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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgattctgtagtttttacatgtcctttggtgtgtgcccacctcggtgttccatctgagcatctcttctaaccatggctaaacatgattgattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAATTAAAGTTGGAAGTTCTAGAGGACACAGGACCCTTTCTTAAGGGTTCGTC

Basic information

species Physcomitrella patens
transcript PP1S14_318V6.2
intron # 9
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:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|18336897|gb|BJ168920.1|BJ168920
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|67727809|gb|BJ978068.1|BJ978068
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|162184795|gb|FC361097.1|FC361097
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|67728278|gb|BJ978537.1|BJ978537
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|67726888|gb|BJ977147.1|BJ977147
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|67728007|gb|BJ978266.1|BJ978266
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|7582787|gb|AW698951.1|AW698951
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|37836566|gb|BJ594574.1|BJ594574
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|67721922|gb|BJ972181.1|BJ972181
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|67725789|gb|BJ976048.1|BJ976048
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|67723947|gb|BJ974206.1|BJ974206
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|37846703|gb|BJ604711.1|BJ604711
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|208373205|gb|DC944904.1|DC944904
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|162235943|gb|FC411686.1|FC411686
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|18340442|gb|BJ172470.1|BJ172470
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|162245025|gb|FC424983.1|FC424983
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|162195398|gb|FC370867.1|FC370867
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|67692593|gb|BJ952826.1|BJ952826
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|67724183|gb|BJ974442.1|BJ974442
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|37849081|gb|BJ607089.1|BJ607089
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|37823060|gb|BJ581126.1|BJ581126
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|162245026|gb|FC424984.1|FC424984
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
EST: gi|162270584|gb|FC446509.1|FC446509
EST:     CAAATGACCCAAATGTTCGGGATGTTTTAGCTTTTTTGCAGACAGACGAG                         GGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT
genomic: CAAATGACCCAAATGTTCGGGATGTTTTAGCTTCTCTGCAGACAGACGAGgtaaattgcc ... gattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgttccatctgagcatctcttctaaccatggctaaacatgattgattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAATTAAAGTTGGAAGTTCTAGAGGACACAGGACCCTTTCTTAAGGGTTCGTC
                                              attcaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgattctgtagtttttacatgtcctttggtgtgtgcccacctcggtgttccatctgagcatctcttctaaccatggctaaacatgattgattcaatagGGGAAGAACGATGATCAAGCAACAAAGGATAAGAGCAAATGAGTATGGAATTAAAGTTGGAAGTTCTAGAGGACACAGGACCCTTTCTTAAGGGTTCGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA