon 3770 bp [gt-ag] intron 19 GenBank accessions 100 bp exon 100 bp exon 426 bp [gt-ag] intron 20 GenBank accessions 255 bp exon 255 bp exon 1485 bp [gt-ag] intron 16 GenBank accessions 3757 bp exon 3757 bp exon 194 accessions, some from brain (seen 34 times) whole brain (24), upper head (11) embryonic stem cell (10) taste buds (8) Validated 3' end, 23 accessions 3757 bp exon 78 bp exon 642 bp [gt-ag] intron 2 GenBank accessions 193 bp exon 15437 bp [gt-ag] intron 14 GenBank accessions 190 bp exon 2689 bp [gt-ag] intron 27 GenBank accessions 70 bp exon 109 bp [gt-ag] intron 33 GenBank accessions 92 bp exon 1347 bp [gt-ag] intron 16 GenBank accessions 199 bp exon 284 bp [gt-ag] intron 14 GenBank accessions 2 accessions 30 bp exon 2216 bp exon 2216 bp exon 14 accessions, some from testis (seen 3 times) pooled organs (2), stomach (2) taste buds (2), tongue (2) 2216 bp exon 622 bp exon 622 bp exon 1 accession from whole embryo including extraembryonictissues at 10.5-days postcoitum 622 bp exon 625 bp exon 625 bp exon 1384 bp [gt-ag] intron 1 GenBank accession 193 bp exon 15437 bp [gt-ag] intron 14 GenBank accessions 190 bp exon 2689 bp [gt-ag] intron 27 GenBank accessions 70 bp exon 109 bp [gt-ag] intron 33 GenBank accessions 92 bp exon 1347 bp [gt-ag] intron 16 GenBank accessions 199 bp exon 284 bp [gt-ag] intron 14 GenBank accessions 2 accessions, some from spinal ganglion (seen once) 30 bp exon 27 bp exon 455 bp [gt-ag] intron 17 GenBank accessions 126 bp exon 1624 bp [gt-ag] intron 1 GenBank accession 127 bp exon 127 bp exon 3073 bp [gt-ag] intron 1 GenBank accession 119 bp exon 623 bp [gt-ag] intron 9 GenBank accessions 1 accession 143 bp exon 583 bp exon 583 bp exon 1 accession 583 bp exon 255 bp exon 255 bp exon 255 bp exon 426 bp [gt-ag] intron 20 GenBank accessions 1 accession 50 bp exon 35 bp exon 476 bp [gt-ag] intron 1 GenBank accession 193 bp exon 193 bp exon 15437 bp [gt-ag] intron 14 GenBank accessions 190 bp exon 2689 bp [gt-ag] intron 27 GenBank accessions 70 bp exon 109 bp [gt-ag] intron 33 GenBank accessions 92 bp exon 1347 bp [gt-ag] intron 16 GenBank accessions 199 bp exon 284 bp [gt-ag] intron 14 GenBank accessions 1 accession 30 bp exon 208 bp exon 15437 bp [gt-ag] intron 14 GenBank accessions 190 bp exon 2689 bp [gt-ag] intron 27 GenBank accessions 70 bp exon 109 bp [gt-ag] intron 33 GenBank accessions 92 bp exon 1347 bp [gt-ag] intron 16 GenBank accessions 116 bp exon 1 accession 116 bp exon 190 bp exon 190 bp exon 2689 bp [gt-ag] intron 27 GenBank accessions 70 bp exon 109 bp [gt-ag] intron 33 GenBank accessions 269 bp exon 17 accessions, some from inner ear (seen once) Validated 3' end, 11 accessions 269 bp exon 576 bp exon 576 bp exon 2 accessions, some from embryonic stem cell (seen once) whole embryo including extraembryonictissues at 13.5-days postcoitum (once) 576 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 uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aSep07 7486 bp 1434 aa 215 bp 2966 bp 2kb possibly including promoter 57588 bp 1kb
bSep07 7667 bp 791 aa 2077 bp 3214 bp 2kb possibly including promoter 65142 bp 1kb
581 aa 366 bp 5555 bp 2kb possibly including promoter 65142 bp 1kb
cSep07 852 bp 284 aa 2kb 21360 bp 1kb
dSep07 1399 bp 275 aa 574 bp 2kb possibly including promoter 22649 bp 1kb
eSep07 809 bp 257 aa 38 bp 2kb possibly including promoter 21151 bp 1kb
fSep07-unspliced 2216 bp 250 aa 1461 bp 750 bp 2kb 2216 bp 1kb
gSep07 676 bp 225 aa 675 bp 2kb 20258 bp 1kb
hSep07 529 bp 117 aa 173 bp 351 bp 2kb 3327 bp 1kb
iSep07-unspliced 576 bp 67 aa 371 bp 201 bp 2kb 576 bp 1kb
jSep07-unspliced 622 bp 59 aa 441 bp 177 bp 2kb 622 bp 1kb
kSep07-unspliced 583 bp 65 aa 384 bp 195 bp 2kb 583 bp 1kb
lSep07 542 bp 52 aa 383 bp 2kb 6317 bp 1kb
mSep07 305 bp 48 aa 107 bp 51 bp 2kb 731 bp 1kb

Gene neighbors and Navigator on chromosome 13 B3|13 36.0 cM back to top
2010111I01Rik C R P R R R 0610007P08Rikand9330134C04Rik C R C R C C R R R D C R P Fancc D C R P Ptch1 R R C030010C08Rik C EG665575 100kb 0 2010111I01Rik, 375 accessions 30 variants reniha, 10 accessions nohimo, 8 accessions, 2 variants farner, 1 accession 0610007P08Rikand9330134C04Rik 163 accessions, 13 variants stynee, 1 accession tenaha, 1 accession stunee, 1 accession stonee, 1 accession starnee, 1 accession stawnee, 1 accession sanaha, 4 accessions sawmoy, 1 accession steenee, 1 accession senaha, 5 accessions sonaha, 3 accessions sternee, 1 accession stornee, 1 accession kanaha, 10 accessions kunaha, 4 accessions swanee, 3 accessions swunee, 2 accessions konaha, 3 accessions raniha, 2 accessions swarnee, 3 accessions riniha, 6 accessions swawnee, 1 accession runiha, 1 accession yaniha, 2 accessions swornee, 1 accession byner, 1 accession yoniha, 1 accession bawner, 1 accession beener, 1 accession daner, 1 accession duner, 1 accession darner, 2 accessions dawner, 2 accessions meniha, 3 accessions faner, 2 accessions fyner, 1 accession funer, 2 accessions foner, 1 accession fawner, 1 accession moniha, 1 accession ferner, 2 accessions feyner, 5 accessions forner, 3 accessions haniha, 1 accession foyner, 1 accession ganer, 1 accession huniha, 2 accessions gyner, 1 accession goner, 1 accession garner, 1 accession honiha, 2 accessions geener, 1 accession sormoy, 1 accession soymoy, 1 accession naniha, 5 accessions goyner, 3 accessions sarmoy, 2 accessions tonaha, 2 accessions sinaha, 1 accession steynee, 1 accession kinaha, 6 accessions stoynee, 3 accessions 2 variants swynee, 1 accession swonee, 1 accession kenaha, 5 accessions roniha, 1 accession sweenee, 1 accession swernee, 1 accession sweynee, 1 accession swoynee, 1 accession baner, 2 accessions sermoy, 2 accessions, 2 variants yuniha, 2 accessions buner, 2 accessions boner, 1 accession barner, 1 accession maniha, 1 accession berner, 1 accession beyner, 2 accessions miniha, 9 accessions borner, 2 accessions boyner, 1 accession dyner, 8 accessions, 2 variants doner, 3 accessions deener, 1 accession derner, 1 accession deyner, 2 accessions dorner, 1 accession doyner, 1 accession muniha, 2 accessions feener, 1 accession hiniha, 1 accession guner, 1 accession gawner, 1 accession heniha, 2 accessions gerner, 2 accessions seymoy, 1 accession geyner, 1 accession gorner, 3 accessions RVT_1.172, 1 accession sunaha, 1 accession RVT_1.173, 1 accession nuhimo, 6 accessions, 2 variants seemoy, 7 accessions waniha, 2 accessions nehimo, 3 accessions Fancc, 176 accessions 17 variants Ptch1, 272 accessions 13 variants tahimo, 5 accessions, 2 variants C030010C08Rik, 12 accessions EG665575, 439 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               373 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f-u, .g, .h, .i-u, .j-u, .k-u, .l, .m 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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