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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttgttttttatgcttgcattaacttacatgaaaatttagctctcttagacataataataaacaattagtgtgcctaaaataaactgattaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAG

Basic information

species Arabidopsis thaliana
transcript AT1G09210.1
intron # 7
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|125060130|gb|EL128807.1|EL128807
EST:     AACCCCAACTACAAGGGCAAGTGGGAGGGCTCCATTGATTGACAACCCTG                         ACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATA
genomic: AACCCCAACTACAAGGGCAAGTGGGA-GGCTCCATTGATTGACAACCCTGgtacattact ... attaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATA
EST: gi|124838986|gb|EH923425.1|EH923425
EST:     AAGTGGGAGGCTCCATTGATTGACAACCCTG                         ACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
genomic: AAGTGGGAGGCTCCATTGATTGACAACCCTGgtacattact ... attaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
EST: gi|164046547|gb|ES089054.1|ES089054
EST:     AACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTG                         ACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
genomic: AACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTGgtacattact ... attaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
EST: gi|116393133|gb|EG435725.1|EG435725
EST:     GAACCCCGACTACAATGGCAAGTGGGAGGCTCCATTGATTGACAACCCTG                         ACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
genomic: GAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTGgtacattact ... attaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
EST: gi|116412926|gb|EG455518.1|EG455518
EST:     GAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTG                         ACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
genomic: GAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTGgtacattact ... attaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
EST: gi|86078431|gb|DR374188.1|DR374188
EST:     GAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTG                         ACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
genomic: GAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTGgtacattact ... attaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
EST: gi|116412928|gb|EG455520.1|EG455520
EST:     GAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTG                         ACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG
genomic: GAACCCCAACTACAAGGGCAAGTGGGAGGCTCCATTGATTGACAACCCTGgtacattact ... attaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttagacataataataaacaattagtgtgcctaaaataaactgattaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAG
                                        aactgat  putative branch site (score: 3)
     agacataataataaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttgttttttatgcttgcattaacttacatgaaaatttagctctcttagacataataataaacaattagtgtgcctaaaataaactgattaccgcagACTTCAAGGATGACCCAGAGCTCTACGTCTTCCCCAAGCTGAAATATGTTGGACTCGAATTGTGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - -acttaca
- - - - - - - - - - - - - - - - - - - - - - - - - -gacataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa