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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGAGCTGCGGCGCGACGACATGGAGGTGGCGGAGGAGGACATCAGCGACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggattgagctccttgctcctctgctcagtttttatgtggggggatgggggtaccatgatcagctttcgaatcagtcgtacgatggctcagacatt...

Basic information

species Oryza sativa
transcript LOC_Os06g47350.1
intron # 2
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|29656148|gb|CB652423.1|CB652423
EST:     ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATG                         GATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
genomic: ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggatt ... tttcattcagGATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
EST: gi|29636778|gb|CB641787.1|CB641787
EST:     ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATG                         GATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
genomic: ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggatt ... tttcattcagGATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
EST: gi|29676742|gb|CB673017.1|CB673017
EST:     ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATG                         GATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
genomic: ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggatt ... tttcattcagGATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
EST: gi|88575206|gb|CI669351.1|CI669351
EST:     ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATG                         GATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
genomic: ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggatt ... tttcattcagGATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
EST: gi|29678964|gb|CB675239.1|CB675239
EST:     ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATG                         GATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
genomic: ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggatt ... tttcattcagGATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
EST: gi|29624118|gb|CB629129.1|CB629129
EST:     ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATG                         GATCCTTTTCAAGTTGACCTAAGGGACAAAGAAGAGTACGATAGCTTGCTA
genomic: ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggatt ... tttcattcagGATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
EST: gi|29685786|gb|CB682061.1|CB682061
EST:     ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATG                         GATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
genomic: ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggatt ... tttcattcagGATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
EST: gi|88736559|gb|CI760067.1|CI760067
EST:     ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATG                         GATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA
genomic: ACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggatt ... tttcattcagGATCCTTTTCAAGTTGATCTAAGGGACAAAGAAGAGTATGATAGCTTGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGGAGCTGCGGCGCGACGACATGGAGGTGGCGGAGGAGGACATCAGCGACTCCCAGGCGTTCCGGTTCGTCGAGCACGTGCTCCAGTCCGTGCGGATGgtatgggattgagctccttgctcctctgctcagtttttatgtggggggatgggggtaccatgatcagctttcgaatcagtcgtacgatggctcagacatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgggg