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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcaaacttggttcaaatgtgtgtttcattgtcaacacacgtaaattgatgatcctaacaagcttctatgttactaagagtatcttttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAAATTGAGAAGACCATCAATACCCTAGGCAAGAAAGCAAATGATGGGAGCA

Basic information

species Physcomitrella patens
transcript PP1S154_6V6.2
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|37822581|gb|BJ580647.1|BJ580647
EST:     TGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: TGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|208368131|gb|DC947691.1|DC947691
EST:     TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|162195145|gb|FC368820.1|FC368820
EST:     TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|37853268|gb|BJ611276.1|BJ611276
EST:     TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|162190098|gb|FC366672.1|FC366672
EST:     CATCTA-CGAGATTTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: CATCTACCGAGA-TTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|162156509|gb|FC332117.1|FC332117
EST:     TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|162156510|gb|FC332118.1|FC332118
EST:     TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAN
genomic: TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|162188818|gb|FC364832.1|FC364832
EST:     ATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: ATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|162163854|gb|FC340076.1|FC340076
EST:     TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|67724548|gb|BJ974807.1|BJ974807
EST:     GACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACNTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: GACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|208360677|gb|DC946429.1|DC946429
EST:     TCATNTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: TCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
EST: gi|37826547|gb|BJ584559.1|BJ584559
EST:     GATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAA                         GGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA
genomic: GATTACGTTGACATCAGCATTGCTGTTGGTACAGCCAAAgtaagttcaa ... tttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaattgatgatcctaacaagcttctatgttactaagagtatcttttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAAATTGAGAAGACCATCAATACCCTAGGCAAGAAAGCAAATGATGGGAGCA
            tcctaac  putative branch site (score: 1)
                                        tatcttttc  putative PPT
                                        tatctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcaaacttggttcaaatgtgtgtttcattgtcaacacacgtaaattgatgatcctaacaagcttctatgttactaagagtatcttttcatgtagGGACTTGTTGTTCCAGTGATCCGTGGAGCAGATCATTTGAACTTCGCTCAAATTGAGAAGACCATCAATACCCTAGGCAAGAAAGCAAATGATGGGAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA