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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacgttgaggactggagctgttgggtttttgatgtttgatttttcgcatttctgacgactgagtcgacacagctaagatatgaaacttgctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTCCACAGAATGATCCCTTATATGAGAGTTCCGAAGGAGCGTATACCAGCTG

Basic information

species Physcomitrella patens
transcript PP1S97_54V6.2
intron # 4
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|18330249|gb|BJ162255.1|BJ162255
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|37841964|gb|BJ599972.1|BJ599972
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|162249476|gb|FC426746.1|FC426746
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|208388641|gb|DC953431.1|DC953431
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGCAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|67696509|gb|BJ956742.1|BJ956742
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|37835663|gb|BJ593675.1|BJ593675
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|18337853|gb|BJ169877.1|BJ169877
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|18338064|gb|BJ170088.1|BJ170088
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|162248874|gb|FC422881.1|FC422881
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|18341780|gb|BJ173815.1|BJ173815
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|37850242|gb|BJ608250.1|BJ608250
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|37845267|gb|BJ603275.1|BJ603275
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|162224213|gb|FC399277.1|FC399277
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|37853392|gb|BJ611400.1|BJ611400
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|162258316|gb|FC434243.1|FC434243
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|37835745|gb|BJ593757.1|BJ593757
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|208368661|gb|DC947936.1|DC947936
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|162258317|gb|FC434244.1|FC434244
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|67692998|gb|BJ953231.1|BJ953231
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|67573124|gb|BJ945948.1|BJ945948
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|67569732|gb|BJ942556.1|BJ942556
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|162210550|gb|FC386846.1|FC386846
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|67697554|gb|BJ957787.1|BJ957787
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
EST: gi|67508263|gb|BJ941132.1|BJ941132
EST:     TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG                         CCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC
genomic: TGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAGgtactactaa ... ctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcatttctgacgactgagtcgacacagctaagatatgaaacttgctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTCCACAGAATGATCCCTTATATGAGAGTTCCGAAGGAGCGTATACCAGCTG
     ttctgac  putative branch site (score: 2)
                                         cttgcttt  putative PPT
                             taagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacgttgaggactggagctgttgggtttttgatgtttgatttttcgcatttctgacgactgagtcgacacagctaagatatgaaacttgctttgcgcagCCTATGCCAGCGGAGCAACTTCAAAAGCTGAAGCATTATAAGGACGTTCTCCACAGAATGATCCCTTATATGAGAGTTCCGAAGGAGCGTATACCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG