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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatagcactgtacaaaatctgacaatggcctactcatgctattaagttcttttgcttcagtcttctttttgaggaaccatccccctgtaaaatttgcagGAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGGACAGTATCAAGATCCTCTGCTACATGATTTCACAAACTGTATAGTGGTA

Basic information

species Oryza sativa
transcript LOC_Os01g67490.2
intron # 5
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|87031599|gb|CI263972.1|CI263972
EST:     GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCT                         GAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
genomic: GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCTgtgagtatag ... aaatttgcagGAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
EST: gi|88992413|gb|CI035551.1|CI035551
EST:     GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCT                         GAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
genomic: GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCTgtgagtatag ... aaatttgcagGAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
EST: gi|89168675|gb|CI038527.1|CI038527
EST:     GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCT                         GAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
genomic: GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCTgtgagtatag ... aaatttgcagGAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
EST: gi|86833096|gb|CI333695.1|CI333695
EST:     GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCT                         GAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
genomic: GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCTgtgagtatag ... aaatttgcagGAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
EST: gi|88991813|gb|CI034951.1|CI034951
EST:     GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCT                         GAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
genomic: GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCTgtgagtatag ... aaatttgcagGAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
EST: gi|88987206|gb|CI034219.1|CI034219
EST:     GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCT                         GAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG
genomic: GGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCTgtgagtatag ... aaatttgcagGAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGG

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: 63 (upstream exon), 46 (downstream exon)
Score: 2

GTCAGGAGTATGGCAAGGACAATCCAATCTGCGTGCTCTACGATGGTTACGGACACTACGATGCGCTGCAGCCATCTCTTGTAAGAACACAATCAAGGCTgtgagtatag ... aaatttgcagGAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGGACAGTATCAAGATCCTCTGCTACATGATTTCACAAACTGTATAGTGGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcttttgcttcagtcttctttttgaggaaccatccccctgtaaaatttgcagGAGAGGAATACAGATAACCGAAGATTACGCTACCTAAGATTGTTCTCAAGGACAGTATCAAGATCCTCTGCTACATGATTTCACAAACTGTATAGTGGTA
                                         tgtaaaattt  TA-rich tract