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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTGATGACACCCCGTGGGATGGAGgtatggctacaccacgttgacttagcggtgtaggaatttggaggacttgtggtttggaaaattgttgatagagtgtgttggtgagatagaaactgcatca...

Basic information

species Physcomitrella patens
transcript PP1S91_88V6.1
intron # 2
splice site 5'
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|67693862|gb|BJ954095.1|BJ954095
EST:     GTCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: GTCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67701080|gb|BJ961313.1|BJ961313
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67569580|gb|BJ942404.1|BJ942404
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67570577|gb|BJ943401.1|BJ943401
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|208380555|gb|DC914944.1|DC914944
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|18368607|gb|BJ200692.1|BJ200692
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67508398|gb|BJ941265.1|BJ941265
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|18349879|gb|BJ181930.1|BJ181930
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67572289|gb|BJ945113.1|BJ945113
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67727247|gb|BJ977506.1|BJ977506
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|162259058|gb|FC436391.1|FC436391
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67578213|gb|BJ950380.1|BJ950380
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67569740|gb|BJ942564.1|BJ942564
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|208393858|gb|DC928694.1|DC928694
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67693006|gb|BJ953239.1|BJ953239
EST:     TGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|208399565|gb|DC908562.1|DC908562
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAGGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|162229344|gb|FC405535.1|FC405535
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|162268444|gb|FC444317.1|FC444317
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67576821|gb|BJ949645.1|BJ949645
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|18357799|gb|BJ189858.1|BJ189858
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67692406|gb|BJ952639.1|BJ952639
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67569162|gb|BJ941986.1|BJ941986
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|37837159|gb|BJ595167.1|BJ595167
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67692848|gb|BJ953081.1|BJ953081
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67695657|gb|BJ955890.1|BJ955890
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCNAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|18366035|gb|BJ198113.1|BJ198113
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|18331935|gb|BJ163947.1|BJ163947
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67576245|gb|BJ949069.1|BJ949069
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|162268443|gb|FC444316.1|FC444316
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|18371730|gb|BJ203332.1|BJ203332
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|162229343|gb|FC405534.1|FC405534
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67699746|gb|BJ959979.1|BJ959979
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|67718896|gb|BJ969155.1|BJ969155
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|208356654|gb|DC922444.1|DC922444
EST:     GTCCTGATGACACCCCGTGGGA-NGAG                         GAACGTTCAAGTTGACGNTGCAATTTACTGAGGATTACCCGAATAGGCCTC
genomic: GTCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|37846151|gb|BJ604159.1|BJ604159
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
EST: gi|208391714|gb|DC942290.1|DC942290
EST:     TCCTGATGACACCCCGTGGGATGGAG                         GAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC
genomic: TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 32 (downstream exon)
Score: 99

TCCTGATGACACCCCGTGGGATGGAGgtatggctac ... tcctccccagGAACGTTCAAGTTGACGTTGCAATTTACTGAGGATTACCCGAATAAGCCTCCCACAGTGCGCTTTGTCTCAAAGATGTTTCACCCTAACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGATGACACCCCGTGGGATGGAGgtatggctacaccacgttgacttagcggtgtaggaatttggaggacttgtggtttggaaaattgttgatagagtgtgttggtgagatagaaactgcatca

- - - - - - - - -  GATGGA