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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCCTCCTCGCGGAAAATCCTAGAAACAGAAAGAAATCGCACTCATGGCGAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcctcgatccatggccatggggggcgcccctcaccccctacgcagcgacatctctgatccgatctgagcctgactcctcctcgcctcgtcttgcag

Basic information

species Oryza sativa
transcript LOC_Os09g32526.1
intron # 1
splice site 5'
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|88694794|gb|CI738832.1|CI738832
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|88376918|gb|CI639243.1|CI639243
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|88733695|gb|CI756872.1|CI756872
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|163925746|gb|EG714582.1|EG714582
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|55432912|gb|CV729479.1|CV729479
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|88827078|gb|CI777643.1|CI777643
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|5004128|gb|AU069277.1|AU069277
EST:     AA--CGCANGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: AAGCCGCA-GCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|33687579|gb|CF315818.1|CF315818
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|66928292|gb|CX115140.1|CX115140
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|218484090|gb|FG956007.1|FG956007
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|163927898|gb|EG713510.1|EG713510
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|58678099|gb|CK066786.1|CK066786
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|88375448|gb|CI681220.1|CI681220
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|88739216|gb|CI762724.1|CI762724
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|58676104|gb|CK064791.1|CK064791
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|86903638|gb|CI300492.1|CI300492
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|33686364|gb|CF314603.1|CF314603
EST:     GAAGCCGCAGCTTCTTCCGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|88347332|gb|CI632617.1|CI632617
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|88574137|gb|CI665906.1|CI665906
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|218491364|gb|FG953091.1|FG953091
EST:     TGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: TGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|163920086|gb|EG709856.1|EG709856
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|88576196|gb|CI670341.1|CI670341
EST:     GAAGCCGNAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGAGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|88332240|gb|CI643657.1|CI643657
EST:     GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
EST: gi|10794952|gb|AU108918.1|AU108918
EST:     GAAGCCGCAGCTTCTTCTGNTCGTCGCCGCCGCCGCACTGCTACTCGTCG                         TTGCAG-CTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG
genomic: GAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcc ... cgtcttgcagTTGCAGCCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCCCTCCTCGCGGAAAATCCTAGAAACAGAAAGAAATCGCACTCATGGCGAAGCCGCAGCTTCTTCTGGTCGTCGCCGCCGCCGCACTGCTACTCGTCGgtaagtagcctcgatccatggccatggggggcgcccctcaccccctacgcagcgacatctctgatccgatctgagcctgactcctcctcgcctcgtcttgcag

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