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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGTCTCTTCAGGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaaattttagcggttgtcgatgattttatttaataagtgcggcttgctttttgtaatttcctatgtggctgttcttctgagggctccaaatgc...

Basic information

species Physcomitrella patens
transcript PP1S61_124V6.1
intron # 4
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|208370975|gb|DC944350.1|DC944350
EST:     GGAAGGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208366029|gb|DC951124.1|DC951124
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208399308|gb|DC916621.1|DC916621
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208362082|gb|DC943509.1|DC943509
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208370558|gb|DC951594.1|DC951594
EST:     GGAAAGGGCGAACCGTGAAGGGTACAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208358614|gb|DC949949.1|DC949949
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208370450|gb|DC952153.1|DC952153
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208370762|gb|DC948271.1|DC948271
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208351242|gb|DC921549.1|DC921549
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208365172|gb|DC947352.1|DC947352
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208385741|gb|DC952902.1|DC952902
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208389602|gb|DC945826.1|DC945826
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|162206888|gb|FC382750.1|FC382750
EST:     AGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATT
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATT
EST: gi|208393558|gb|DC949720.1|DC949720
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208384193|gb|DC919679.1|DC919679
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208396517|gb|DC915829.1|DC915829
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208389378|gb|DC953216.1|DC953216
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208389174|gb|DC945750.1|DC945750
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208355255|gb|DC949791.1|DC949791
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208348899|gb|DC921671.1|DC921671
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208388748|gb|DC953482.1|DC953482
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAGATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208368721|gb|DC947954.1|DC947954
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|162206887|gb|FC382749.1|FC382749
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208373226|gb|DC945166.1|DC945166
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|37845977|gb|BJ603985.1|BJ603985
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208381467|gb|DC919469.1|DC919469
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208392762|gb|DC953659.1|DC953659
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAGATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208367375|gb|DC951293.1|DC951293
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208367870|gb|DC950951.1|DC950951
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208365476|gb|DC954717.1|DC954717
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208369168|gb|DC956043.1|DC956043
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208388577|gb|DC953395.1|DC953395
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208353508|gb|DC946330.1|DC946330
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208358599|gb|DC946560.1|DC946560
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208388861|gb|DC945437.1|DC945437
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208397452|gb|DC916364.1|DC916364
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
EST: gi|208359478|gb|DC954031.1|DC954031
EST:     GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAG                         GGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC
genomic: GGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGC

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), 30 (downstream exon)
Score: 12

GTGGGTCTCTTCAGGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaa ... atttcctcagGGACAAATAGTTAAGGAGGGTCAAGTGGTGTGCTATTTGGAGCAGCTCGGCACGCAACAACCTGTAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGTCTCTTCAGGAAAGGGCGAACCGTGAAGGGTAAAAGTGGTCCTCCACTCTGCGAAGAGgtatcctcaaattttagcggttgtcgatgattttatttaataagtgcggcttgctttttgtaatttcctatgtggctgttcttctgagggctccaaatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA