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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggatatcacactagacccccggaaagatgcagtggatttatgccgatctagtgatattcaccgtcaatgcttccgagtgtgaaaatcataaggtgattttgaacttcggtctcctttcctgtttgttttgatctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCCAAAACTTCACCGTCCTCACCTTGGGCCAGAAGAACGTCTTCCCTGGATC

Basic information

species Physcomitrella patens
transcript PP1S100_198V6.1
intron # 8
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|18334408|gb|BJ166425.1|BJ166425
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37837868|gb|BJ595876.1|BJ595876
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37821512|gb|BJ579578.1|BJ579578
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37850809|gb|BJ608817.1|BJ608817
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37839144|gb|BJ597152.1|BJ597152
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18333580|gb|BJ165595.1|BJ165595
EST:     TCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: TCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18333712|gb|BJ165727.1|BJ165727
EST:     CCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: CCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18339217|gb|BJ171244.1|BJ171244
EST:     CCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: CCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37847733|gb|BJ605741.1|BJ605741
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACNTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18333467|gb|BJ165482.1|BJ165482
EST:     GCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: GCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18340909|gb|BJ172940.1|BJ172940
EST:     CCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: CCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18340469|gb|BJ172497.1|BJ172497
EST:     CCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: CCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18338076|gb|BJ170100.1|BJ170100
EST:     CCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: CCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18335474|gb|BJ167494.1|BJ167494
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37828305|gb|BJ586317.1|BJ586317
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18341643|gb|BJ173678.1|BJ173678
EST:     GTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: GTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37832716|gb|BJ590728.1|BJ590728
EST:     CGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: CGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18333568|gb|BJ165583.1|BJ165583
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18339461|gb|BJ171488.1|BJ171488
EST:     AAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18339420|gb|BJ171447.1|BJ171447
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18339173|gb|BJ171200.1|BJ171200
EST:     GGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: GGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18341161|gb|BJ173194.1|BJ173194
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37826821|gb|BJ584833.1|BJ584833
EST:     CCGTCCCCGNTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: CCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|18334572|gb|BJ166589.1|BJ166589
EST:     CCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: CCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37829601|gb|BJ587613.1|BJ587613
EST:     CGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: CGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
EST: gi|37834527|gb|BJ592539.1|BJ592539
EST:     AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAG                         TGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC
genomic: AGCCGCGGCGGCTGTGAAGGCCGTTTCCGTCCCCGCTAAAGTTGGCACAGgtaggatatc ... atctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcataaggtgattttgaacttcggtctcctttcctgtttgttttgatctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCCAAAACTTCACCGTCCTCACCTTGGGCCAGAAGAACGTCTTCCCTGGATC
                                        ttttgat  putative branch site (score: 4)
          attttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggatatcacactagacccccggaaagatgcagtggatttatgccgatctagtgatattcaccgtcaatgcttccgagtgtgaaaatcataaggtgattttgaacttcggtctcctttcctgtttgttttgatctgtgcagTGCGGCCGGCAGTATATCTCGGAAACCTGAGGAAGGGTCTCGCCGAAATCCAAAACTTCACCGTCCTCACCTTGGGCCAGAAGAACGTCTTCCCTGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC