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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagatttcaataattaccaaagccagaacaatgcaaaatctttgtttatatttgtcccgcttttaatctctctatgtcgttctcctgttttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTGGAAGAACAAGTAAGGAAGATAAGAGAAGTTGGGAAGGTAATGACAATGG

Basic information

species Arabidopsis thaliana
transcript AT5G24314.1
intron # 3
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|86062440|gb|DR358197.1|DR358197
EST:     GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTG                         ACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
genomic: GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTGgtaagtacta ... ttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
EST: gi|86087301|gb|DR383060.1|DR383060
EST:     GGATTCAGAGAGATGATAATGGACSCCGTGTTTGGCGGAGGAGAACATTG                         ACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
genomic: GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTGgtaagtacta ... ttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
EST: gi|86062439|gb|DR358196.1|DR358196
EST:     GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTG                         ACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
genomic: GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTGgtaagtacta ... ttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
EST: gi|86062438|gb|DR358195.1|DR358195
EST:     GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTG                         ACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
genomic: GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTGgtaagtacta ... ttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
EST: gi|86062437|gb|DR358194.1|DR358194
EST:     GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTG                         ACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
genomic: GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTGgtaagtacta ... ttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
EST: gi|86062441|gb|DR358198.1|DR358198
EST:     GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTG                         ACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
genomic: GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTGgtaagtacta ... ttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
EST: gi|86062443|gb|DR358200.1|DR358200
EST:     GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTG                         ACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
genomic: GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTGgtaagtacta ... ttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
EST: gi|86075735|gb|DR371492.1|DR371492
EST:     GGATCCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTG                         ACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
genomic: GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTGgtaagtacta ... ttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
EST: gi|86062442|gb|DR358199.1|DR358199
EST:     GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTG                         ACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG
genomic: GGATTCAGAGAGATGATAATGGACGCCGTGTTTGGCGGAGGAGAACATTGgtaagtacta ... ttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatatttgtcccgcttttaatctctctatgtcgttctcctgttttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTGGAAGAACAAGTAAGGAAGATAAGAGAAGTTGGGAAGGTAATGACAATGG
                ttttaat  putative branch site (score: 3)
                                   ttctcctgttttgtct  putative PPT
                ttttaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagatttcaataattaccaaagccagaacaatgcaaaatctttgtttatatttgtcccgcttttaatctctctatgtcgttctcctgttttgtctgtagACGAAGAAGGACGATATGTTGCGTTACAAAATGCAAAGAGTTCCATTTGTGGAAGAACAAGTAAGGAAGATAAGAGAAGTTGGGAAGGTAATGACAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - -taccaaa
- - - - - - - - - - - -ccagaac
- - - - - - - - - - - - - - - - - caaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctcct