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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgttgctgatgtttttttcttttacactatgctcatgtgattctcattgattgaggatattttttttatcaatctccagGTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g58080.1
intron # 12
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|89193755|gb|CI116388.1|CI116388
EST:     CTGGAACAGGAGGTGGACAAG                         GTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAG
genomic: CTGGAACAGGAGGTGGACAAGgtttgtgttg ... caatctccagGTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAG
EST: gi|86485320|gb|CI127953.1|CI127953
EST:     GACTGCTGAGCTGACTGCTGGAACAGGAGGTGGACAAG                         TTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAG
genomic: GACTGCTGAGCTGACTGCTGGAACAGGAGGTGGACAAGgtttgtgttg ... caatctccagGTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAG
EST: gi|25798277|gb|CA754238.1|CA754238
EST:     TCCTTTTTCTGTGACTGCTGAGCTGACTGCTGGAACAGGAGGTGGACAAG                         GTCTGGGCA-CAGGAGTCCTGAACCTTGNCA-TCGTTGTTCCGCAG
genomic: TCCTTTTTCTGTGACTGCTGAGCTGACTGCTGGAACAGGAGGTGGACAAGgtttgtgttg ... caatctccagGTCTGG-CAACAGGAGTCCTGAACCTTG-CAATCGTTGTTCCGCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 64 (upstream exon), 44 (downstream exon)
Score: 6

ATCACATATAGCGTTCCTTTTTCTGTGACTGCTGAGCTGACTGCTGGAACAGGAGGTGGACAAGgtttgtgttg ... caatctccagGTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactatgctcatgtgattctcattgattgaggatattttttttatcaatctccagGTCTGGCAACAGGAGTCCTGAACCTTGCAATCGTTGTTCCGCAG
                    cattgat  putative branch site (score: 6)
                                   ttttttttatc  putative PPT
                                atattttttttatcaa  TA-rich tract