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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGGCCGCACGGTCTCTCGCTCCACCTGAGGCCGCCTGCTATGGCCTCCGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctgcgtcgtcgattaggcttttgttctgttgcgcttcatgtgatttgctaccatgctatgcttgacatctccactagcagtaggcagtagcagtagctattccaagagttcttactctcttttgtgaaagctaatcctatttaatttgattttttaaactctggtttgtgttcggaattctcag

Basic information

species Oryza sativa
transcript LOC_Os04g52710.3
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|58588701|gb|CF987009.1|CF987009
EST:     CGCCGCGGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAG                         CGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
genomic: CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctg ... gaattctcagCGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
EST: gi|29658246|gb|CB654521.1|CB654521
EST:     CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAG                         CGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
genomic: CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctg ... gaattctcagCGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
EST: gi|88424747|gb|CI606546.1|CI606546
EST:     CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAG                         CGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
genomic: CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctg ... gaattctcagCGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
EST: gi|38471849|gb|CF955980.1|CF955980
EST:     CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAG                         CGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
genomic: CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctg ... gaattctcagCGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
EST: gi|88357594|gb|CI623648.1|CI623648
EST:     CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAG                         CGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
genomic: CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctg ... gaattctcagCGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
EST: gi|58668546|gb|CK057232.1|CK057232
EST:     CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAG                         CGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
genomic: CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctg ... gaattctcagCGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
EST: gi|29676398|gb|CB672673.1|CB672673
EST:     CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAG                         CGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
genomic: CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctg ... gaattctcagCGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
EST: gi|218497506|gb|FG955300.1|FG955300
EST:     CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAG                         CGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC
genomic: CGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctg ... gaattctcagCGTTGTCCAGGATAGGAGAAGTCAAGAGGGTGACCAAGGAGACGAATGTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCGGCCGCACGGTCTCTCGCTCCACCTGAGGCCGCCTGCTATGGCCTCCGCCGCCGCCGCCGGGAACGGCTCTCCTTCCGCGCCGGAGGACTCCACAGgtggattctgcgtcgtcgattaggcttttgttctgttgcgcttcatgtgatttgctaccatgctatgcttgacatctccactagcagtaggcagtagcagtagctattccaagagttcttactctcttttgtgaaagctaatcctatttaatttgattttttaaactctggtttgtgttcggaattctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA