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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattgatatctcgtgttctagctttggtggatccgtgtgttaattttgttggttaaactattttaacatgttaatatttgaatttgtaatcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCACAGGATGTTGTAG

Basic information

species Arabidopsis thaliana
transcript AT3G55440.1
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|116434595|gb|EG477187.1|EG477187
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434695|gb|EG477287.1|EG477287
EST:     TTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: TTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|125124711|gb|EL170522.1|EL170522
EST:     TTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGAATTGTGAACACTCTTAATGAAGC
genomic: TTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGA-TTGTGAACACTCTTAATGAAGC
EST: gi|116434684|gb|EG477276.1|EG477276
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|125300387|gb|EL314472.1|EL314472
EST:     CAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAGGCT
genomic: CAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434506|gb|EG477098.1|EG477098
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434673|gb|EG477265.1|EG477265
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434661|gb|EG477253.1|EG477253
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|124915705|gb|EH989579.1|EH989579
EST:     TGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: TGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116443947|gb|EG486539.1|EG486539
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116443934|gb|EG486526.1|EG486526
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434539|gb|EG477131.1|EG477131
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434639|gb|EG477231.1|EG477231
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434584|gb|EG477176.1|EG477176
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434617|gb|EG477209.1|EG477209
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGACAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACATTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434495|gb|EG477087.1|EG477087
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434717|gb|EG477309.1|EG477309
EST:     AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|125126717|gb|EL171784.1|EL171784
EST:     TGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTACTTAATGAAGC
genomic: TGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACT-CTTAATGAAGC
EST: gi|124795706|gb|EH885385.1|EH885385
EST:     CTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGAATTAGTGAACACTCTTAATGAAG
genomic: CTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGA-TT-GTGAACACTCTTAATGAAG
EST: gi|125024193|gb|EL096462.1|EL096462
EST:     CAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: CAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116430495|gb|EG473087.1|EG473087
EST:     NNTTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
EST: gi|116434650|gb|EG477242.1|EG477242
EST:     AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGT                         AACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT
genomic: AATTTGAGATAATGGCCAGAAAGTTCTTCGTCGGAGGCAACTGGAAATGTgtaagtgatc ... tcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttggttaaactattttaacatgttaatatttgaatttgtaatcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCACAGGATGTTGTAG
              tattttaacatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattgatatctcgtgttctagctttggtggatccgtgtgttaattttgttggttaaactattttaacatgttaatatttgaatttgtaatcttatatagAACGGAACTGCTGAGGAGGTGAAGAAGATTGTGAACACTCTTAATGAAGCTCAGGTTCCTTCACAGGATGTTGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - -gctttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aaactat