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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtatttgttgattgattgatttacatgtcatgatttgaaatctttgtattgctaattgctattgctctgtttactgattttcttttctggggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G55280.1
intron # 1
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|125048792|gb|EL121061.1|EL121061
EST:     AACCACCAAGCAACTTGGATCTACTCTAGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTA
genomic: AACCACCAAGCAACTTGGATCTACTCTAGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTA
EST: gi|152035088|gb|BP844212.2|BP844212
EST:     ACTCTAGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG
genomic: ACTCTAGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG
EST: gi|116415207|gb|EG457799.1|EG457799
EST:     ACTCTAGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG
genomic: ACTCTAGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG
EST: gi|86083163|gb|DR378922.1|DR378922
EST:     CTAGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG
genomic: CTAGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG
EST: gi|152033917|gb|BP819853.2|BP819853
EST:     ACTCTAGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG
genomic: ACTCTAGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG
EST: gi|124940075|gb|EL016559.1|EL016559
EST:     AAGCAACTTGGATCTACTCTAGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTATCTTGAGCAA
genomic: AAGCAACTTGGATCTACTCTAGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAA
EST: gi|164149190|gb|ES160507.1|ES160507
EST:     ACTCTAGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAGTTG
genomic: ACTCTAGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAGTTG
EST: gi|164218126|gb|ES030476.1|ES030476
EST:     AGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAGTTGA
genomic: AGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAGTTGA
EST: gi|124766636|gb|EH856766.1|EH856766
EST:     AAGCAACTTGGATCTACTCTAGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTATCTTGAGCAATGT
genomic: AAGCAACTTGGATCTACTCTAGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGT
EST: gi|125075179|gb|EL138844.1|EL138844
EST:     AGGGTTTCTGTTTCGCCGCTCAG                         GTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAGTTGATGT
genomic: AGGGTTTCTGTTTCGCCGCTCAGgttcgtcaat ... gggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAGTTGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtattgctaattgctattgctctgtttactgattttcttttctggggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG
                           tactgat  putative branch site (score: 2)
                                attttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtatttgttgattgattgatttacatgtcatgatttgaaatctttgtattgctaattgctattgctctgtttactgattttcttttctggggttatcagGTTTCGTGAAAAGAATCTATCTTGAGCAATGTCTCCAGCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA