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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtttcttttctggtttggtcagatgctctttggatacattttctgattgaacttttctcttatatttccttcttggtttgttttcagACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAATGCGCCACTTGTAGTAAAACTGTGTATCCTATTGAAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G55770.6
intron # 5
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|164129476|gb|ES026513.1|ES026513
EST:     CTCCTGAGCTG                         ACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAA
genomic: CTCCTGAGCTGgtaaatgttt ... ttgttttcagACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAA
EST: gi|47829977|gb|CK119661.1|CK119661
EST:     CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG                         ACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAANGAGAA
genomic: CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTGgtaaatgttt ... ttgttttcagACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAA-GAGAA
EST: gi|125100058|gb|EL155652.1|EL155652
EST:     CAACTCCTGAGCTG                         ACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAA
genomic: CAACTCCTGAGCTGgtaaatgttt ... ttgttttcagACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAA
EST: gi|124757831|gb|EH847961.1|EH847961
EST:     CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG                         ACAAGGACGCCTAGCCG
genomic: CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTGgtaaatgttt ... ttgttttcagACAAGGACGCCTAGCCG
EST: gi|125078742|gb|EL141010.1|EL141010
EST:     CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG                         ACAAGGACGCCTAGCCGAGTTGCTGGCAGG
genomic: CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTGgtaaatgttt ... ttgttttcagACAAGGACGCCTAGCCGAGTTGCTGGCAGG
EST: gi|301502045|gb|HO207585.1|HO207585
EST:     CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG                         ACAAGGACGCCTAGCCGACTTGCTGGCAGGTTCTCTGGTACACAAGAGAAA
genomic: CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTGgtaaatgttt ... ttgttttcagACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAA
EST: gi|124824735|gb|EH909601.1|EH909601
EST:     CAAATCAACTCCTGAGCTG                         ACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAA
genomic: CAAATCAACTCCTGAGCTGgtaaatgttt ... ttgttttcagACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAA
EST: gi|124979033|gb|EL052135.1|EL052135
EST:     CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG                         ACAAGGACGCCTAGCCGAGTTG
genomic: CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTGgtaaatgttt ... ttgttttcagACAAGGACGCCTAGCCGAGTTG
EST: gi|125009929|gb|EL082198.1|EL082198
EST:     CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTG                         ACAAGGACGCCTAGCCGAGTTG
genomic: CTGCAAAATCGGCTGACAAATCAACTCCTGAGCTGgtaaatgttt ... ttgttttcagACAAGGACGCCTAGCCGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacattttctgattgaacttttctcttatatttccttcttggtttgttttcagACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAATGCGCCACTTGTAGTAAAACTGTGTATCCTATTGAAAAG
        ttctgat  putative branch site (score: 3)
                   cttttctcttatattt  putative PPT
                    ttttctcttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgtttcttttctggtttggtcagatgctctttggatacattttctgattgaacttttctcttatatttccttcttggtttgttttcagACAAGGACGCCTAGCCGAGTTGCTGGCAGGTTCTCTGGTACACAAGAGAAATGCGCCACTTGTAGTAAAACTGTGTATCCTATTGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA