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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacgtatctcgtctgtaccgaagattacttaagaagctcgaagtatttgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcaccttggtgttcgctgttgcag

Basic information

species Physcomitrella patens
transcript PP1S17_286V6.1
intron # 5
splice site 5'
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|208365978|gb|DC955497.1|DC955497
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTT-GGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162184832|gb|FC361134.1|FC361134
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162195745|gb|FC371136.1|FC371136
EST:     ATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: ATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|208378728|gb|DC914702.1|DC914702
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTANTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTNGGG-ACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|208398836|gb|DC920784.1|DC920784
EST:     GAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: GAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162243725|gb|FC421846.1|FC421846
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|208381790|gb|DC928453.1|DC928453
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162245393|gb|FC421295.1|FC421295
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|19780877|gb|BQ039620.1|BQ039620
EST:     TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|100401328|gb|BY990947.1|BY990947
EST:     GATGAACGGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGGTCTTGCTGTCTC
genomic: GATGAACGGG-AACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTC
EST: gi|208352662|gb|DC921396.1|DC921396
EST:     TGATGAACNGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: TGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
EST: gi|162229107|gb|FC405090.1|FC405090
EST:     GGTGGAGTAGTCATGTGGTCTG                         GCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC
genomic: GGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 31 (downstream exon)
Score: 28

CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacg ... gctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTTCCACTTTCCACTGACCACAAGCCCAATCGACATGATGAACGGGAACGAATTGAGAAATCTGGTGGAGTAGTCATGTGGTCTGgtgagtcacgtatctcgtctgtaccgaagattacttaagaagctcgaagtatttgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcaccttggtgttcgctgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG