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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatggatttttgaatgccttgcagaacacgaaatatgctaattgcagagtctaagaggttcaagttcatggtggcttactagatatgttctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG

Basic information

species Physcomitrella patens
transcript PP1S41_70V6.1
intron # 4
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|18334808|gb|BJ166825.1|BJ166825
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|18326829|gb|BJ158829.1|BJ158829
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|208372651|gb|DC944630.1|DC944630
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAGATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|208353940|gb|DC930094.1|DC930094
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAGATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|162241394|gb|FC418559.1|FC418559
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|162244584|gb|FC423446.1|FC423446
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|67721131|gb|BJ971390.1|BJ971390
EST:     AGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGA-TTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: AGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|162184696|gb|FC361934.1|FC361934
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|7148048|gb|AW509970.1|AW509970
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|18351691|gb|BJ183743.1|BJ183743
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|19780510|gb|BQ039570.1|BQ039570
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|18327559|gb|BJ159562.1|BJ159562
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|37831031|gb|BJ589043.1|BJ589043
EST:     ACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: ACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|67720438|gb|BJ970697.1|BJ970697
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|67709266|gb|BJ965082.1|BJ965082
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|162244583|gb|FC423445.1|FC423445
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|162241395|gb|FC418560.1|FC418560
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
EST: gi|18354254|gb|BJ186310.1|BJ186310
EST:     GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAG                         CAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA
genomic: GCCCAAGAACTTTGAAGCTTTTTGCAAATAGACCAAATATGGGTTTCAGgtaagatacg ... ctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagagtctaagaggttcaagttcatggtggcttactagatatgttctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG
                            ggcttac  putative branch site (score: 3)
                                           ttctgtt  putative PPT
                                   tagatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatggatttttgaatgccttgcagaacacgaaatatgctaattgcagagtctaagaggttcaagttcatggtggcttactagatatgttctgttggcagCAACGTTACGGATTTTCCTCCAAATGACACAGTTATTGCATCTTTGGAGAATCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA