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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcgcaatgcgacaatcgtgtccccctcttgttttgtagcaatgtcgttcgatcgatcgccctcccggcatcgcgcggtccagtgcagtcatgtctagccgggaccgattcgctcaggagctgaattgtacagcggcgaaggtcctgtggacagatcgcagtctgacgatcgtcatttcgcgcaatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCACCGCCGGAAGGTGTTGATGGCCGAGGTTGCAGCAGGCGTGGTGGGAGCTG

Basic information

species Physcomitrella patens
transcript PP1S77_158V6.1
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|162271315|gb|FC446693.1|FC446693
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|100422546|gb|BY976427.1|BY976427
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|18328626|gb|BJ160631.1|BJ160631
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|208395910|gb|DC911891.1|DC911891
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|162255717|gb|FC431377.1|FC431377
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|100414339|gb|BY992727.1|BY992727
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|162271086|gb|FC446620.1|FC446620
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|162258262|gb|FC434661.1|FC434661
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|100421074|gb|BY993599.1|BY993599
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|162258327|gb|FC434254.1|FC434254
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|162271797|gb|FC448930.1|FC448930
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|67576540|gb|BJ949364.1|BJ949364
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|162256384|gb|FC432394.1|FC432394
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|162269146|gb|FC445014.1|FC445014
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|162269346|gb|FC445851.1|FC445851
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|208378644|gb|DC903675.1|DC903675
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
EST: gi|162262787|gb|FC439037.1|FC439037
EST:     GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGAT                         GTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC
genomic: GCGATGGCATTCCAGACGAGTTCGAGAAGAGCCAATACAACAGGGAAGATgtaagtgcgc ... caatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaggtcctgtggacagatcgcagtctgacgatcgtcatttcgcgcaatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCACCGCCGGAAGGTGTTGATGGCCGAGGTTGCAGCAGGCGTGGTGGGAGCTG
                       gtctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcgcaatgcgacaatcgtgtccccctcttgttttgtagcaatgtcgttcgatcgatcgccctcccggcatcgcgcggtccagtgcagtcatgtctagccgggaccgattcgctcaggagctgaattgtacagcggcgaaggtcctgtggacagatcgcagtctgacgatcgtcatttcgcgcaatgtgcagGTCGAGGACTTGAAGAACCGCACGGACATTGACGACGAAGAGAGGGATCACCGCCGGAAGGTGTTGATGGCCGAGGTTGCAGCAGGCGTGGTGGGAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT