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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttctgttctggaatatttacattgcttagaagaattattccgaatgtattttaattttctcagcatattattttggtcatttgttgtttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG

Basic information

species Physcomitrella patens
transcript PP1S222_130V6.2
intron # 2
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:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18370288|gb|BJ201890.1|BJ201890
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18367574|gb|BJ199657.1|BJ199657
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGANATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18374528|gb|BJ206106.1|BJ206106
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|67570167|gb|BJ942991.1|BJ942991
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|162181666|gb|FC358696.1|FC358696
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|100443300|gb|BY963596.1|BY963596
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18362678|gb|BJ194749.1|BJ194749
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|67574627|gb|BJ947451.1|BJ947451
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18372863|gb|BJ204465.1|BJ204465
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|162170244|gb|FC347364.1|FC347364
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18365275|gb|BJ197349.1|BJ197349
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18374599|gb|BJ206177.1|BJ206177
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18365381|gb|BJ197456.1|BJ197456
EST:     ATCTAGCANAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18358877|gb|BJ190936.1|BJ190936
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|162220370|gb|FC395738.1|FC395738
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18363986|gb|BJ196059.1|BJ196059
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|162196667|gb|FC374632.1|FC374632
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18347979|gb|BJ180026.1|BJ180026
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18365214|gb|BJ197288.1|BJ197288
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|162257683|gb|FC433610.1|FC433610
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18350462|gb|BJ182513.1|BJ182513
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18373428|gb|BJ205006.1|BJ205006
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|162168431|gb|FC344407.1|FC344407
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18359898|gb|BJ191959.1|BJ191959
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18374996|gb|BJ206574.1|BJ206574
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18360287|gb|BJ192349.1|BJ192349
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|100434971|gb|BY960896.1|BY960896
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|162149665|gb|FC326716.1|FC326716
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|18355255|gb|BJ187314.1|BJ187314
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
EST: gi|162162513|gb|FC338607.1|FC338607
EST:     ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAG                         GGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG
genomic: ATCTAGCAAAGAAAAAGACTTTTCCAGCCATCTTCAATCTTTACAAGCAGgtacaattat ... ttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtattttaattttctcagcatattattttggtcatttgttgtttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG
      ttttaat  putative branch site (score: 3)
                                         ttgtttc  putative PPT
     attttaattttctcag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttctgttctggaatatttacattgcttagaagaattattccgaatgtattttaattttctcagcatattattttggtcatttgttgtttcgtggcagGGTTTCTTGCCGGACGAGATGCATGTTTTTGGGTATGCGAGATCCAATATGACCAACGAGGAGCTGCATGAGAAGCTTCTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC