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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatttgtgacatcttttggcttgttttactgattactccacgagcgtttttgttttcttgtgcctaactttctttgtttggatcatattagGTTAAGTTGGAGCAAGGTTTGAAGATTGTGAAAATTTTCAAGGAGCATAGCAGCAAGACTTGCATTTTGGATGATTTCTCATTCTACGAGGTTCGACAGA

Basic information

species Arabidopsis thaliana
transcript AT3G13460.2
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|124892856|gb|EH971758.1|EH971758
EST:     CAATGAGAACAAACCTGTTACCAACAGCAGAGACACACAAGAG                         GTTAAGTTGGAGCAAGGTTTGAAGATTGTGAAAA
genomic: CAATGAGAACAAACCTGTTACCAACAGCAGAGACACACAAGAGgtaaatattt ... atcatattagGTTAAGTTGGAGCAAGGTTTGAAGATTGTGAAAA
EST: gi|125194081|gb|EL209035.1|EL209035
EST:     CAGAGACACACAAGAG                         GTTAAGTTGGAGCAAGGTTTGAAGATTGTGAAAATTTTCAAGGAGCATAGC
genomic: CAGAGACACACAAGAGgtaaatattt ... atcatattagGTTAAGTTGGAGCAAGGTTTGAAGATTGTGAAAATTTTCAAGGAGCATAGC
EST: gi|125132114|gb|EL174366.1|EL174366
EST:     GAGAACAATGAGAACAAACCTGTTACCAACAGCTAGTAGACACACAAGAG                         GTTAAGTTGGAGCAAGGTTTGAAG
genomic: GAGAACAATGAGAACAAACCTGTTACCAACAGC-AG-AGACACACAAGAGgtaaatattt ... atcatattagGTTAAGTTGGAGCAAGGTTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacgagcgtttttgttttcttgtgcctaactttctttgtttggatcatattagGTTAAGTTGGAGCAAGGTTTGAAGATTGTGAAAATTTTCAAGGAGCATAGCAGCAAGACTTGCATTTTGGATGATTTCTCATTCTACGAGGTTCGACAGA
                         gcctaac  putative branch site (score: 2)
          tttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatttgtgacatcttttggcttgttttactgattactccacgagcgtttttgttttcttgtgcctaactttctttgtttggatcatattagGTTAAGTTGGAGCAAGGTTTGAAGATTGTGAAAATTTTCAAGGAGCATAGCAGCAAGACTTGCATTTTGGATGATTTCTCATTCTACGAGGTTCGACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA