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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccactgaagtggatcaattcatatcatacaattttacaaatgcaatcttcctcatttctgccaatgtttgctcatccatatgctcctgcttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATACCTCCAAAGTGGATGTAACAATTCTGTGGGGAGCAAAGCCTCATCACTC

Basic information

species Oryza sativa
transcript LOC_Os03g58530.2
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|9865574|gb|AU101324.1|AU101324
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATNTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|88987559|gb|CI034472.1|CI034472
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|88849191|gb|CI087713.1|CI087713
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|88839650|gb|CI015741.1|CI015741
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|15008655|gb|AU223043.1|AU223043
EST:     GAAAGGATCTCCAAAAGTCCAATGGTGCTACTGTGCAATNTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCNATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|86536262|gb|CI176468.1|CI176468
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|44673976|gb|CR287410.1|CR287410
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGCGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|88204685|gb|CI204534.1|CI204534
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|87032905|gb|CI187529.1|CI187529
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|15008654|gb|AU223042.1|AU223042
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|88239337|gb|CI240499.1|CI240499
EST:     GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: GAAAGGATCTACAAAAGTCCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|88284937|gb|CI406383.1|CI406383
EST:     CAATGGTGGTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: CAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
EST: gi|86873864|gb|CI334396.1|CI334396
EST:     CCAATGGTGCTACTGTGCAATCTGAAGAAAAG                         GTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA
genomic: CCAATGGTGCTACTGTGCAATCTGAAGAAAAGgtaaactgag ... cttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcttcctcatttctgccaatgtttgctcatccatatgctcctgcttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATACCTCCAAAGTGGATGTAACAATTCTGTGGGGAGCAAAGCCTCATCACTC
                                       ctcctgctt  CT-rich tract
                   aatgttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccactgaagtggatcaattcatatcatacaattttacaaatgcaatcttcctcatttctgccaatgtttgctcatccatatgctcctgcttgcatcagGTGCAGTCCAAACGACGGCGGAGGTGATGCCATGGAGACAGAATCTCAATACCTCCAAAGTGGATGTAACAATTCTGTGGGGAGCAAAGCCTCATCACTC

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