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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcattgtgatgattctgtttatttttctagtatgaggtgaatatcacaaggtttctcacatacacttttttttttgctgactgtgcggcgtagattagACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAGTTTCATGGCAACCCTGCAGGCTTCAAACGCTACAGTCTCTTTGCAGGGACAGAA

Basic information

species Physcomitrella patens
transcript PP1S77_163V6.2
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|18360619|gb|BJ192682.1|BJ192682
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|18360619|gb|BJ192682.1|BJ192682
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|18360619|gb|BJ192682.1|BJ192682
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|67569137|gb|BJ941961.1|BJ941961
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|67569137|gb|BJ941961.1|BJ941961
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|67569137|gb|BJ941961.1|BJ941961
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|18327068|gb|BJ159069.1|BJ159069
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|18327068|gb|BJ159069.1|BJ159069
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|18327068|gb|BJ159069.1|BJ159069
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|15327009|gb|BI487464.1|BI487464
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|15327009|gb|BI487464.1|BI487464
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|15327009|gb|BI487464.1|BI487464
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|162214635|gb|FC390666.1|FC390666
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|162214635|gb|FC390666.1|FC390666
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|162214635|gb|FC390666.1|FC390666
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|100412337|gb|BY956532.1|BY956532
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|100412337|gb|BY956532.1|BY956532
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|100412337|gb|BY956532.1|BY956532
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|100396568|gb|BY990190.1|BY990190
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGAT                         ACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAGTTTCA
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATgtaagtagaa ... cgtagattagACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAGTTTCA
EST: gi|162253435|gb|FC430069.1|FC430069
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|162253435|gb|FC430069.1|FC430069
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|162253435|gb|FC430069.1|FC430069
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|208382112|gb|DC914787.1|DC914787
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|208382112|gb|DC914787.1|DC914787
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt
EST: gi|208382112|gb|DC914787.1|DC914787
EST:     CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTGATATT                       
genomic: CTGCACTTCCGTAGAGACCGTTTCGTAGTGAAATTCGATCAAGATTTG--A-Tgtaagtagaa ... cgtagatt


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacaaggtttctcacatacacttttttttttgctgactgtgcggcgtagattagACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAGTTTCATGGCAACCCTGCAGGCTTCAAACGCTACAGTCTCTTTGCAGGGACAGAA
                               tgctgac  putative branch site (score: 2)
                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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcattgtgatgattctgtttatttttctagtatgaggtgaatatcacaaggtttctcacatacacttttttttttgctgactgtgcggcgtagattagACGACTGTATCGTGATTACTCTCCTTCATCGGTGGCAACAAGGCAGTTTCATGGCAACCCTGCAGGCTTCAAACGCTACAGTCTCTTTGCAGGGACAGAA

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