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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacatttaggccatggcggacggttcgtgtaatttttaggttggaggtttgttgtggattggttatttgctgatttgattttgctgaaattggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACCTTGAACATTGCGACTTTGATAGCCATGCTGGGTCCGGAGGCGGACTCCC

Basic information

species Physcomitrella patens
transcript PP1S83_6V6.1
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|208388972|gb|DC933000.1|DC933000
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|41107737|gb|BJ157912.1|BJ157912
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|100353601|gb|BY964888.1|BY964888
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|100394101|gb|BY971939.1|BY971939
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|100399969|gb|BY990712.1|BY990712
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|100421900|gb|BY957777.1|BY957777
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGNGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|208399831|gb|DC904703.1|DC904703
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|100355595|gb|BY946013.1|BY946013
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTTGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|67573837|gb|BJ946661.1|BJ946661
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|162166468|gb|FC343165.1|FC343165
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGCCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|162217637|gb|FC393729.1|FC393729
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGCCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|208386049|gb|DC956565.1|DC956565
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|162248674|gb|FC424527.1|FC424527
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGCCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|100389238|gb|BY970988.1|BY970988
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTTCGGGAC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTT-CGGGAC
EST: gi|100427683|gb|BY977620.1|BY977620
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|100353047|gb|BY945580.1|BY945580
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|67720023|gb|BJ970282.1|BJ970282
EST:     GCAATGGANAGGGGTCGGNGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCNATTTTGTGTTGGGGNCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACC
EST: gi|41107739|gb|BJ158924.1|BJ158924
EST:     GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAA                         ATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGAC
genomic: GCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 24 (upstream exon), 35 (downstream exon)
Score: 19

TTTGATCAACCCTTCGGAGACTGATCCTGATGTGAGATCGTTTAAGGGTGGCAATGGAGAGGGGTCGGTGACTCTGCGAGCTGGCCGGGCTGGGTCTAAAgtatatatat ... tggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACCTTGAACATTGCGACTTTGATAGCCATGCTGGGTCCGGAGGCGGACTCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttgttgtggattggttatttgctgatttgattttgctgaaattggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACCTTGAACATTGCGACTTTGATAGCCATGCTGGGTCCGGAGGCGGACTCCC
                           atttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacatttaggccatggcggacggttcgtgtaatttttaggttggaggtttgttgtggattggttatttgctgatttgattttgctgaaattggtgtgcagATCGATTTTGTGTTGGGGTCGTGGCTGAATTGCACGCTGGCCTTCGGGACCTTGAACATTGCGACTTTGATAGCCATGCTGGGTCCGGAGGCGGACTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG