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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagtgtgattgttatatatcattgatatttgctgaatcctgttgcatttctttcttcttttttttttgagagtgaatcctgttgcatttctgatgtcatctgtttgcactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCTGGGATCACATAAAGGTGACAATTCGGTTCCATGAATATTCTGCCCTTAG

Basic information

species Oryza sativa
transcript LOC_Os04g43220.1
intron # 8
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|88843020|gb|CI371920.1|CI371920
EST:     TT-GTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|29674337|gb|CB670612.1|CB670612
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|88843030|gb|CI371930.1|CI371930
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|86427341|gb|CI072438.1|CI072438
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|88289588|gb|CI522721.1|CI522721
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|87005739|gb|CI316158.1|CI316158
EST:     TTTGTGATACGATCCCCCGCTTGCCATCCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|88289758|gb|CI525090.1|CI525090
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|29667534|gb|CB663809.1|CB663809
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|88455774|gb|CI524193.1|CI524193
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|86860667|gb|CI324938.1|CI324938
EST:     TTGGTGATACGATCCCCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|88291197|gb|CI527587.1|CI527587
EST:     CGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: CGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|86841664|gb|CI337363.1|CI337363
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|88320841|gb|CI527993.1|CI527993
EST:     TGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|88375787|gb|CI528091.1|CI528091
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|89183386|gb|CI045951.1|CI045951
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|86835123|gb|CI346598.1|CI346598
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|88977912|gb|CI384394.1|CI384394
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|86887032|gb|CI324453.1|CI324453
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|89177761|gb|CI390940.1|CI390940
EST:     TTGGTGATACGATCCCCCGCTTTCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|89177589|gb|CI390768.1|CI390768
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
EST: gi|29642643|gb|CB647650.1|CB647650
EST:     TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAA                         TGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT
genomic: TTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCT

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: 54 (upstream exon), 68 (downstream exon)
Score: 7

TCAAATATTGAAGAGCCGTGTGCAGTTTGCCTTGATAATCCCTCTATTGGTGATACGATCCGCCGCTTGCCATGCTTTCACATGTTCCATAAAGAAgtatgcagtg ... cactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCTGGGATCACATAAAGGTGACAATTCGGTTCCATGAATATTCTGCCCTTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgagagtgaatcctgttgcatttctgatgtcatctgtttgcactctgcagTGCATAGACGAATGGCTAAGAAGGAAGAAACTATGTCCAGTTTGCAAGTCTGGGATCACATAAAGGTGACAATTCGGTTCCATGAATATTCTGCCCTTAG
                          ttctgat  putative branch site (score: 7)