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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaggagttgcagctgattcctgataatatgcgccctattttttagctatgaaaatgttcttttagtgacgaagaaatcgttaccattttttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG

Basic information

species Physcomitrella patens
transcript PP1S47_18V6.2
intron # 11
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|162190447|gb|FC365669.1|FC365669
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|162209036|gb|FC385588.1|FC385588
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|162167335|gb|FC342323.1|FC342323
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|162159093|gb|FC334888.1|FC334888
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCNTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|37832387|gb|BJ590399.1|BJ590399
EST:     TTTTACGGGACAAGCNTTTGCTCAGTTCAGATACTTCACAGACCTTCNTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: TTTTAC-GGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|37835979|gb|BJ593991.1|BJ593991
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|162158872|gb|FC335395.1|FC335395
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|37821841|gb|BJ579907.1|BJ579907
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCNTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|162190446|gb|FC365668.1|FC365668
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|162169730|gb|FC345267.1|FC345267
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|37832682|gb|BJ590694.1|BJ590694
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCNTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|37843775|gb|BJ601783.1|BJ601783
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|162167336|gb|FC342324.1|FC342324
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|18336041|gb|BJ168063.1|BJ168063
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|162172645|gb|FC348026.1|FC348026
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
EST: gi|37823211|gb|BJ581277.1|BJ581277
EST:     GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCNTG                         CGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA
genomic: GTTTTACGGACAAGCCTTTGCTCAGTTCAGATACTTCACAGACCTTCCTGgtatgttcaa ... ttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatgaaaatgttcttttagtgacgaagaaatcgttaccattttttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG
                                      ccatttttt  CT-rich tract
      aaaatgttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaggagttgcagctgattcctgataatatgcgccctattttttagctatgaaaatgttcttttagtgacgaagaaatcgttaccattttttgcatgcagCGCCAGAAAGTGCCATGCGGGATGTGATTTCAAAGCCTGCTGCTGCAAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA