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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcacctgtcctctccattcaagttgttccactcttgtcttgcaaacgtgccaaaagtggagccgcatgcaaattctctaacagaaattacgtggcttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAACAAACGGAATTTACCGCAGTCGGTTTTCATAGATCCGAGAATTGGAGTTT

Basic information

species Physcomitrella patens
transcript PP1S217_91V6.1
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|162222778|gb|FC399032.1|FC399032
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|162239202|gb|FC416484.1|FC416484
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|18372342|gb|BJ203944.1|BJ203944
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|37821957|gb|BJ580023.1|BJ580023
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|67507466|gb|BJ940348.1|BJ940348
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|18325545|gb|BJ157542.1|BJ157542
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|162223114|gb|FC399693.1|FC399693
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|37850127|gb|BJ608135.1|BJ608135
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|37838928|gb|BJ596936.1|BJ596936
EST:     TGGCCTTCAATACCCCCTCNTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: TGGCCTTCAATA-CCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|162227771|gb|FC402387.1|FC402387
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|67578724|gb|BJ950891.1|BJ950891
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|18368840|gb|BJ200925.1|BJ200925
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|37852029|gb|BJ610037.1|BJ610037
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|162233101|gb|FC408508.1|FC408508
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|18333507|gb|BJ165522.1|BJ165522
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGNAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|18372510|gb|BJ204112.1|BJ204112
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|162233100|gb|FC408507.1|FC408507
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|162227772|gb|FC402388.1|FC402388
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|37834706|gb|BJ592718.1|BJ592718
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
EST: gi|18342813|gb|BJ174849.1|BJ174849
EST:     GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTAC                         GCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC
genomic: GTGGCCTTCAATACCCCTCCTGGTGTATTAAGTGCCCCTTTTAAGTCTACgtgagttcac ... cttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaaagtggagccgcatgcaaattctctaacagaaattacgtggcttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAACAAACGGAATTTACCGCAGTCGGTTTTCATAGATCCGAGAATTGGAGTTT
                         ctctaac  putative branch site (score: 2)
                                agaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcacctgtcctctccattcaagttgttccactcttgtcttgcaaacgtgccaaaagtggagccgcatgcaaattctctaacagaaattacgtggcttgtaatagGCACGGGTATCACATCATCTTGGCCGAGGGAAGGAAAAACTAAATTCAAACAAACGGAATTTACCGCAGTCGGTTTTCATAGATCCGAGAATTGGAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG