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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacccacacagcaattttcgttcgatgtttgactattaaagttcataaattttatcatttcgctcaatagttaacacctatcacaatgtgacgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACATTGTCAAGTCAGCAGCTGACGCTGATGATGTCCTTGAAAGCCAGGCTCCC

Basic information

species Physcomitrella patens
transcript PP1S422_7V6.1
intron # 1
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|18348478|gb|BJ180527.1|BJ180527
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|162257578|gb|FC433712.1|FC433712
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|162166450|gb|FC342432.1|FC342432
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|162171848|gb|FC348985.1|FC348985
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|18375278|gb|BJ206856.1|BJ206856
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|18348587|gb|BJ180636.1|BJ180636
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|162218094|gb|FC394957.1|FC394957
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|18355396|gb|BJ187455.1|BJ187455
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAA
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAA
EST: gi|162170029|gb|FC345082.1|FC345082
EST:     GCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: GCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|18348075|gb|BJ180122.1|BJ180122
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTG
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTG
EST: gi|18325035|gb|BJ157031.1|BJ157031
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAG
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAG
EST: gi|162167529|gb|FC344220.1|FC344220
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|100367163|gb|BY984833.1|BY984833
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|162248488|gb|FC420935.1|FC420935
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|67718767|gb|BJ969026.1|BJ969026
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|100419910|gb|BY975902.1|BY975902
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|100392230|gb|BY953259.1|BY953259
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|100409294|gb|BY991940.1|BY991940
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|18374236|gb|BJ205814.1|BJ205814
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGAACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|162198843|gb|FC372870.1|FC372870
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|100434142|gb|BY978979.1|BY978979
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|18328202|gb|BJ160206.1|BJ160206
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAA
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAA
EST: gi|18331716|gb|BJ163727.1|BJ163727
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGT
EST: gi|100378248|gb|BY949755.1|BY949755
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTNCA-CA
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGT-CAACA
EST: gi|208399903|gb|DC904971.1|DC904971
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|208346932|gb|DC913129.1|DC913129
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|208357820|gb|DC902330.1|DC902330
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAG                         CGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACAT
EST: gi|100378848|gb|BY968719.1|BY968719
EST:     TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAC                         CGATGATTTCGTCAACTGGGTTGAAAA-GAGAATGGGACCTGCTGTCA
genomic: TTTTTCTTCGTCGATGGCGAGAAGAGACCTTACAATGGCGGACGAAACAGgtttgctttt ... acgaatgcagCGATGATATCGTCAACTGGGT-GAAAAAGAGAATGGGACCTGCTGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattttatcatttcgctcaatagttaacacctatcacaatgtgacgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACATTGTCAAGTCAGCAGCTGACGCTGATGATGTCCTTGAAAGCCAGGCTCCC
                       agttaac  putative branch site (score: 3)
     tttatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacccacacagcaattttcgttcgatgtttgactattaaagttcataaattttatcatttcgctcaatagttaacacctatcacaatgtgacgaatgcagCGATGATATCGTCAACTGGGTGAAAAAGAGAATGGGACCTGCTGTCAACATTGTCAAGTCAGCAGCTGACGCTGATGATGTCCTTGAAAGCCAGGCTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT