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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgattgacaaaagagcagcattgttcactgtaattgtacaagtcacgagtttagtctgttgattgcttgagagaaggatgactggttgccgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAGTCACGAAATACCTTGTACCTTACTG

Basic information

species Physcomitrella patens
transcript PP1S9_317V6.2
intron # 15
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|100398950|gb|BY990597.1|BY990597
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGGCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37827954|gb|BJ585966.1|BJ585966
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37839102|gb|BJ597110.1|BJ597110
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37829800|gb|BJ587812.1|BJ587812
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|162242962|gb|FC416471.1|FC416471
EST:     AATNTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|208350253|gb|DC925729.1|DC925729
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|18340695|gb|BJ172725.1|BJ172725
EST:     CTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: CTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37824608|gb|BJ582674.1|BJ582674
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|162160170|gb|FC337067.1|FC337067
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|162178384|gb|FC355206.1|FC355206
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37829477|gb|BJ587489.1|BJ587489
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37829305|gb|BJ587317.1|BJ587317
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37841967|gb|BJ599975.1|BJ599975
EST:     AATTTCATACGGAGGTTTTAGTACCNTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37841095|gb|BJ599103.1|BJ599103
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37827427|gb|BJ585439.1|BJ585439
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|162252661|gb|FC428698.1|FC428698
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|18334134|gb|BJ166150.1|BJ166150
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|162197253|gb|FC372540.1|FC372540
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37825373|gb|BJ583439.1|BJ583439
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|18336149|gb|BJ168171.1|BJ168171
EST:     CCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: CCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|162197252|gb|FC372539.1|FC372539
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37828150|gb|BJ586162.1|BJ586162
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|37851908|gb|BJ609916.1|BJ609916
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
EST: gi|162174854|gb|FC351646.1|FC351646
EST:     AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAG                         AGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG
genomic: AATTTCATACGGAGGTTTTAGTACCCTCGCAGGCATTACTTTCACTCCAGgtattcaatt ... cgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgagtttagtctgttgattgcttgagagaaggatgactggttgccgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAGTCACGAAATACCTTGTACCTTACTG
            tgttgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgattgacaaaagagcagcattgttcactgtaattgtacaagtcacgagtttagtctgttgattgcttgagagaaggatgactggttgccgtggtgcagAGCTTTACAAGTGTGCTGCCGAATTAGTTGGCCCATCGCAGCTCTTCACAGTCACGAAATACCTTGTACCTTACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC