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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttcaaactcttcttcttcttcttcgttgaccattttcccacttctcttattaagctcggtcatattttactatcagGTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAAGA

Basic information

species Arabidopsis thaliana
transcript AT5G63890.2
intron # 2
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|86068844|gb|DR364601.1|DR364601
EST:     ATAGTTTGAAGTCACGCCCTAGCATTGACTTCTCTTCTATTTTCGCCACT                         GTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAA
genomic: ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACTgtaactttca ... ttactatcagGTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAA
EST: gi|86068846|gb|DR364603.1|DR364603
EST:     ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACT                         GTGAACCCGATTATCGATGCTGTTCGTANCAATGGGGATAATGCTGTCAAA
genomic: ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACTgtaactttca ... ttactatcagGTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAA
EST: gi|86068847|gb|DR364604.1|DR364604
EST:     ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACT                         GTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAA
genomic: ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACTgtaactttca ... ttactatcagGTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAA
EST: gi|86068843|gb|DR364600.1|DR364600
EST:     ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACT                         GTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAA
genomic: ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACTgtaactttca ... ttactatcagGTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAA
EST: gi|86068841|gb|DR364598.1|DR364598
EST:     ATAGTTTGAAGTCACGCCCTCGCNTTGACTTCTCTTCTATTTTCGCCACT                         GTGAACCCGATTATCGATGCTG
genomic: ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACTgtaactttca ... ttactatcagGTGAACCCGATTATCGATGCTG
EST: gi|86068845|gb|DR364602.1|DR364602
EST:     ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACT                         GTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAA
genomic: ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACTgtaactttca ... ttactatcagGTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAA
EST: gi|125122336|gb|EL169011.1|EL169011
EST:     ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACT                         GTGAACCCGATTAT
genomic: ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACTgtaactttca ... ttactatcagGTGAACCCGATTAT
EST: gi|86068842|gb|DR364599.1|DR364599
EST:     ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACT                         GTGAACCCGATTATCGATGCTG
genomic: ATAGTTTGAAGTCACGCCCTCGCATTGACTTCTCTTCTATTTTCGCCACTgtaactttca ... ttactatcagGTGAACCCGATTATCGATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgttgaccattttcccacttctcttattaagctcggtcatattttactatcagGTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAAGA
  cgttgac  putative branch site (score: 4)
                                           ttttact  putative PPT
                                      tcatattttactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactttcaaactcttcttcttcttcttcgttgaccattttcccacttctcttattaagctcggtcatattttactatcagGTGAACCCGATTATCGATGCTGTTCGTAGCAATGGGGATAATGCTGTCAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG