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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttcttgtattcttgattctttatttctacttttaaacatctttcacatttcattggatggatattttgggtggtaactttgttcctctcatgaggcagAACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g56640.1
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|4715475|gb|AU056592.1|AU056592
EST:     AGATTGGTGGATAAGGAGATG                         AACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTT
genomic: AGATTGGTGGATAAGGAGATGgtacgcccca ... catgaggcagAACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTT
EST: gi|4715422|gb|AU056539.1|AU056539
EST:     AGATTGGTGGATAAGGAGATG                         AACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTT
genomic: AGATTGGTGGATAAGGAGATGgtacgcccca ... catgaggcagAACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTT
EST: gi|33680312|gb|CF308551.1|CF308551
EST:     GAGCAGATTGGTGGATAAGGAGATG                         AACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTT
genomic: GAGCAGATTGGTGGATAAGGAGATGgtacgcccca ... catgaggcagAACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTT
EST: gi|5803388|gb|AI978336.1|AI978336
EST:     GCAGATTGGTGGATAAGGAGATG                         AACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTT
genomic: GCAGATTGGTGGATAAGGAGATGgtacgcccca ... catgaggcagAACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatttcattggatggatattttgggtggtaactttgttcctctcatgaggcagAACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAG
                           tggtaac  putative branch site (score: 2)
                                 ctttgttcctctcat  CT-rich tract
                 atatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttcttgtattcttgattctttatttctacttttaaacatctttcacatttcattggatggatattttgggtggtaactttgttcctctcatgaggcagAACAAAATGGTGCAGGAGAATTCTGTTTCTTGTTCAAAAGGTACAACTGTTTGTCAGCCTACAGATGAAGAATCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA