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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgggtgcacatcttctgctttgctcctgatatattagatgatcacatttgaattgattttagaataaacttttcttcaagtctgattatttggaatgggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG

Basic information

species Physcomitrella patens
transcript PP1S129_147V6.1
intron # 27
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|162186786|gb|FC362822.1|FC362822
EST:     TGAAAGTAGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|162197287|gb|FC372249.1|FC372249
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|162167451|gb|FC343154.1|FC343154
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATNGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|162177883|gb|FC355133.1|FC355133
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|162243942|gb|FC424286.1|FC424286
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|162197288|gb|FC372250.1|FC372250
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|37848274|gb|BJ606282.1|BJ606282
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|162196025|gb|FC372703.1|FC372703
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|18337956|gb|BJ169980.1|BJ169980
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|208385867|gb|DC956705.1|DC956705
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|37844500|gb|BJ602508.1|BJ602508
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|162196024|gb|FC372702.1|FC372702
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
EST: gi|162161758|gb|FC337899.1|FC337899
EST:     TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAG                         GAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
genomic: TGAAAGTTGGCTACGAACTACCTCTTAATATTGCCGTCATGACTCTTCAGgttgggtgca ... gggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgattttagaataaacttttcttcaagtctgattatttggaatgggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG
                            gtctgat  putative branch site (score: 4)
     ttttagaataaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgggtgcacatcttctgctttgctcctgatatattagatgatcacatttgaattgattttagaataaacttttcttcaagtctgattatttggaatgggagtgcagGAGCTAAATGAAGAGGAAGTGCTTCTAAGACTCGCCAATCTTTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA