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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatcgattttgcagcgaatactgaagcttgaaacagacttctttttgtcctaaaacctgaagaaatgatcttctttttctctctgaattctctcgcagTATTTCCCGGCCAAGTTGAGATGGTGAAGAAGAGGGAGAGAACATAAAAAAAATTGGTCGAAATTATCCTGTAATATGATGTAATTGCAGGAGTTCAGTT

Basic information

species Oryza sativa
transcript LOC_Os06g36560.2
intron # 9
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|29674860|gb|CB671135.1|CB671135
EST:     GGATAGACGTTGAGAAGGTGAAGCCCTACTACATGTCACTCATCGAAAAG                         TATTTCCCGGCCAAGTTGAGATGGTGAAGAAGAGGGAGAGAACATNNNNNN
genomic: GGATAGACGTTGAGAAGGTGAAGCCCTACTACATGTCACTCATCGAAAAGgtatgatcga ... tctctcgcagTATTTCCCGGCCAAGTTGAGATGGTGAAGAAGAGGGAGAGAACATAAAAAA
EST: gi|88834589|gb|CI077872.1|CI077872
EST:     GGATAGACGTTGAGAAGGTGAAGCCCTACTACATGTCACTCATCGAAAAG                         TATTTCCCGGCCAAGTTGAGATGGTGAAGAAGAGGGAGAGAACATNNNNNN
genomic: GGATAGACGTTGAGAAGGTGAAGCCCTACTACATGTCACTCATCGAAAAGgtatgatcga ... tctctcgcagTATTTCCCGGCCAAGTTGAGATGGTGAAGAAGAGGGAGAGAACATAAAAAA

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: 75 (upstream exon), 75 (downstream exon)
Score: 320

AATGGTTTTCTTCTGCAGCAAATACGACCTGTACAGCAAGAGCAATGAGAGGATAGACGTTGAGAAGGTGAAGCCCTACTACATGTCACTCATCGAAAAGgtatgatcga ... tctctcgcagTATTTCCCGGCCAAGTTGAGATGGTGAAGAAGAGGGAGAGAACATAAAAAAAATTGGTCGAAATTATCCTGTAATATGATGTAATTGCAGGAGTTCAGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtcctaaaacctgaagaaatgatcttctttttctctctgaattctctcgcagTATTTCCCGGCCAAGTTGAGATGGTGAAGAAGAGGGAGAGAACATAAAAAAAATTGGTCGAAATTATCCTGTAATATGATGTAATTGCAGGAGTTCAGTT
    tcctaaa  putative branch site (score: 320)
                         tcttctttttctctct  putative PPT
                           ttcttttt  TA-rich tract