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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcgtcgtggagtttttgggtcgattttggtttctatggacggagttcttggttgatttttgagagagcaggagcctttatctgttaggatggattctagcgtttaattcagtatccttactcaaacaatggctgtttacaatttccagtgtgggttttgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGCCTTTTTAACCATGTGGATCTCGTGAACAAATTGGGAATTGTTGAGCTTG

Basic information

species Physcomitrella patens
transcript PP1S142_120V6.1
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|208399121|gb|DC912392.1|DC912392
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|67718504|gb|BJ968763.1|BJ968763
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTANAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|100447765|gb|CJ972064.1|CJ972064
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|18361483|gb|BJ193549.1|BJ193549
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGA
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGA
EST: gi|100364655|gb|BY947842.1|BY947842
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|208394382|gb|DC942542.1|DC942542
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|100448482|gb|CJ972781.1|CJ972781
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|100447644|gb|CJ971943.1|CJ971943
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|100446744|gb|CJ971043.1|CJ971043
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|100394755|gb|BY989909.1|BY989909
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|208384748|gb|DC915281.1|DC915281
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAN                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTATAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|162179840|gb|FC355911.1|FC355911
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|67717323|gb|BJ967582.1|BJ967582
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTANAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
EST: gi|67574064|gb|BJ946888.1|BJ946888
EST:     GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAG                         GACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC
genomic: GCTTGGTTGGCAACTTGGTGCACGACTCCGTGCCTGTGGATAACAATGAGgtaggcgtcg ... tgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccttactcaaacaatggctgtttacaatttccagtgtgggttttgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGCCTTTTTAACCATGTGGATCTCGTGAACAAATTGGGAATTGTTGAGCTTG
 tccttac  putative branch site (score: 2)
                      tttacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcgtcgtggagtttttgggtcgattttggtttctatggacggagttcttggttgatttttgagagagcaggagcctttatctgttaggatggattctagcgtttaattcagtatccttactcaaacaatggctgtttacaatttccagtgtgggttttgtggaacagGACAATAACCAGGTCGTTCGGAAATGGGGAACTCTTAGAGAAGAAGCCGGCCTTTTTAACCATGTGGATCTCGTGAACAAATTGGGAATTGTTGAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT