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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagcgggtataagtattgatgtttggatgtggttcagtcttctggtactgatgcttggtttgtttttgcgtggttggctggggaacttggaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTAAGCACTTTCTTGGAGCAGGGGATGTTCGGACTTGTGGACGGTGGTCG

Basic information

species Physcomitrella patens
transcript PP1S505_6V6.2
intron # 13
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|208394906|gb|DC924125.1|DC924125
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGNCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|67697104|gb|BJ957337.1|BJ957337
EST:     TTACCCCGATCGGNCGGTTCTTCACTCATAACATG                         GNGCGTGTGTNGGAAGCTGTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|37845058|gb|BJ603066.1|BJ603066
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208394780|gb|DC924083.1|DC924083
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|162166439|gb|FC342421.1|FC342421
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208346584|gb|DC916850.1|DC916850
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208388484|gb|DC957066.1|DC957066
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|67727357|gb|BJ977616.1|BJ977616
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208367883|gb|DC955346.1|DC955346
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208387195|gb|DC945494.1|DC945494
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208396976|gb|DC924658.1|DC924658
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|162166440|gb|FC342422.1|FC342422
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208380622|gb|DC919380.1|DC919380
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208386208|gb|DC952921.1|DC952921
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|37838233|gb|BJ596241.1|BJ596241
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|37853228|gb|BJ611236.1|BJ611236
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208371896|gb|DC951714.1|DC951714
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|208354679|gb|DC918705.1|DC918705
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
EST: gi|67720489|gb|BJ970748.1|BJ970748
EST:     TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATG                         GTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA
genomic: TTTCCACTCTTCGGCTTACCCCGATCGGGCGGTTCTTCACTCATAACATGgtttgttatt ... gaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactgatgcttggtttgtttttgcgtggttggctggggaacttggaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTAAGCACTTTCTTGGAGCAGGGGATGTTCGGACTTGTGGACGGTGGTCG
 tactgat  putative branch site (score: 2)
              tttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagcgggtataagtattgatgtttggatgtggttcagtcttctggtactgatgcttggtttgtttttgcgtggttggctggggaacttggaacgtgcagGTGCGTGTGTTGGAAGCTTTGAAAATCGCTCCGGAGGGGAGCGCCAGAGTAAGCACTTTCTTGGAGCAGGGGATGTTCGGACTTGTGGACGGTGGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG