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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taagggttttatgtagtccatctcatcagtaggtggactttcactcatatttgtatttcgttttgttgataatgttaaatgggtgtaacagctgctgcagCTATTCACTTCGTCCATAGCACGTAGATGGCAGAAAAGGCCTGTATAAAACGTCTTCAAAAGGAATATAGAGCACTTTGCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G17280.2
intron # 1
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|86056971|gb|DR352728.1|DR352728
EST:     TAACGAGAAACCCCAAGAGAGAAAATCTTCATCGACAAAATTCGATTCAG                         CTATTCACTTCGTCCATAGCACGTAGATGGCAGAAAAGGCCTGTATAAAAC
genomic: TAACGAGAAACCCCAAGAGAGAAAATCTTCATCGACAAAATTCGATTCAGgtgatcaatt ... gctgctgcagCTATTCACTTCGTCCATAGCACGTAGATGGCAGAAAAGGCCTGTATAAAAC
EST: gi|116477746|gb|EG520338.1|EG520338
EST:     GAGAAACCCCAAGAGAGAAAATCTTCATCGACAAAATTCGATTCAGCTGCTGCAG                 
genomic: GAGAAACCCCAAGAGAGAAAATCTTCATCGACAAAATTCG----A--T--T-CAGgtgatcaatt ... gc
EST: gi|86056972|gb|DR352729.1|DR352729
EST:     TAACGAGAAACCCCAAGAGAGAAAATCTTCATCGACAAAATTCGATTCAG                         CTATTCACTTCGTCCATAGCACGTAGATGGCAGAAAAGGCCTGTATAAAAC
genomic: TAACGAGAAACCCCAAGAGAGAAAATCTTCATCGACAAAATTCGATTCAGgtgatcaatt ... gctgctgcagCTATTCACTTCGTCCATAGCACGTAGATGGCAGAAAAGGCCTGTATAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatttgtatttcgttttgttgataatgttaaatgggtgtaacagctgctgcagCTATTCACTTCGTCCATAGCACGTAGATGGCAGAAAAGGCCTGTATAAAACGTCTTCAAAAGGAATATAGAGCACTTTGCAAG
                                     gtgtaac  putative branch site (score: 3)
                    ttgataatgttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taagggttttatgtagtccatctcatcagtaggtggactttcactcatatttgtatttcgttttgttgataatgttaaatgggtgtaacagctgctgcagCTATTCACTTCGTCCATAGCACGTAGATGGCAGAAAAGGCCTGTATAAAACGTCTTCAAAAGGAATATAGAGCACTTTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - ggtttta
- - - - - - - - - - -ctcatca
- - - - - - - - - - - - - - - - - - - - - actcata