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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatataccaaggcctttttctcatcacatcatcgtattgtcagggaagaaacaacagctccagtaaaccaaaagcctaaaatcatgtttctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCATCATTCTTGGTCTGTACTGAG

Basic information

species Oryza sativa
transcript LOC_Os01g18800.4
intron # 9
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|29681596|gb|CB677871.1|CB677871
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|86851934|gb|CI316503.1|CI316503
EST:     GGATTCCAAGTCCAGAGGGGTAATAACAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: GGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|4716471|gb|AU057587.1|AU057587
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|58691448|gb|CK080135.1|CK080135
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAAGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|89178091|gb|CI391270.1|CI391270
EST:     GGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: GGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|29620378|gb|CB625390.1|CB625390
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAAGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|86908767|gb|CI319031.1|CI319031
EST:     AGAATTTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATACCAAG                         CTAAAGGTCATGAAAAATGGCA-GGGTTCAAAGAACCTCA-GAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|4714970|gb|AU056087.1|AU056087
EST:     AGAATGTTGTGACGGAGATGGGATTCCAANTCCAGAGGGGTAATACCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|2317562|gb|C22616.1|C22616
EST:     AGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|86852707|gb|CI321827.1|CI321827
EST:     AGAATGTTGTGAC-GAGAT-GGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|33794290|gb|CF323032.1|CF323032
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|4714969|gb|AU056086.1|AU056086
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|29685924|gb|CB682199.1|CB682199
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|33656212|gb|CF278826.1|CF278826
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|29614338|gb|CB619351.1|CB619351
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAAGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|86873660|gb|CI341093.1|CI341093
EST:     GAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: GAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|29626405|gb|CB631416.1|CB631416
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAAGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|86841350|gb|CI336379.1|CI336379
EST:     ATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: ATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|88843115|gb|CI372015.1|CI372015
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|7608753|gb|AU090534.1|AU090534
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|89181904|gb|CI113410.1|CI113410
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|29638650|gb|CB643659.1|CB643659
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|88270625|gb|CI385883.1|CI385883
EST:     AGAATGTT-TGACGGAGAT-GGATTCCAAGTCCAGAGGGGTAATACCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|86908580|gb|CI318936.1|CI318936
EST:     AGAATG-TGTGAC-GAGAT-GGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGGTCATGAAAAATGCCAGGGGTTCAAAGAACCTCACGGAATCCAT
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAA-GGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCA-GGAATCCAT
EST: gi|88197193|gb|CI197043.1|CI197043
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|88548764|gb|CI478588.1|CI478588
EST:     GTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: GTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|86876443|gb|CI318423.1|CI318423
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCA-GAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|88905990|gb|CI089576.1|CI089576
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|29687811|gb|CB684086.1|CB684086
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|88264315|gb|CI368089.1|CI368089
EST:     ATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: ATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|58681853|gb|CK070540.1|CK070540
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAAGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA
EST: gi|58593223|gb|CF991531.1|CF991531
EST:     AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAG                         CTAAAGGTCATGAAAAATGGCAAGGGTTCAAAGAACCTCAGGAATCCATCA
genomic: AGAATGTTGTGACGGAGATGGGATTCCAAGTCCAGAGGGGTAATAGCAAGgtagatatac ... ctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaaacaacagctccagtaaaccaaaagcctaaaatcatgtttctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCATCATTCTTGGTCTGTACTGAG
                             gcctaaa  putative branch site (score: 3)
                                     tcatgtttctcttt  CT-rich tract
                                taaaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatataccaaggcctttttctcatcacatcatcgtattgtcagggaagaaacaacagctccagtaaaccaaaagcctaaaatcatgtttctctttgcagCTAAAGGTCATGAAAAATGGCAGGGGTTCAAAGAACCTCAGGAATCCATCATCATTCTTGGTCTGTACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC