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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcattaggatatggttttatgtacatgtagcaagattcttttcacccctctcgagcgacttcaagaatctcaactcttacaacggatggttatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG

Basic information

species Physcomitrella patens
transcript PP1S9_386V6.1
intron # 3
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:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|18358114|gb|BJ190173.1|BJ190173
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|100399659|gb|BY972829.1|BY972829
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|100427615|gb|BY977586.1|BY977586
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|22492231|gb|BU052154.1|BU052154
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|208347568|gb|DC912827.1|DC912827
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|100417743|gb|BY975631.1|BY975631
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|67717655|gb|BJ967914.1|BJ967914
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|100416732|gb|BY993060.1|BY993060
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACGGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|18348196|gb|BJ180243.1|BJ180243
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|100446593|gb|CJ970892.1|CJ970892
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|162164761|gb|FC340483.1|FC340483
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|208373792|gb|DC936577.1|DC936577
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|208349326|gb|DC910385.1|DC910385
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|208344626|gb|DC912572.1|DC912572
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGGGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|67719577|gb|BJ969836.1|BJ969836
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|67717904|gb|BJ968163.1|BJ968163
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|100393447|gb|BY953403.1|BY953403
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|162249194|gb|FC421537.1|FC421537
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|208358732|gb|DC942926.1|DC942926
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|100401417|gb|BY990992.1|BY990992
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|162150303|gb|FC326388.1|FC326388
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|208368260|gb|DC935643.1|DC935643
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|18362966|gb|BJ195038.1|BJ195038
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|67704727|gb|BJ964960.1|BJ964960
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAN
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|100428929|gb|BY959504.1|BY959504
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG
EST: gi|18359430|gb|BJ191491.1|BJ191491
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGA
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGA
EST: gi|67719148|gb|BJ969407.1|BJ969407
EST:     ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACNAGCCTCCCCAGAAG                         ATGGGTGATCAAGATGTGGAGGTGACAGAGGANAANATGGACGAGGCTCAN
genomic: ACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAG

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: 29 (upstream exon), 35 (downstream exon)
Score: 11

ACCTAAGACATATGAAGATGAAAATGTCACTGATGATGAGTCGGATATTGACCTAGACACCGAGGGTGTTGTGGAACCTGACGACGAGCCTCCCCAGAAGgcaagtttct ... tatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctctcgagcgacttcaagaatctcaactcttacaacggatggttatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG
                            ctcttac  putative branch site (score: 11)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcattaggatatggttttatgtacatgtagcaagattcttttcacccctctcgagcgacttcaagaatctcaactcttacaacggatggttatgctgcagATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG