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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAAGCCAATTTCATGTACGAAGATGTTGAGGCGGAGCCCAAGGTGGATTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggactctcttcttgcaataccctacggcttaattgtagggttgcattgttggtcctagtgatgtctatcaaaatctcgtacaagctagatgcggg...

Basic information

species Physcomitrella patens
transcript PP1S285_10V6.1
intron # 1
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|100405523|gb|BY973719.1|BY973719
EST:     TTGGCGCCTGAAGGGGGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGGCGTTTTCTGCGGTCGGTTCGGTTTGA-GGAGTGAATGC
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGG-CGTTTTCTGCGGTCGGTTCGGTT-GAAGGAGTGAATGC
EST: gi|162185297|gb|FC360871.1|FC360871
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|162186545|gb|FC363309.1|FC363309
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|162157752|gb|FC335466.1|FC335466
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|100361795|gb|BY947631.1|BY947631
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTT-CTGCGGTCGGTTCGGTTGAAGGAGTGAATGCA
EST: gi|100396097|gb|BY972245.1|BY972245
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAG
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAG
EST: gi|162265158|gb|FC441245.1|FC441245
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|100397603|gb|BY990309.1|BY990309
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGC
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGC
EST: gi|162255174|gb|FC431484.1|FC431484
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|100405708|gb|BY973814.1|BY973814
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAGGGAGTG
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTG
EST: gi|100385224|gb|BY950816.1|BY950816
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|67718463|gb|BJ968722.1|BJ968722
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|100388519|gb|BY952121.1|BY952121
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|162177962|gb|FC354068.1|FC354068
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|100397513|gb|BY990264.1|BY990264
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|67569865|gb|BJ942689.1|BJ942689
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|100433239|gb|BY978858.1|BY978858
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|162163721|gb|FC340307.1|FC340307
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|162172914|gb|FC348919.1|FC348919
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|162234971|gb|FC411758.1|FC411758
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
EST: gi|100447462|gb|CJ971761.1|CJ971761
EST:     TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTG                         GGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA
genomic: TTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 30

AAGGAAGCCAATTTCATGTACGAAGATGTTGAGGCGGAGCCCAAGGTGGATTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggact ... tgtgattcagGGAGTTGCTGGGCGTTTTCTGCGGTCGGTTCGGTTGAAGGAGTGAATGCAATTAAAACCGGAGAATTGGTTTCCTTGTCTGAGCAGGAGCTCGTGGACTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGAAGCCAATTTCATGTACGAAGATGTTGAGGCGGAGCCCAAGGTGGATTGGCGCCTGAAGGGTGCGGTCACGGACGTCAAAGATCAAGGCGCATGTGgtaatggactctcttcttgcaataccctacggcttaattgtagggttgcattgttggtcctagtgatgtctatcaaaatctcgtacaagctagatgcggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA