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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataaacctcttcaatttcagatttatctgttccctttgtctctatttgagtattttgtgactgattatgtgtctttgttacagCTGCAAAGAGAAAAAGTATGCTTGAAGCTATTGAACGCGAGTTTGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G52410.1
intron # 10
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|164213808|gb|ES170280.1|ES170280
EST:     ACAACTAAAGGTTAATGACTTCACCGGGGACAAAGATGACGAAGAACACT                         CTGCAGAGAGAAAAAGTATGCTTGAAGCTATTGAACGCGAGTTTGAAGC
genomic: ACAACTAAAGGTTAATGACTTCACCGGGGACAAAGATGACGAAGAACACTgtaataaacc ... tttgttacagCTGCAAAGAGAAAAAGTATGCTTGAAGCTATTGAACGCGAGTTTGAAGC
EST: gi|125242722|gb|EL256807.1|EL256807
EST:     ACAACTAAAGGTTAATGACTTCACCGGGGACAAAGATGACGAAGAACACT                         CTGCAAAGAAGAAAAAGTAT
genomic: ACAACTAAAGGTTAATGACTTCACCGGGGACAAAGATGACGAAGAACACTgtaataaacc ... tttgttacagCTGCAAAGA-GAAAAAGTAT
EST: gi|164230260|gb|ES107233.1|ES107233
EST:     CTAAAGGTTAATGACTTCACCGGGGACAAAGATGACGAAGAACACT                         CTGCAGAGAGAAAAAGTATGCTTGAAGTCTATTGAACGCGAGTTTGAAG
genomic: CTAAAGGTTAATGACTTCACCGGGGACAAAGATGACGAAGAACACTgtaataaacc ... tttgttacagCTGCAAAGAGAAAAAGTATGCTTGAAG-CTATTGAACGCGAGTTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccctttgtctctatttgagtattttgtgactgattatgtgtctttgttacagCTGCAAAGAGAAAAAGTATGCTTGAAGCTATTGAACGCGAGTTTGAAG
                              gactgat  putative branch site (score: 3)
                                           tctttgtt  putative PPT
              tatttgagtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataaacctcttcaatttcagatttatctgttccctttgtctctatttgagtattttgtgactgattatgtgtctttgttacagCTGCAAAGAGAAAAAGTATGCTTGAAGCTATTGAACGCGAGTTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG