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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggttgggtcacttatttatttcatatcaacactctagctctggttatctgtgtcgatgaggtcaattttttcaaaaacttttactcaccatgtcttcgatcattttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGTTTGTTGAATTTTTGGGTCGTGGAGATTTTCCACAGTTACAG

Basic information

species Physcomitrella patens
transcript PP1S63_171V6.2
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|208377226|gb|DC932376.1|DC932376
EST:     AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTG                         AACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
genomic: AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTGgtacggttgg ... ttttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
EST: gi|67575223|gb|BJ948047.1|BJ948047
EST:     AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTG                         AACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
genomic: AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTGgtacggttgg ... ttttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
EST: gi|18358603|gb|BJ190662.1|BJ190662
EST:     AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTACATTG                         AACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
genomic: AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTGgtacggttgg ... ttttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
EST: gi|18359532|gb|BJ191593.1|BJ191593
EST:     AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTG                         AACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
genomic: AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTGgtacggttgg ... ttttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
EST: gi|162267820|gb|FC444421.1|FC444421
EST:     AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTG                         AACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
genomic: AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTGgtacggttgg ... ttttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
EST: gi|18366309|gb|BJ198388.1|BJ198388
EST:     AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTG                         AACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
genomic: AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTGgtacggttgg ... ttttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
EST: gi|67703759|gb|BJ963992.1|BJ963992
EST:     AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTG                         AACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT
genomic: AGCCACTCAACTGGAAGCTACCACTCATTTCCGGAAGCTTCTGTCCATTGgtacggttgg ... ttttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggtcaattttttcaaaaacttttactcaccatgtcttcgatcattttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGTTTGTTGAATTTTTGGGTCGTGGAGATTTTCCACAGTTACAG
                        tactcac  putative branch site (score: 1)
                                          tcatttttt  putative PPT
      aattttttcaaaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggttgggtcacttatttatttcatatcaacactctagctctggttatctgtgtcgatgaggtcaattttttcaaaaacttttactcaccatgtcttcgatcattttttgcagAACGCAGTCCCCCAATCGATGAGGTTATAGCGGCGGGTGTTGTACCTCGGTTTGTTGAATTTTTGGGTCGTGGAGATTTTCCACAGTTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT