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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtctgtgaggaagcggggtgcccctaccattattagtgtgtcttttgctaagctggttgaaaaagtcctttatatgttaacaatttgtttgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG

Basic information

species Physcomitrella patens
transcript PP1S222_130V6.2
intron # 3
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|162200922|gb|FC377325.1|FC377325
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18370288|gb|BJ201890.1|BJ201890
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18374528|gb|BJ206106.1|BJ206106
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAN                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAA
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAA
EST: gi|67570167|gb|BJ942991.1|BJ942991
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|162181666|gb|FC358696.1|FC358696
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|100443300|gb|BY963596.1|BY963596
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18362678|gb|BJ194749.1|BJ194749
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|67574627|gb|BJ947451.1|BJ947451
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18372863|gb|BJ204465.1|BJ204465
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|162170244|gb|FC347364.1|FC347364
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18365275|gb|BJ197349.1|BJ197349
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAN                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAG
EST: gi|18374599|gb|BJ206177.1|BJ206177
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18358877|gb|BJ190936.1|BJ190936
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATG
EST: gi|162220370|gb|FC395738.1|FC395738
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18363986|gb|BJ196059.1|BJ196059
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|162196667|gb|FC374632.1|FC374632
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18347979|gb|BJ180026.1|BJ180026
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18365214|gb|BJ197288.1|BJ197288
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|162257683|gb|FC433610.1|FC433610
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18350462|gb|BJ182513.1|BJ182513
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGAT
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGAT
EST: gi|18373428|gb|BJ205006.1|BJ205006
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|162168431|gb|FC344407.1|FC344407
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18359898|gb|BJ191959.1|BJ191959
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18374996|gb|BJ206574.1|BJ206574
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18360287|gb|BJ192349.1|BJ192349
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|100434971|gb|BY960896.1|BY960896
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|162149665|gb|FC326716.1|FC326716
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|18355255|gb|BJ187314.1|BJ187314
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
EST: gi|162162513|gb|FC338607.1|FC338607
EST:     TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG                         GTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG
genomic: TATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAGgtataatgtt ... tgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctaagctggttgaaaaagtcctttatatgttaacaatttgtttgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG
                              tgttaac  putative branch site (score: 2)
                                       tttgttt  putative PPT
                        tttatatgttaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtctgtgaggaagcggggtgcccctaccattattagtgtgtcttttgctaagctggttgaaaaagtcctttatatgttaacaatttgtttgtgattcagGTATTTGAAAGCAGAAAGGACAGATCCTACAACAAATCCTGAAGATGTGAGAAAGCAGTTTCTTAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG