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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaccagtggatgttccagtgttttctctttttatagttgtactgctcatatattacttactattgtgttctctttgttctgctggacttccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGGCGGTACCATAAAAAATATAACACTTGGTTTCAACGTCACGAAGAGCCCA

Basic information

species Physcomitrella patens
transcript PP1S101_120V6.1
intron # 18
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|162194885|gb|FC369002.1|FC369002
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|162203132|gb|FC378527.1|FC378527
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|162157765|gb|FC335479.1|FC335479
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|162164420|gb|FC341559.1|FC341559
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|162194884|gb|FC369001.1|FC369001
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|162164419|gb|FC341558.1|FC341558
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|37853190|gb|BJ611198.1|BJ611198
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|162203133|gb|FC378528.1|FC378528
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|37851584|gb|BJ609592.1|BJ609592
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|37851635|gb|BJ609643.1|BJ609643
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
EST: gi|162157764|gb|FC335478.1|FC335478
EST:     GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAG                         GGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG
genomic: GGGAACGACTAGACAAAGATGTTCTTTTCTATGCCTTCTATTATCAACAGgtgttttaca ... tccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcatatattacttactattgtgttctctttgttctgctggacttccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGGCGGTACCATAAAAAATATAACACTTGGTTTCAACGTCACGAAGAGCCCA
          tacttac  putative branch site (score: 1)
                                           cttccac  putative PPT
     tatattacttactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaccagtggatgttccagtgttttctctttttatagttgtactgctcatatattacttactattgtgttctctttgttctgctggacttccacaacagGGTACTTACCAACAGTATTTAGCAGCTCGGGAGCTAAAAAAGCAATCATGGCGGTACCATAAAAAATATAACACTTGGTTTCAACGTCACGAAGAGCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - -ctgctca