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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcgtagtctattcacaacttcaaatcttacttgattattacaaggttgttgttttttgacaataggtaactgacatcctgatggcttgttgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGGGGAGTGCCGATGTGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTC

Basic information

species Physcomitrella patens
transcript PP1S14_318V6.2
intron # 7
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|162159572|gb|FC335750.1|FC335750
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|18336897|gb|BJ168920.1|BJ168920
EST:     AGACGACCCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: AGACGA-CCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|67727809|gb|BJ978068.1|BJ978068
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|162235944|gb|FC411687.1|FC411687
EST:     TGATACTTCTATGGAAGAATCANGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGNNCA-CA-GCAGCTGCTGCAGCATCCGCA
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATG--CAACAAGCAGCTGCTGCAGCATCCGCA
EST: gi|67728278|gb|BJ978537.1|BJ978537
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCGACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|67726888|gb|BJ977147.1|BJ977147
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|67728007|gb|BJ978266.1|BJ978266
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|7582787|gb|AW698951.1|AW698951
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|37836566|gb|BJ594574.1|BJ594574
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|67725789|gb|BJ976048.1|BJ976048
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|67723947|gb|BJ974206.1|BJ974206
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|37846703|gb|BJ604711.1|BJ604711
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|208373205|gb|DC944904.1|DC944904
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|162235943|gb|FC411686.1|FC411686
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|18340442|gb|BJ172470.1|BJ172470
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCGGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|162245025|gb|FC424983.1|FC424983
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|162195398|gb|FC370867.1|FC370867
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|67692593|gb|BJ952826.1|BJ952826
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|67724183|gb|BJ974442.1|BJ974442
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|37849081|gb|BJ607089.1|BJ607089
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|37823060|gb|BJ581126.1|BJ581126
EST:     AGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: AGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|162245026|gb|FC424984.1|FC424984
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG
EST: gi|162270584|gb|FC446509.1|FC446509
EST:     TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATG                         CTTTGCAGATGTCGATGCAACAAGCAGCTGTTGCAGCATCCGCAGCACAGG
genomic: TGATACTTCTATGGAAGAATCAGGCGGAGACGACCAAGACCTTGCATATGgttggttgtt ... tgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttgttttttgacaataggtaactgacatcctgatggcttgttgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGGGGAGTGCCGATGTGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTC
     tgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcgtagtctattcacaacttcaaatcttacttgattattacaaggttgttgttttttgacaataggtaactgacatcctgatggcttgttgaaattcagCTCTGCAGATGTCGATGCAACAAGCAGCTGCTGCAGCATCCGCAGCACAGGGGAGTGCCGATGTGAACCAGGTTCTGGGTGATCAGAGCTTTGTTTCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT