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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagacacttgtgcgatatgctttcttgtttccgactattgtaaatttaataatttcgtgcattgttcatttgagatttaagttcaatgttgactttgcagCTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGGGGGGAGATCGTGATTGGTGGACCTAGTGTAACATTGGGGTACTTCAAGA

Basic information

species Physcomitrella patens
transcript PP1S186_65V6.1
intron # 8
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|162174770|gb|FC352186.1|FC352186
EST:     TGGACCTCCTGTACCGCACTGCTATGTCAAG                         CTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG
genomic: TGGACCTCCTGTACCGCACTGCTATGTCAAGgtgcattttt ... gactttgcagCTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG
EST: gi|162213167|gb|FC389052.1|FC389052
EST:     GCTATGTCAAG                         CTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG
genomic: GCTATGTCAAGgtgcattttt ... gactttgcagCTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG
EST: gi|162270431|gb|FC447547.1|FC447547
EST:     ACACTTCTGTTGGACGTGTTGGACCTCCTGTACCGCACTGCTATGTCAAG                         CTCGTAAACTGGGAG
genomic: ACACTTCTGTTGGACGTGTTGGACCTCCTGTACCGCACTGCTATGTCAAGgtgcattttt ... gactttgcagCTCGTAAACTGGGAG
EST: gi|100385385|gb|BY950977.1|BY950977
EST:     ACACTTCTGTTGGACGTGTTGNACCTCCTGTACCGCACTGCTATGTCAAG                         CTCGTNAACTGGGGAG-AGGGGCA-CTACAAGACCACAGATGATCCACCAA
genomic: ACACTTCTGTTGGACGTGTTGGACCTCCTGTACCGCACTGCTATGTCAAGgtgcattttt ... gactttgcagCTCGTAAACTGGG-AGGAGGG-CAACTACAAGACCACAGATGATCCACCAA
EST: gi|162196325|gb|FC374368.1|FC374368
EST:     ACACTTCTGTTGGACGTGTTGGACCTCCTGTACCGCACTGCTATGTCAAG                         CTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG
genomic: ACACTTCTGTTGGACGTGTTGGACCTCCTGTACCGCACTGCTATGTCAAGgtgcattttt ... gactttgcagCTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG
EST: gi|162273457|gb|FC449906.1|FC449906
EST:     ACACTTCTGTTGGACGTGTTGGACCTCCTGTACCGCACTGCTATGTCAAG                         CTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG
genomic: ACACTTCTGTTGGACGTGTTGGACCTCCTGTACCGCACTGCTATGTCAAGgtgcattttt ... gactttgcagCTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG
EST: gi|162188839|gb|FC364853.1|FC364853
EST:     ACACTTCTGTTGGACGTGTTGGACCTCCTGTACCGCACTGCTATGTCAAG                         CTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG
genomic: ACACTTCTGTTGGACGTGTTGGACCTCCTGTACCGCACTGCTATGTCAAGgtgcattttt ... gactttgcagCTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaataatttcgtgcattgttcatttgagatttaagttcaatgttgactttgcagCTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGGGGGGAGATCGTGATTGGTGGACCTAGTGTAACATTGGGGTACTTCAAGA
                                         tgttgac  putative branch site (score: 3)
                             atttaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagacacttgtgcgatatgctttcttgtttccgactattgtaaatttaataatttcgtgcattgttcatttgagatttaagttcaatgttgactttgcagCTCGTAAACTGGGAGGAGGGCAACTACAAGACCACAGATGATCCACCAAGGGGGGAGATCGTGATTGGTGGACCTAGTGTAACATTGGGGTACTTCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA