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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatccaaaagtgatccaagcataaccttttcacccttgctcatctaagatgtttgttctgattgttttggtggtgattgtttttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAGATAACTACCACTGTTAGTGGTGTCAAAATCTCAGAGCTTCTAAGTTACC

Basic information

species Arabidopsis thaliana
transcript AT4G26850.1
intron # 5
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|124917603|gb|EH991477.1|EH991477
EST:     GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTT
genomic: GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTT
EST: gi|125283640|gb|EL297725.1|EL297725
EST:     GGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
genomic: GGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
EST: gi|124902353|gb|EH976433.1|EH976433
EST:     GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAG
genomic: GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAG
EST: gi|125110072|gb|EL162212.1|EL162212
EST:     CACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
genomic: CACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
EST: gi|86058721|gb|DR354478.1|DR354478
EST:     GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
genomic: GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
EST: gi|164050106|gb|ES168153.1|ES168153
EST:     GCTTTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
genomic: GCTTTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
EST: gi|124961548|gb|EL036067.1|EL036067
EST:     GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCA
genomic: GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCA
EST: gi|125228729|gb|EL242814.1|EL242814
EST:     TTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
genomic: TTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
EST: gi|86058720|gb|DR354477.1|DR354477
EST:     GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
genomic: GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
EST: gi|125309867|gb|EL323952.1|EL323952
EST:     GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTAC
genomic: GTTACAACAGCTTGGGTGCTTTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTAC
EST: gi|125040078|gb|EL112347.1|EL112347
EST:     TGCTTTTGCCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
genomic: TGCTTTTGCCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
EST: gi|124952291|gb|EL027574.1|EL027574
EST:     CCACTATCAATCATCTCCACTTTCAG                         GCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG
genomic: CCACTATCAATCATCTCCACTTTCAGgtatatccaa ... ttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcatctaagatgtttgttctgattgttttggtggtgattgtttttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAGATAACTACCACTGTTAGTGGTGTCAAAATCTCAGAGCTTCTAAGTTACC
                  ttctgat  putative branch site (score: 3)
                                       ttgttttt  putative PPT
                                      attgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatccaaaagtgatccaagcataaccttttcacccttgctcatctaagatgtttgttctgattgttttggtggtgattgtttttggaaacagGCTTATTACTTGGCCATGCCTTTCCCACTGGAGAAAGCTCCTACCAAGAAGATAACTACCACTGTTAGTGGTGTCAAAATCTCAGAGCTTCTAAGTTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT