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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatattttgaattttcttgggtggtgctatattgtcaggggttccatattgttatatttagtattattaactgatcattgttcatgcttttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTACAGGCCATGTGACCTATGATGGTTACCATAATGCAAACTATTCTCAGCTG

Basic information

species Oryza sativa
transcript LOC_Os02g47410.1
intron # 16
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|86437401|gb|CI119123.1|CI119123
EST:     ATTGCAAACTCAAACTCTTTATCCATGAATCAAAG                         AGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
genomic: ATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|87039717|gb|CI194339.1|CI194339
EST:     AACTCTTTATCCATGAATCAAAG                         AGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
genomic: AACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|87038519|gb|CI193141.1|CI193141
EST:     ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAG                         AGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
genomic: ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|29638403|gb|CB643412.1|CB643412
EST:     ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAG                         AGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
genomic: ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|87041686|gb|CI196308.1|CI196308
EST:     ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAG                         AGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
genomic: ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|87040692|gb|CI195314.1|CI195314
EST:     CTCTTTATCCATGAATCAAAG                         AGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
genomic: CTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|58601341|gb|CK011869.1|CK011869
EST:     ATCCAAAGCCATGCTATTGCAAACTCAAACGCTGTATCCATGAATCAAAG                         AGGTGACCACCTGTTCCATGCATCAACTCTTACAGAGACTAGTGCCTCTAC
genomic: ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|87016346|gb|CI271757.1|CI271757
EST:     ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAG                         AGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGT-GTGCCTCTAC
genomic: ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|29622303|gb|CB627314.1|CB627314
EST:     ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAG                         AGGTGACCACCTGTTCCATGCATCAACTCTTACAGAGACTAGTGCCTCTAC
genomic: ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|87040709|gb|CI195331.1|CI195331
EST:     ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAG                         AGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
genomic: ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|218498653|gb|FG968593.1|FG968593
EST:     ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAG                         AGGTGACCACCTGTTCCATGCATCAACTCTTACAGAGACTAGTGCCTCTAC
genomic: ATCCAAAGCCATGCTATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
EST: gi|87018950|gb|CI256835.1|CI256835
EST:     ATTGCAAACTCGAACTCTTTATCCATGAATCAAAG                         AGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC
genomic: ATTGCAAACTCAAACTCTTTATCCATGAATCAAAGgtacttaagt ... tttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatattgttatatttagtattattaactgatcattgttcatgcttttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTACAGGCCATGTGACCTATGATGGTTACCATAATGCAAACTATTCTCAGCTG
                                     ttcatgcttttcct  CT-rich tract
        ttatatttagtattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatattttgaattttcttgggtggtgctatattgtcaggggttccatattgttatatttagtattattaactgatcattgttcatgcttttcctatagAGGTGACCGCCTGTTCCATGCATCAACTCTTACAGAGAGTAGTGCCTCTACAGGCCATGTGACCTATGATGGTTACCATAATGCAAACTATTCTCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG