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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatatgattggatatatttaaccactaatataactccatggatattaaagcccttgactgctactaatgcacttttctctttttcttttcccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGATGCATCTGAAATCAAGTCTTGCGGGCTCTCGCTGTAGTTGGAGGGCATA

Basic information

species Physcomitrella patens
transcript PP1S269_30V6.2
intron # 17
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|37840929|gb|BJ598937.1|BJ598937
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|162255598|gb|FC431596.1|FC431596
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|162279090|gb|FC455429.1|FC455429
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208386299|gb|DC953012.1|DC953012
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|18339902|gb|BJ171929.1|BJ171929
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208348107|gb|DC916917.1|DC916917
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|67696733|gb|BJ956966.1|BJ956966
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|18341451|gb|BJ173486.1|BJ173486
EST:     GTAAGAGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208376570|gb|DC922601.1|DC922601
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|162183659|gb|FC359900.1|FC359900
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208381414|gb|DC927850.1|DC927850
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|162189304|gb|FC366774.1|FC366774
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208394434|gb|DC928486.1|DC928486
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208354437|gb|DC926614.1|DC926614
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208397506|gb|DC916390.1|DC916390
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|18334107|gb|BJ166123.1|BJ166123
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208347298|gb|DC925322.1|DC925322
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCGCTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208356794|gb|DC926805.1|DC926805
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|18340631|gb|BJ172659.1|BJ172659
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208395040|gb|DC924175.1|DC924175
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208380224|gb|DC919060.1|DC919060
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208355907|gb|DC926668.1|DC926668
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAATCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
EST: gi|208354673|gb|DC918699.1|DC918699
EST:     GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAG                         GATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA
genomic: GTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGA

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: 10 (upstream exon), 35 (downstream exon)
Score: 12

CTTCACTTTACGGCCACTTTGTTGTAAGTGTTATTCATGAGATTACAGAGGCACTTGGCATCCATTGCTTCAGgtgatgtgct ... cccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGATGCATCTGAAATCAAGTCTTGCGGGCTCTCGCTGTAGTTGGAGGGCATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaagcccttgactgctactaatgcacttttctctttttcttttcccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGATGCATCTGAAATCAAGTCTTGCGGGCTCTCGCTGTAGTTGGAGGGCATA
                 tactaat  putative branch site (score: 12)
                ctactaatgcactttt  CT-rich tract
                                   tttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatatgattggatatatttaaccactaatataactccatggatattaaagcccttgactgctactaatgcacttttctctttttcttttcccttttcagGATTGGTAAAGTCAAAGACGGGAAAGGAACCTAAGCAAGAGGAATCTTTGATGCATCTGAAATCAAGTCTTGCGGGCTCTCGCTGTAGTTGGAGGGCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG