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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCTTCTCTTACTTGCCCCCATTGTCCGATGACGCCATCGCTAAGCAGGTGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattattgtttcgtgaaattatcactactttttgaatcaccaactgagccgttgggcagaatgtaggaaaggatatgagttagctatctctttcga...

Basic information

species Physcomitrella patens
transcript PP1S46_42V6.1
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|37849395|gb|BJ607403.1|BJ607403
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162245811|gb|FC420777.1|FC420777
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162252872|gb|FC429245.1|FC429245
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162227605|gb|FC402611.1|FC402611
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|19783181|gb|BQ039974.1|BQ039974
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|15590649|gb|BI675265.1|BI675265
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162218460|gb|FC394842.1|FC394842
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|18346213|gb|BJ178256.1|BJ178256
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|16137521|gb|BI894379.1|BI894379
EST:     TGGAGTACATGATTCANCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162253646|gb|FC430384.1|FC430384
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162227604|gb|FC402610.1|FC402610
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|18348675|gb|BJ180724.1|BJ180724
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162278356|gb|FC454234.1|FC454234
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162253647|gb|FC430385.1|FC430385
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162259810|gb|FC436777.1|FC436777
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|67575357|gb|BJ948181.1|BJ948181
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|18354460|gb|BJ186516.1|BJ186516
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162250779|gb|FC426628.1|FC426628
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162221380|gb|FC398138.1|FC398138
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|19789498|gb|BQ041341.1|BQ041341
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|37829325|gb|BJ587337.1|BJ587337
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162265088|gb|FC440967.1|FC440967
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|16137935|gb|BI894799.1|BI894799
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162269175|gb|FC444731.1|FC444731
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCTCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|18340429|gb|BJ172457.1|BJ172457
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162277910|gb|FC453833.1|FC453833
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162259809|gb|FC436776.1|FC436776
EST:     TGGAGTACATGATTCAGCAGAAGTTGTTCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTATTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162265087|gb|FC440966.1|FC440966
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162245810|gb|FC420776.1|FC420776
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162218459|gb|FC394841.1|FC394841
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|67704491|gb|BJ964724.1|BJ964724
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162252873|gb|FC429246.1|FC429246
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|67698821|gb|BJ959054.1|BJ959054
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|37827973|gb|BJ585985.1|BJ585985
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162221379|gb|FC398137.1|FC398137
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTATTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162230070|gb|FC406010.1|FC406010
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|37825323|gb|BJ583389.1|BJ583389
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|162269176|gb|FC444732.1|FC444732
EST:     TGGAGTACATGATTCAGCAGAAGTTGATCCTCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
EST: gi|16137472|gb|BI894336.1|BI894336
EST:     TTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTG                         AACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC
genomic: TTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGAC

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: 35 (upstream exon), 35 (downstream exon)
Score: 121

GACCTTCTCTTACTTGCCCCCATTGTCCGATGACGCCATCGCTAAGCAGGTGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattat ... ctcgttacagAACTCCAAGGGTGTGACCCGCGAGAACAACTCCTCCCCAGGGTACTATGACGGCCGCTACTGGACCATGTGGAAGTTGCCCATGTTCGGATGCCAAGACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCTTCTCTTACTTGCCCCCATTGTCCGATGACGCCATCGCTAAGCAGGTGGAGTACATGATTCAGCAGAAGTTGATCCCCTGCCTCGAGTTCGACGTGgtaagattattgtttcgtgaaattatcactactttttgaatcaccaactgagccgttgggcagaatgtaggaaaggatatgagttagctatctctttcga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT