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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcggaggttcgagcaattcggtatcttagagggttccacacaaagtttttaaatgtttttttcattggggatgttttattttatatgatttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGCCGGTGGTTGCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGT

Basic information

species Physcomitrella patens
transcript PP1S9_386V6.1
intron # 1
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|162275962|gb|FC452030.1|FC452030
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|18358114|gb|BJ190173.1|BJ190173
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67702514|gb|BJ962747.1|BJ962747
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|100399659|gb|BY972829.1|BY972829
EST:     GCGATGCTGGCCACTCCGACGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|100427615|gb|BY977586.1|BY977586
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|22492231|gb|BU052154.1|BU052154
EST:     CGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: CGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|208347568|gb|DC912827.1|DC912827
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67702635|gb|BJ962868.1|BJ962868
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|100417743|gb|BY975631.1|BY975631
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67702204|gb|BJ962437.1|BJ962437
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67717655|gb|BJ967914.1|BJ967914
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|100416732|gb|BY993060.1|BY993060
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|18348196|gb|BJ180243.1|BJ180243
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|100446593|gb|CJ970892.1|CJ970892
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|162164761|gb|FC340483.1|FC340483
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|208373792|gb|DC936577.1|DC936577
EST:     GCGATGCTGGCCACTCCAGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|208349326|gb|DC910385.1|DC910385
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67704132|gb|BJ964365.1|BJ964365
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|208344626|gb|DC912572.1|DC912572
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67719577|gb|BJ969836.1|BJ969836
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67717904|gb|BJ968163.1|BJ968163
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67702495|gb|BJ962728.1|BJ962728
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|100393447|gb|BY953403.1|BY953403
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|18353366|gb|BJ185421.1|BJ185421
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|162249194|gb|FC421537.1|FC421537
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|208358732|gb|DC942926.1|DC942926
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|100401417|gb|BY990992.1|BY990992
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|162150303|gb|FC326388.1|FC326388
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|208368260|gb|DC935643.1|DC935643
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|18362966|gb|BJ195038.1|BJ195038
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|18352940|gb|BJ184995.1|BJ184995
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCNGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67704727|gb|BJ964960.1|BJ964960
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|100428929|gb|BY959504.1|BY959504
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|18359430|gb|BJ191491.1|BJ191491
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
EST: gi|67719148|gb|BJ969407.1|BJ969407
EST:     GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGANAG                         GTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC
genomic: GCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGC

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: 15 (upstream exon), 30 (downstream exon)
Score: 7

CGAAGCTGAAGGAGCTTAAGGTGTTCGTGCAGCAGGTGGAGGCGTATCCGGCGATGCTGGCCACTCCGGCGCTTCGATTCTTTCGGGACTTCCTGGAGAGgtagcgtagt ... ttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGCCGGTGGTTGCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttaaatgtttttttcattggggatgttttattttatatgatttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGCCGGTGGTTGCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGT
                          atgttttattttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcggaggttcgagcaattcggtatcttagagggttccacacaaagtttttaaatgtttttttcattggggatgttttattttatatgatttgtgatcagGTTTGGAGCGACTCTGCCGTCAGTTGCGTATGCGGAGGAAGCCAAATCTGCCGGTGGTTGCGGAAAACCTGCTGGAGGCTGTTGTCCTCACCCCCATGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT