Arabidopsis thaliana gene AT4G38350, encoding patched family protein.
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SUMMARY back to top
TAIR annotates one representative transcript (NM included in AceView variant.a), but Arabidopsis thaliana 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 2 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 0.5 times the average gene in this release. The sequence of this gene is defined by 17 GenBank accessions, some from ovule (seen 6 times), aerial (5), hormone treated callus (2), see description (once), seedling hypocotyl (once).
Alternative mRNA variants and regulation: The gene contains 39 distinct gt-ag introns. Transcription produces 2 alternatively spliced mRNAs. There are 2 probable alternative promotors (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of 5 cassette exons, overlapping exons with different boundaries.
Proteins are expected to have molecular function (hedgehog receptor activity) and to localize in membrane. No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Please see the Arabidopsis TAIR site TAIR:AT4G38350 for in depth functional annotation of this gene.
Protein coding potential: The 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (1 complete, 1 COOH complete), containing Patched domain [Pfam], some transmembrane domains [Psort2].
Isoform AT4G38350.bOct08 is annotated using as Met a Kozak-compatible a..GTGg start, thereby gaining 259 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 4, links to other databases and other names
Map: This gene AT4G38350 maps on chromosome 4. In AceView, it covers 8.24 kb, from 17966411 to 17958174 (NCBI 7_1, April 2007), on the reverse strand.
Links to: manual annotations from TAIR:AT4G38350, the SNP view, gene overviews from Entrez Gene 829992, expression data from UniGene.
Other names: The gene is also known as AT4G38350, F22I13.120 or F22I13_120, LOC829992. It has been described as patched family protein.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene NPC1 (e=4 10-76).
The closest mouse gene, according to BlastP, is the AceView gene Npc1 (e=2 10-76).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene ncr-1 (e=10-38), 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 AT4G38350 5' 3' encoded on minus strand of chromosome 4 from 17,966,411 to 17,958,174 a [NM] b 10kb 0 72 bp exon 88 bp [gt-ag] intron only supported by one RefSeq model 108 bp exon 86 bp [gt-ag] intron only supported by one RefSeq model 117 bp exon 87 bp [gt-ag] intron only supported by one RefSeq model 151 bp exon 89 bp [gt-ag] intron only supported by one RefSeq model 129 bp exon 48 bp [gt-ag] intron only supported by one RefSeq model 71 bp exon 89 bp [gt-ag] intron only supported by one RefSeq model 186 bp exon 155 bp [gt-ag] intron only supported by one RefSeq model 56 bp exon 103 bp [gt-ag] intron only supported by one RefSeq model 118 bp exon 103 bp [gt-ag] intron 2 GenBank accessions 84 bp exon 90 bp [gt-ag] intron 2 GenBank accessions 96 bp exon 116 bp [gt-ag] intron 4 GenBank accessions 102 bp exon 175 bp [gt-ag] intron 2 GenBank accessions 69 bp exon 152 bp [gt-ag] intron 2 GenBank accessions 96 bp exon 72 bp [gt-ag] intron 3 GenBank accessions 108 bp exon 111 bp [gt-ag] intron 2 GenBank accessions 114 bp exon 116 bp [gt-ag] intron 2 GenBank accessions 84 bp exon 351 bp [gt-ag] intron 2 GenBank accessions 129 bp exon 91 bp [gt-ag] intron 2 GenBank accessions 199 bp exon 71 bp [gt-ag] intron only supported by one RefSeq model 144 bp exon 93 bp [gt-ag] intron only supported by one RefSeq model 38 bp exon 138 bp [gt-ag] intron only supported by one RefSeq model 84 bp exon 811 bp [gt-ag] intron only supported by one RefSeq model 150 bp exon 333 bp [gt-ag] intron only supported by one RefSeq model 145 bp exon 104 bp [gt-ag] intron 4 GenBank accessions 65 bp exon 274 bp [gt-ag] intron only supported by one RefSeq model 94 bp exon 406 bp [gt-ag] intron only supported by one RefSeq model 92 bp exon 227 bp [gt-ag] intron 2 GenBank accessions 68 bp exon 149 bp [gt-ag] intron 3 GenBank accessions 67 bp exon 86 bp [gt-ag] intron 4 GenBank accessions 69 bp exon 85 bp [gt-ag] intron 3 GenBank accessions 6 accessions, NM_119997 some from aerial (seen 2 times) ovule (2), hormone treated callus (once) 90 bp exon 83 bp exon 83 bp exon 93 bp [gt-ag] fuzzy intron 2 GenBank accessions 70 bp exon 188 bp [gt-ag] intron 2 GenBank accessions 150 bp exon 201 bp [gt-ag] intron 2 GenBank accessions 66 bp exon 66 bp [gt-ag] intron 3 GenBank accessions 145 bp exon 104 bp [gt-ag] intron 4 GenBank accessions 65 bp exon 71 bp [gt-ag] intron 5 GenBank accessions 66 bp exon 137 bp [gt-ag] intron 3 GenBank accessions 94 bp exon 86 bp [gt-ag] intron 3 GenBank accessions 37 bp exon 87 bp [gt-ag] intron 3 GenBank accessions 58 bp exon 119 bp [gt-ag] intron 2 GenBank accessions 111 bp exon 227 bp [gt-ag] intron 2 GenBank accessions 68 bp exon 149 bp [gt-ag] intron 3 GenBank accessions 67 bp exon 86 bp [gt-ag] intron 4 GenBank accessions 69 bp exon 85 bp [gt-ag] intron 3 GenBank accessions 234 bp exon 11 accessions, some from ovule (seen 4 times) aerial (3), hormone treated callus (once) see description (once) seedling hypocotyl (once) 234 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
aOct08 3195 bp 1064 aa 2kb 8094 bp 1kb
bOct08 1383 bp 399 aa 39 bp 144 bp 2kb possibly including promoter 3082 bp 1kb

Gene neighbors and Navigator on chromosome 4 back to top
C R AT4G38070 C P AT4G38080 C AT4G38092 C PDE191 C R FRS9 C R AT4G38200 C R P AT4G38215 C R AT4G38220 C R AT4G38225 C R AT4G38250 C R P GAUT3 C R P AT4G38280andAT4G38290 C R AT4G38310andHHP5 C R P AT4G38330 C R AT4G38340 C AT4G38360 C R AT4G38390 C R AT4G38410 C SKS9 C P ATROPGEF1/ROPGEF1 C R P AT4G38440 C GGR C P AT4G38470 C R P AT4G38480 C AT4G38490 C AT4G38500 C R P ATPLC1andAT4G38540 C R P AT4G38550 C AT4G38560 C R R ATFP6 C P BGAL14 C R C R MYB4 D C P AT4G38650 AT4G38401 AT4G38405 C P C AT4G38060 C R AT4G38090 C R P AT4G38100 C R AT4G38120 D C P HD1 C P AT4G38140 C AT4G38150 C R FRS5 C ATCSLD4 C P ATEXPA20 D C R P CGL1andCPK26 C R AT4G38260 C AT4G38300 R R C R AT4G38350 C R AT4G38380andAT4G38370 C P ATEXLA2 C R AT4G38495 C R C R AT4G38510 C R AT4G38520 R AT4G38545 C R C R P PIS2 D C R P KAK D C P RPN10 10 20kb 0 AT4G38020, 18 accessions AT4G38040, 31 accessions 3 variants AT4G38070, 10 accessions 2 variants AT4G38080, 32 accessions AT4G38092, 2 accessions PDE191, 71 accessions 2 variants FRS9, 24 accessions, 2 variants AT4G38200, 20 accessions 2 variants AT4G38215, 7 accessions AT4G38220, 188 accessions 3 variants AT4G38225, 69 accessions 3 variants AT4G38250, 85 accessions GAUT3, 18 accessions AT4G38280andAT4G38290 41 accessions, 5 variants AT4G38310andHHP5, 54 accessions 2 variants AT4G38330, 5 accessions 2 variants AT4G38340, 3 accessions AT4G38360, 32 accessions 3 variants AT4G38390, 2 accessions AT4G38410, 9 accessions SKS9, 31 accessions, 2 variants ATROPGEF1/ROPGEF1, 104 accessions AT4G38440, 22 accessions GGR, 131 accessions AT4G38470, 20 accessions 2 variants AT4G38480, 13 accessions AT4G38490, 26 accessions AT4G38500, 39 accessions ATPLC1andAT4G38540, 63 accessions 2 variants AT4G38550, 62 accessions AT4G38560, 12 accessions 3 variants kloybee, 2 accessions ATFP6, 71 accessions, 2 variants BGAL14, 2 accessions plybee, 1 accession MYB4, 43 accessions klordoy, 1 accession AT4G38052, 1 accession klawbee, 1 accession AT4G38401, 1 accession AT4G38405, 1 accession klorbee, 1 accession kleydoy, 1 accession AT4G38030, 3 accessions 2 variants AT4G38050, 9 accessions AT4G38060, 64 accessions 3 variants AT4G38090, 28 accessions 3 variants AT4G38100, 16 accessions AT4G38120, 14 accessions 5 variants HD1, 129 accessions, 2 variants AT4G38140, 5 accessions AT4G38150, 25 accessions 2 variants FRS5, 12 accessions ATCSLD4, 3 accessions ATEXPA20, 7 accessions CGL1andCPK26, 29 accessions 5 variants AT4G38260, 41 accessions 3 variants AT4G38300, 8 accessions 2 variants klawdoy, 2 accessions kleybee, 1 accession AT4G38350, 17 accessions 2 variants AT4G38380andAT4G38370 21 accessions, 3 variants ATEXLA2, 35 accessions AT4G38495, 14 accessions kleedoy, 3 accessions AT4G38510, 162 accessions 5 variants AT4G38520, 95 accessions 2 variants AT4G38545, 18 accessions 4 variants klerdoy, 7 accessions PIS2, 22 accessions, 2 variants KAK, 61 accessions, 2 variants RPN10, 142 accessions ZOOM IN                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 C

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 !