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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatttttcatgtgttaaagattaaaatattaaggatttgatgttgttgatatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCGGAACTCGCATTGTTCTCCAAACTG

Basic information

species Arabidopsis thaliana
transcript AT4G20095.2
intron # 4
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|116482081|gb|EG524673.1|EG524673
EST:     GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAG                         ATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
genomic: GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAGgtgagatttt ... tatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
EST: gi|116482080|gb|EG524672.1|EG524672
EST:     GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAG                         ATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
genomic: GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAGgtgagatttt ... tatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
EST: gi|116482099|gb|EG524691.1|EG524691
EST:     GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAG                         ATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
genomic: GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAGgtgagatttt ... tatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
EST: gi|116482093|gb|EG524685.1|EG524685
EST:     GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAG                         ATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
genomic: GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAGgtgagatttt ... tatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
EST: gi|116482092|gb|EG524684.1|EG524684
EST:     GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAG                         ATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
genomic: GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAGgtgagatttt ... tatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
EST: gi|116482100|gb|EG524692.1|EG524692
EST:     GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAG                         ATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
genomic: GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAGgtgagatttt ... tatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
EST: gi|116482082|gb|EG524674.1|EG524674
EST:     GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAG                         ATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG
genomic: GGATGCCGGAAGATGCACTAACGGGAAGGGACAAGCTGCAATACTATGAGgtgagatttt ... tatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatgtgttaaagattaaaatattaaggatttgatgttgttgatatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCGGAACTCGCATTGTTCTCCAAACTG
                                       tgttgat  putative branch site (score: 4)
         ttaaagattaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatttttcatgtgttaaagattaaaatattaaggatttgatgttgttgatatggtacagATGAAAGATTCAGAGTTAGAAGAAGAGAAGGAATGGCTTCATCTATACGCGGAACTCGCATTGTTCTCCAAACTG

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