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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtctaacctcttttcaacataaactccaaaaatatatgcaaacattgggctgtatgactaactctgtgattatgatttgattacagGACGAGCTCTAAGCAAAGGTGGAGGATTAAAAAGTTTTCAGAGTCTTAATTGTTCTTTTAAACTTTTCTTTTAAAAGGAATTCTTTAGCTCTAGTTTGGT

Basic information

species Arabidopsis thaliana
transcript AT1G56340.1
intron # 11
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|164009513|gb|ES097017.1|ES097017
EST:     CCAAGGAGGCCGAGGAAACCAAGGAAGCCGAGGAAACCGATGCCGCCCAT                         GACGAGCTCTAAGC
genomic: CCAAGGAGGCCGAGGAAACCAAGGAAGCCGAGGAAACCGATGCCGCCCATgtatgtgtct ... ttgattacagGACGAGCTCTAAGC
EST: gi|124801038|gb|EH890561.1|EH890561
EST:     CCAAGGAGGCCGAGGAAACCAAGGAAGCCGAGGAAACCGATGCCGCCCAT                         GACGAGCTCTAAGCAAAGG
genomic: CCAAGGAGGCCGAGGAAACCAAGGAAGCCGAGGAAACCGATGCCGCCCATgtatgtgtct ... ttgattacagGACGAGCTCTAAGCAAAGG
EST: gi|125259214|gb|EL273299.1|EL273299
EST:     GATGCCGCCCAT                         GACGAGCTCTAAGTCAAAGGTGGAGGATTAAAAAGTTTTCAGAGTCTTAAT
genomic: GATGCCGCCCATgtatgtgtct ... ttgattacagGACGAGCTCTAAG-CAAAGGTGGAGGATTAAAAAGTTTTCAGAGTCTTAAT
EST: gi|164038721|gb|ES110882.1|ES110882
EST:     CCAAGGAGGCCGAGGAAACCAAGGAAGCCGAGGAAACCGATGCCGCCCAT                         GACGAGCTCTAAG
genomic: CCAAGGAGGCCGAGGAAACCAAGGAAGCCGAGGAAACCGATGCCGCCCATgtatgtgtct ... ttgattacagGACGAGCTCTAAG
EST: gi|125265253|gb|EL279338.1|EL279338
EST:     CCAAGGAGGCCGAGGAAACCAAGGAAGCCGAGGAAACCGATGCCGCCCAT                         GACGAGCTCTAAGCAAAGGTGGAGGATTAAAAAGTTTTCAGAGTCTTAATT
genomic: CCAAGGAGGCCGAGGAAACCAAGGAAGCCGAGGAAACCGATGCCGCCCATgtatgtgtct ... ttgattacagGACGAGCTCTAAGCAAAGGTGGAGGATTAAAAAGTTTTCAGAGTCTTAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatgcaaacattgggctgtatgactaactctgtgattatgatttgattacagGACGAGCTCTAAGCAAAGGTGGAGGATTAAAAAGTTTTCAGAGTCTTAATTGTTCTTTTAAACTTTTCTTTTAAAAGGAATTCTTTAGCTCTAGTTTGGT
                                     attatgatttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtctaacctcttttcaacataaactccaaaaatatatgcaaacattgggctgtatgactaactctgtgattatgatttgattacagGACGAGCTCTAAGCAAAGGTGGAGGATTAAAAAGTTTTCAGAGTCTTAATTGTTCTTTTAAACTTTTCTTTTAAAAGGAATTCTTTAGCTCTAGTTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA