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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgacaatcattgtgatgattctgtttatttttctagtatgaggtgaatatcacaaggtttctcacatacacttttttttttgctgactgtgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAGTTTCATGGCAACCCTGCAGGCTTCAAACGCTACAGTCTCTTTGCAGGGA

Basic information

species Physcomitrella patens
transcript PP1S77_163V6.1
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|100390647|gb|BY971402.1|BY971402
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|15327009|gb|BI487464.1|BI487464
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|18360619|gb|BJ192682.1|BJ192682
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|208382112|gb|DC914787.1|DC914787
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|18327068|gb|BJ159069.1|BJ159069
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|100396568|gb|BY990190.1|BY990190
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--                         A-T--ACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|100412337|gb|BY956532.1|BY956532
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|67569137|gb|BJ941961.1|BJ941961
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|162214635|gb|FC390666.1|FC390666
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTCCTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|100372283|gb|BY985523.1|BY985523
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG
EST: gi|162253435|gb|FC430069.1|FC430069
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ATTAGACGACTGTATCGTGATTCCTCTCCTTCATCGGTGGCAACAAGGCAG
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAG

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

AACTTGTGCCACCGCCTGTAGACCAATTTCTTTCTTTCGGGTGTTCGGAGCTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... tgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAGTTTCATGGCAACCCTGCAGGCTTCAAACGCTACAGTCTCTTTGCAGGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatatcacaaggtttctcacatacacttttttttttgctgactgtgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAGTTTCATGGCAACCCTGCAGGCTTCAAACGCTACAGTCTCTTTGCAGGGA
                                    tgctgac  putative branch site (score: 10)
                     atacactttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgacaatcattgtgatgattctgtttatttttctagtatgaggtgaatatcacaaggtttctcacatacacttttttttttgctgactgtgcggcgtagATTAGACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAGTTTCATGGCAACCCTGCAGGCTTCAAACGCTACAGTCTCTTTGCAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG