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
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...
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the intron and exons table.
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron. ]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). ] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries. ]-[ Pink and ] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal, blue flags to any single letter variant of the main . More explanations are given in the gene help file
The mRNAs diagrams with the aligned cDNA sequence accessions and their mismatches are available in the mRNA pages accessible from the tab at the top of the page, or here:
In Flash: .b, .a.
or in GIF: .b, .a
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 !