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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctagcgtgtcatttttaacagaactccctcacaaaaccaacgtacctgatccgattggacctgctgataactattgttctccttgcattttctgtcagGGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAATGCTTCGAGTAAAACAGCCGGCAACAAGAAACCTGCCAAGGCTGGAACC

Basic information

species Oryza sativa
transcript LOC_Os01g10690.1
intron # 7
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|88376043|gb|CI530547.1|CI530547
EST:     GCTGCAAACAG                         GGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
genomic: GCTGCAAACAGgtaatgtctt ... tttctgtcagGGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
EST: gi|27921126|gb|CB096934.1|CB096934
EST:     GCAGGTGATAAGGCTGAGAAGAATGTGAGCGATATTGGTGCTGCAAACAG                         GGCAACTCTCTCA-GCAAGCCGCAGCCAGTAGCAAAGACCGAAAAA-GCAA
genomic: GCAGGTGATAAGGCTGAGAAGAATGTGAGCGATACTGGTGCTGCAAACAGgtaatgtctt ... tttctgtcagGGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
EST: gi|88380593|gb|CI521162.1|CI521162
EST:     GGTGCTGCAAACAG                         GGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
genomic: GGTGCTGCAAACAGgtaatgtctt ... tttctgtcagGGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
EST: gi|89188223|gb|CI115472.1|CI115472
EST:     GCAGGTGATAAGGCTGAGAAGAATGTGAGCGATACTGGTGCTGCAAACAG                         GGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
genomic: GCAGGTGATAAGGCTGAGAAGAATGTGAGCGATACTGGTGCTGCAAACAGgtaatgtctt ... tttctgtcagGGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
EST: gi|25807256|gb|CA763217.1|CA763217
EST:     GCAGGTGATAAGGCTGAGAAGAATGTGAGCGATATTGGTGCTGCAAACAG                         GGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
genomic: GCAGGTGATAAGGCTGAGAAGAATGTGAGCGATACTGGTGCTGCAAACAGgtaatgtctt ... tttctgtcagGGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
EST: gi|88842027|gb|CI081283.1|CI081283
EST:     GCAGGTGATAAGGCTGAGAAGAATGTGAGCGATACTGGTGCTGCAAACAG                         GGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA
genomic: GCAGGTGATAAGGCTGAGAAGAATGTGAGCGATACTGGTGCTGCAAACAGgtaatgtctt ... tttctgtcagGGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgatccgattggacctgctgataactattgttctccttgcattttctgtcagGGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAATGCTTCGAGTAAAACAGCCGGCAACAAGAAACCTGCCAAGGCTGGAACC
                     tgataac  putative branch site (score: 2)
                                 ttctccttgcattttc  putative PPT
                       ataactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctagcgtgtcatttttaacagaactccctcacaaaaccaacgtacctgatccgattggacctgctgataactattgttctccttgcattttctgtcagGGCAACTCTCTCAAGCAAGCCGCAGCCAGTAGCAAAGACCGAAAAAAGCAATGCTTCGAGTAAAACAGCCGGCAACAAGAAACCTGCCAAGGCTGGAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - aacagaac
- - - - - - - - - - - - - - - - - -aaaccaa
- - - - - - - - - - - - - - - - - - - - - -gtacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgat