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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagcttggctattattctaacatgcggcaagagcttttttttttcggtaaaaatttacatatttacattctaaaattctcattacttggttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCACTCCATCTCACCAGAGAAGTTGGAAATGTTCAAGTCCCTTGAAGGCTGG

Basic information

species Physcomitrella patens
transcript PP1S146_17V6.3
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|67575280|gb|BJ948104.1|BJ948104
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|162220399|gb|FC395754.1|FC395754
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|162158539|gb|FC334542.1|FC334542
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|208394235|gb|DC933903.1|DC933903
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|67507633|gb|BJ940513.1|BJ940513
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100364909|gb|BY947969.1|BY947969
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100444048|gb|BY963946.1|BY963946
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|162181623|gb|FC357925.1|FC357925
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100440863|gb|BY962351.1|BY962351
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100386266|gb|BY987933.1|BY987933
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100445755|gb|CJ970054.1|CJ970054
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|162256527|gb|FC432837.1|FC432837
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|162216943|gb|FC391943.1|FC391943
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100448931|gb|CJ973230.1|CJ973230
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|22132922|gb|BQ827438.1|BQ827438
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100426446|gb|BY958902.1|BY958902
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|18343661|gb|BJ175699.1|BJ175699
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|18325821|gb|BJ157818.1|BJ157818
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|162188015|gb|FC365005.1|FC365005
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|162241856|gb|FC418111.1|FC418111
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100423120|gb|BY958156.1|BY958156
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGNAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|162187542|gb|FC363804.1|FC363804
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|18372829|gb|BJ204431.1|BJ204431
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100419057|gb|BY975836.1|BY975836
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
EST: gi|100411895|gb|BY992393.1|BY992393
EST:     GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAA                         AGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA
genomic: GTTGGTCCATTGGAAGTATTTATGACTGCTACTCTGCCCCCTAAAACAAAgtaagcacca ... ttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtaaaaatttacatatttacattctaaaattctcattacttggttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCACTCCATCTCACCAGAGAAGTTGGAAATGTTCAAGTCCCTTGAAGGCTGG
                       ttctaaa  putative branch site (score: 2)
     aaaatttacatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcttggctattattctaacatgcggcaagagcttttttttttcggtaaaaatttacatatttacattctaaaattctcattacttggttggttacagAGGTGCACCTATAAGTAAGCGACCAACGGAGAAGCACTCCAAAGTTATGCACTCCATCTCACCAGAGAAGTTGGAAATGTTCAAGTCCCTTGAAGGCTGG

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