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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaccatcctccacccaaaaatctagtctaattgcaaataagtcaagtagtaatcaacaacttgttgtatgtttctttgttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC

Basic information

species Arabidopsis thaliana
transcript AT1G56340.1
intron # 9
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|86064682|gb|DR360439.1|DR360439
EST:     GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG                         GAGTCAAAGGATGCTCCTGCTGAATCCGAC
genomic: GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAGgtaataacca ... gttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC
EST: gi|116465699|gb|EG508291.1|EG508291
EST:     GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG                         GAATCAAAGGATGCTCCTGCTGAATCCGAC
genomic: GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAGgtaataacca ... gttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC
EST: gi|116465718|gb|EG508310.1|EG508310
EST:     GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG                         GAATCAAAGGATGCTCCTGCTGAATCCGAC
genomic: GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAGgtaataacca ... gttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC
EST: gi|116465735|gb|EG508327.1|EG508327
EST:     GCGGAGAAAGCAGCATTTGACGAAGCTGATAAGAAGAGAGAGGAAGAG                         GAATCAAAGGATGCTCCTGCTGAATCCGAC
genomic: GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAGgtaataacca ... gttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC
EST: gi|116482410|gb|EG525002.1|EG525002
EST:     GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG                         GAATCAAAGGATGCTCCTGCTGAATCCGAC
genomic: GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAGgtaataacca ... gttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC
EST: gi|164121228|gb|ES188340.1|ES188340
EST:     CATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAG                         GAATCAAAGGATGCTCCTGCTGAATCCGAC
genomic: CATTTGACGAAGCTGAGAAGAAGAGAGAGGAAGAGgtaataacca ... gttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC
EST: gi|164084037|gb|ES163914.1|ES163914
EST:     CTGAGAAGAAGAGAGAGGAAGAG                         GAATCAAAGGATGCTCCTGCTGAATCCGACGCTGAGG
genomic: CTGAGAAGAAGAGAGAGGAAGAGgtaataacca ... gttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGACGCTGAGG
EST: gi|124738560|gb|EH829814.1|EH829814
EST:     AAGAAGAGAGAGGAAGAG                         GAATCAAAGGATGCTCCTGCTGAATCCGAC
genomic: AAGAAGAGAGAGGAAGAGgtaataacca ... gttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC
EST: gi|164065432|gb|EL985271.1|EL985271
EST:     GCGGAGAAAGCAGCATTTGACGAAGCTGAGAAAGAAGAGAGAGGAAGAG                         GAATCAAAGGAT
genomic: GCGGAGAAAGCAGCATTTGACGAAGCTGAGAA-GAAGAGAGAGGAAGAGgtaataacca ... gttttaccagGAATCAAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaataagtcaagtagtaatcaacaacttgttgtatgtttctttgttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC
                                      tttctttgttttacc  CT-rich tract
                                          tttgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaccatcctccacccaaaaatctagtctaattgcaaataagtcaagtagtaatcaacaacttgttgtatgtttctttgttttaccagGAATCAAAGGATGCTCCTGCTGAATCCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG