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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgcttgcgcaggctctgcctcgtcattgattgtttatgtttaggaagttggagtcgcttcgaaagttaagttgcccttgcattggtgatgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGACATTTTATAAAATTTTCTGTATTCTACTGGTGACGAGGTAGAGATCATG

Basic information

species Physcomitrella patens
transcript PP1S62_236V6.7
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|18362287|gb|BJ194357.1|BJ194357
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|208345526|gb|DC909216.1|DC909216
EST:     ATCGTGAGGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18347183|gb|BJ179229.1|BJ179229
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18347971|gb|BJ180018.1|BJ180018
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18367392|gb|BJ199475.1|BJ199475
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|100396442|gb|BY990131.1|BY990131
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAGTGA                      
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAA-T--T-Agtgagtacgc ... tgtcatg
EST: gi|67573545|gb|BJ946369.1|BJ946369
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18346137|gb|BJ178180.1|BJ178180
EST:     CTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: CTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18344013|gb|BJ176052.1|BJ176052
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18368324|gb|BJ200409.1|BJ200409
EST:     AATTTGTTGCAGGAGGTTGAATTAGTGA                      
genomic: AATTTGTTGCAGGAGGTTGAA-T--T-Agtgagtacgc ... tgtcatg
EST: gi|18347004|gb|BJ179050.1|BJ179050
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18349338|gb|BJ181387.1|BJ181387
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|162275836|gb|FC451397.1|FC451397
EST:     TACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: TACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|162162143|gb|FC337717.1|FC337717
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTCAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18332363|gb|BJ164376.1|BJ164376
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18361105|gb|BJ193169.1|BJ193169
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|67573218|gb|BJ946042.1|BJ946042
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18367879|gb|BJ199962.1|BJ199962
EST:     AATTTGTTGCAGGAGGTTGAATTAGTGA                      
genomic: AATTTGTTGCAGGAGGTTGAA-T--T-Agtgagtacgc ... tgtcatg
EST: gi|18365057|gb|BJ197131.1|BJ197131
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|18361352|gb|BJ193418.1|BJ193418
EST:     AATTTGTTGCAGGAGGTTGAATTAGTGA                      
genomic: AATTTGTTGCAGGAGGTTGAA-T--T-Agtgagtacgc ... tgtcatg
EST: gi|100428878|gb|BY959478.1|BY959478
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
EST: gi|67571932|gb|BJ944756.1|BJ944756
EST:     ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTA                         TGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA
genomic: ATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGA

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: 20 (upstream exon), 30 (downstream exon)
Score: 5

TTTTGACCTTTGGGGTTCGCAGAGGACATCTTTGTGTTCTTATTTTATTTATCGTGAAGCTGCTTACCAAGTGCTCAATTTGTTGCAGGAGGTTGAATTAgtgagtacgc ... tgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGACATTTTATAAAATTTTCTGTATTCTACTGGTGACGAGGTAGAGATCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagttggagtcgcttcgaaagttaagttgcccttgcattggtgatgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGACATTTTATAAAATTTTCTGTATTCTACTGGTGACGAGGTAGAGATCATG
                  aaagttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgcttgcgcaggctctgcctcgtcattgattgtttatgtttaggaagttggagtcgcttcgaaagttaagttgcccttgcattggtgatgtcatgcagTGGTACAGAGTTGGGGTTAATTTTGCGACGTAGGAGGGAGGAGGTTTCGGACATTTTATAAAATTTTCTGTATTCTACTGGTGACGAGGTAGAGATCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA