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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccctgctgttcagtttcctttctcgtctttgctttgtcacgtaatcgtctgtgtttttttggtcgtaatgtcattagctgcattatatagGTAACAATGCTTAGTGGTATTTCAACAACGAGCACAAAACTAAGCAGCCCAATGGCAGGACCAAAACTATTTAAAGAATTTATAAG

Basic information

species Arabidopsis thaliana
transcript AT3G13930.1
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|164134926|gb|ES083809.1|ES083809
EST:     GCCTGAATTATTCCTCTGTAGAGAGAATTTCAAAATGTGGTACTGGCAAT                         GTAACAATGCTTAGTGGTATTTCA
genomic: GCCTGAATTATTCCTCTGTAGAGAGAATTTCAAAATGTGGTACTGGCAATgtaagtccct ... cattatatagGTAACAATGCTTAGTGGTATTTCA
EST: gi|152038127|gb|BP808947.2|BP808947
EST:     GCCTGAATTATTCCTCTGTAGAGAGAATTTCAAAATGTGGTACTGGCAAT                         GTAACAATGCTTAGTGGTATTTCAACAACGAGCACA
genomic: GCCTGAATTATTCCTCTGTAGAGAGAATTTCAAAATGTGGTACTGGCAATgtaagtccct ... cattatatagGTAACAATGCTTAGTGGTATTTCAACAACGAGCACA
EST: gi|152037856|gb|BP800329.2|BP800329
EST:     GCCTGAATTATTCCTCTGTAGAGAGAATTTCAAAATGTGGTACTGGCAAT                         GTAACAATGCTTAGTGGTATTTCAACAACGAGCACAAAAGTAAGCAG
genomic: GCCTGAATTATTCCTCTGTAGAGAGAATTTCAAAATGTGGTACTGGCAATgtaagtccct ... cattatatagGTAACAATGCTTAGTGGTATTTCAACAACGAGCACAAAACTAAGCAG
EST: gi|124946307|gb|EL022241.1|EL022241
EST:     GCCTGAATTATTCCTCTGTAGAGAGAATTTCAAAATGTGGTACTGGCAAT                         GTAACAATGCTTAGTGGTATTTCAACAACGAGCA
genomic: GCCTGAATTATTCCTCTGTAGAGAGAATTTCAAAATGTGGTACTGGCAATgtaagtccct ... cattatatagGTAACAATGCTTAGTGGTATTTCAACAACGAGCA
EST: gi|164145389|gb|ES126983.1|ES126983
EST:     TGGTACTGGCAAT                         GTAACAATGCTTAGTGGTATTTCAACAACGAGCACAAAACTAAGCAGCCCA
genomic: TGGTACTGGCAATgtaagtccct ... cattatatagGTAACAATGCTTAGTGGTATTTCAACAACGAGCACAAAACTAAGCAGCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcacgtaatcgtctgtgtttttttggtcgtaatgtcattagctgcattatatagGTAACAATGCTTAGTGGTATTTCAACAACGAGCACAAAACTAAGCAGCCCAATGGCAGGACCAAAACTATTTAAAGAATTTATAAG
                                              attatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccctgctgttcagtttcctttctcgtctttgctttgtcacgtaatcgtctgtgtttttttggtcgtaatgtcattagctgcattatatagGTAACAATGCTTAGTGGTATTTCAACAACGAGCACAAAACTAAGCAGCCCAATGGCAGGACCAAAACTATTTAAAGAATTTATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA