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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatattttatggacttattggctatcgaggaaaacctcttgatttttgagtttagacatttttatacgtggggacaatcgtgtctgtatgtctaatacgtaaaattattgttctactgtcgcaactccattgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGATCACCACTACCGAAAGGCGTTCTCGGTTTCTGCAAGCTTTAGCCCCAAC

Basic information

species Physcomitrella patens
transcript PP1S79_254V6.1
intron # 9
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|162158020|gb|FC334954.1|FC334954
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37841176|gb|BJ599184.1|BJ599184
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|162269549|gb|FC445105.1|FC445105
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37836542|gb|BJ594550.1|BJ594550
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|208381754|gb|DC928417.1|DC928417
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTNGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|208354680|gb|DC918706.1|DC918706
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|208347734|gb|DC925607.1|DC925607
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37849158|gb|BJ607166.1|BJ607166
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|208366175|gb|DC955276.1|DC955276
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|162238634|gb|FC418997.1|FC418997
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37833353|gb|BJ591365.1|BJ591365
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37845130|gb|BJ603138.1|BJ603138
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37850186|gb|BJ608194.1|BJ608194
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37844185|gb|BJ602193.1|BJ602193
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|7648262|gb|AW739245.1|AW739245
EST:     CTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAACCTACAATG                         ATANACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: CTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37843376|gb|BJ601384.1|BJ601384
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37835860|gb|BJ593872.1|BJ593872
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37843420|gb|BJ601428.1|BJ601428
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|162192771|gb|FC369622.1|FC369622
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|67699119|gb|BJ959352.1|BJ959352
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37842304|gb|BJ600312.1|BJ600312
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37824362|gb|BJ582428.1|BJ582428
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|18340062|gb|BJ172090.1|BJ172090
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|208380520|gb|DC915422.1|DC915422
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|162276878|gb|FC452560.1|FC452560
EST:     TCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|208348822|gb|DC925894.1|DC925894
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|162191817|gb|FC367966.1|FC367966
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|208382347|gb|DC919335.1|DC919335
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37822622|gb|BJ580688.1|BJ580688
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|162164830|gb|FC341345.1|FC341345
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37834032|gb|BJ592044.1|BJ592044
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|162192867|gb|FC369354.1|FC369354
EST:     CTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTANCA-TG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAG
genomic: CTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTA-CAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAG
EST: gi|162162092|gb|FC338883.1|FC338883
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|162195496|gb|FC369353.1|FC369353
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
EST: gi|37831038|gb|BJ589050.1|BJ589050
EST:     GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATG                         ATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA
genomic: GCTTCATGCTATGAACCAAGCTTTACAGTTTTTGCAGGAAAACTACAATGgtaagatatt ... attgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtatgtctaatacgtaaaattattgttctactgtcgcaactccattgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGATCACCACTACCGAAAGGCGTTCTCGGTTTCTGCAAGCTTTAGCCCCAAC
      gtctaat  putative branch site (score: 3)
                                         ctccatt  putative PPT
         taatacgtaaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatattttatggacttattggctatcgaggaaaacctcttgatttttgagtttagacatttttatacgtggggacaatcgtgtctgtatgtctaatacgtaaaattattgttctactgtcgcaactccattgtcgcagATAAACTTGTGGGAGTTTTCACCTTTACGAAGAGCGCCAATAATTTTGAGATCACCACTACCGAAAGGCGTTCTCGGTTTCTGCAAGCTTTAGCCCCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT