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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacggcgtcaacaagtgatatagtgcaatgaaacgattgagacttgtgaactggttttgactgtttagatcttaattggatctgtctatgacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTGTGTACAGCTCTAGGCCTTGGGCCTGACAG

Basic information

species Physcomitrella patens
transcript PP1S205_59V6.2
intron # 6
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|208381557|gb|DC923143.1|DC923143
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162165614|gb|FC341453.1|FC341453
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|208376776|gb|DC918731.1|DC918731
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162200281|gb|FC376322.1|FC376322
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162200282|gb|FC376323.1|FC376323
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162255054|gb|FC430927.1|FC430927
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162168295|gb|FC344609.1|FC344609
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|67695588|gb|BJ955821.1|BJ955821
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|67693124|gb|BJ953357.1|BJ953357
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162165615|gb|FC341454.1|FC341454
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162248720|gb|FC424573.1|FC424573
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162258766|gb|FC434565.1|FC434565
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162181475|gb|FC358089.1|FC358089
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|162168296|gb|FC344610.1|FC344610
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|208394748|gb|DC924079.1|DC924079
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
EST: gi|37849627|gb|BJ607635.1|BJ607635
EST:     AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCA                         GGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG
genomic: AGCTTTGGGCCAAAGCTAAGCTGGCATGGGAGGAAATTTTGTCAGCCCCAgtaagattat ... gacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaactggttttgactgtttagatcttaattggatctgtctatgacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTGTGTACAGCTCTAGGCCTTGGGCCTGACAG
                         tcttaat  putative branch site (score: 3)
                   tttagatcttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaacggcgtcaacaagtgatatagtgcaatgaaacgattgagacttgtgaactggttttgactgtttagatcttaattggatctgtctatgacgttccagGGTGAAAGATTGCTGGTGGTCACACACAAGTCCATATTGCGAGCCATGCTGTGTACAGCTCTAGGCCTTGGGCCTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC