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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggagaagattttgactctttcttcctacttttctacagtgtgggtcagttccatatattccagatgatcgttttcaatatagttcaaattacgaatcttaacaagcatatgttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAGGAGACTGAAACTGGAGACTTCTTGCAACAAATCCGAACACAAGTGAGTG

Basic information

species Arabidopsis thaliana
transcript AT1G29170.2
intron # 6
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|116429024|gb|EG471616.1|EG471616
EST:     AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAG                         GCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
genomic: AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAGgtatggagaa ... gttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
EST: gi|116428888|gb|EG471480.1|EG471480
EST:     AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAG                         GCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
genomic: AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAGgtatggagaa ... gttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
EST: gi|116451506|gb|EG494098.1|EG494098
EST:     AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAG                         GCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
genomic: AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAGgtatggagaa ... gttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
EST: gi|116428885|gb|EG471477.1|EG471477
EST:     AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAG                         GCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
genomic: AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAGgtatggagaa ... gttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
EST: gi|116428903|gb|EG471495.1|EG471495
EST:     AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAG                         GCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
genomic: AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAGgtatggagaa ... gttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
EST: gi|116428889|gb|EG471481.1|EG471481
EST:     AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAG                         GCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
genomic: AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAGgtatggagaa ... gttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
EST: gi|116451428|gb|EG494020.1|EG494020
EST:     AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAG                         GCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
genomic: AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAGgtatggagaa ... gttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
EST: gi|116451430|gb|EG494022.1|EG494022
EST:     AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAG                         GCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
genomic: AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAGgtatggagaa ... gttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG
EST: gi|116451486|gb|EG494078.1|EG494078
EST:     AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAG                         GCCCATCTGAAGAATAATGTCAGGGATGAGAAACAAAGTGCCAACGCAAAG
genomic: AGAACGAACTGCCTAGCATGGTGACTTCTGCTCCTAAACCAGAAATTAAGgtatggagaa ... gttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcgttttcaatatagttcaaattacgaatcttaacaagcatatgttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAGGAGACTGAAACTGGAGACTTCTTGCAACAAATCCGAACACAAGTGAGTG
                              tcttaac  putative branch site (score: 2)
                                            tgttctc  putative PPT
     ttttcaatatagttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggagaagattttgactctttcttcctacttttctacagtgtgggtcagttccatatattccagatgatcgttttcaatatagttcaaattacgaatcttaacaagcatatgttctcatagGCCCATCTGAAGAATAATGTCAGGGAGGAGAAACAAAGTGCCAACGCAAAGGAGACTGAAACTGGAGACTTCTTGCAACAAATCCGAACACAAGTGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA