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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatagcaaatagacagtctcaatgacaaacttttcataactctgggtttgtctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACTTGCTGGAATG

Basic information

species Arabidopsis thaliana
transcript AT5G48090.2
intron # 16
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|116390563|gb|EG433155.1|EG433155
EST:     GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAG                         GGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
genomic: GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAGgtaaatagca ... ctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
EST: gi|116390509|gb|EG433101.1|EG433101
EST:     GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAG                         GGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
genomic: GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAGgtaaatagca ... ctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
EST: gi|116390557|gb|EG433149.1|EG433149
EST:     GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAG                         GGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
genomic: GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAGgtaaatagca ... ctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
EST: gi|116390564|gb|EG433156.1|EG433156
EST:     GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAG                         GGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
genomic: GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAGgtaaatagca ... ctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
EST: gi|116390511|gb|EG433103.1|EG433103
EST:     GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAG                         GGTCGATGCGATTGATGACTATGAGTTGATTTGGGAGGACAGAAATTTACT
genomic: GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAGgtaaatagca ... ctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
EST: gi|116390558|gb|EG433150.1|EG433150
EST:     GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAG                         GGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
genomic: GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAGgtaaatagca ... ctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
EST: gi|116390510|gb|EG433102.1|EG433102
EST:     GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAG                         GGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
genomic: GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAGgtaaatagca ... ctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
EST: gi|116390522|gb|EG433114.1|EG433114
EST:     GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAG                         GGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
genomic: GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAGgtaaatagca ... ctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
EST: gi|116390547|gb|EG433139.1|EG433139
EST:     GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAG                         GGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT
genomic: GAGTTTAAACCGAAGATCTTAATCCTCATCGTACCAAGTGAAACAAAAAGgtaaatagca ... ctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatagacagtctcaatgacaaacttttcataactctgggtttgtctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACTTGCTGGAATG
                           tcataac  putative branch site (score: 2)
                                        tttgtct  putative PPT
                        ttttcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatagcaaatagacagtctcaatgacaaacttttcataactctgggtttgtctacattcagGGTCGATGCGATTGATGATTATGAGTTGATTTGGGAGGACAGAAATTTACTTGCTGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA