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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgagctactcattacttgcctgtgattttcgtgctgttcagtgaatttgctgaaagctgcctggtcatttcatgggtgtggtcttttttgatctctctttttgaatggaagtccatttggtgtgctgtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAACTTGGCCGACGCCATGGACCGAGCTCGTGTGTTGGACATTGACTTGCAGA

Basic information

species Physcomitrella patens
transcript PP1S267_10V6.1
intron # 3
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|100365484|gb|BY966619.1|BY966619
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGG-ATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|162226051|gb|FC401329.1|FC401329
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|18325029|gb|BJ157025.1|BJ157025
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|18359347|gb|BJ191408.1|BJ191408
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTG
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTG
EST: gi|162165793|gb|FC340922.1|FC340922
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|162172373|gb|FC348314.1|FC348314
EST:     GGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: GGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|162150837|gb|FC327109.1|FC327109
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|18363706|gb|BJ195778.1|BJ195778
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATA
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATA
EST: gi|100446640|gb|CJ970939.1|CJ970939
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|162269000|gb|FC445492.1|FC445492
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|100427579|gb|BY977568.1|BY977568
EST:     CTTTCCAGGGCGAGGAA-TTCACGTACCATTCAAGAGTATTCTGCCAATG                         GGTTGACCCCAATGACCTCGTGATTTGGAGGGTGGGATATTTCGGACATGA
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagG-TTGACCCCAATGACCTCGTGATT-GGAGGGTGGGATATTTCGAACATGA
EST: gi|100446102|gb|CJ970401.1|CJ970401
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|100442189|gb|BY963082.1|BY963082
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|100450197|gb|CJ974142.1|CJ974142
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|162169895|gb|FC346251.1|FC346251
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|208356703|gb|DC902535.1|DC902535
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|100403191|gb|BY991080.1|BY991080
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|100430782|gb|BY978394.1|BY978394
EST:     CTTTCCAGGGCGAGGAA-TTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|100441349|gb|BY962638.1|BY962638
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCCATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|162166972|gb|FC343357.1|FC343357
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|100447987|gb|CJ972286.1|CJ972286
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCNATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|67704669|gb|BJ964902.1|BJ964902
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGG
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGG
EST: gi|162279671|gb|FC455904.1|FC455904
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|67574163|gb|BJ946987.1|BJ946987
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|100446153|gb|CJ970452.1|CJ970452
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|18374739|gb|BJ206317.1|BJ206317
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAG
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAG
EST: gi|18359531|gb|BJ191592.1|BJ191592
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGG
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGG
EST: gi|162241553|gb|FC418614.1|FC418614
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|162153386|gb|FC329896.1|FC329896
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|162180539|gb|FC356181.1|FC356181
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
EST: gi|7207697|gb|AW561694.1|AW561694
EST:     CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATG                         GTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC
genomic: CTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAAC

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: 35 (upstream exon), 34 (downstream exon)
Score: 54

CGCTAACTACTTTGGGTCTCTTACTCAAGCATCCACCTGCCGCGTGGGCGCTTTCCAGGGCGAGGAAATTCACGTACCATTCAAGAGTATTCTGCCAATGgtagtgagct ... gtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAACTTGGCCGACGCCATGGACCGAGCTCGTGTGTTGGACATTGACTTGCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttttgatctctctttttgaatggaagtccatttggtgtgctgtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAACTTGGCCGACGCCATGGACCGAGCTCGTGTGTTGGACATTGACTTGCAGA
    ttttgat  putative branch site (score: 54)
                tttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgagctactcattacttgcctgtgattttcgtgctgttcagtgaatttgctgaaagctgcctggtcatttcatgggtgtggtcttttttgatctctctttttgaatggaagtccatttggtgtgctgtatgtgcagGTTGACCCCAATGACCTCGTGATTGGAGGGTGGGATATTTCGAACATGAACTTGGCCGACGCCATGGACCGAGCTCGTGTGTTGGACATTGACTTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA