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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctccaaatcgtacctgtgcctgttcagtgtatcttcggtgttctccaggagacaggaagacgtgaaggatacatgcagttatagcatcaacaatgtgtattctgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATAAGACCTTGACAACTAATAAGGGCGATATTTACGAGTATGGGACTCTGAT

Basic information

species Physcomitrella patens
transcript PP1S90_28V6.4
intron # 5
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|100355472|gb|BY945951.1|BY945951
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100391837|gb|BY989572.1|BY989572
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|67573440|gb|BJ946264.1|BJ946264
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|18365163|gb|BJ197237.1|BJ197237
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100377879|gb|BY986439.1|BY986439
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|162278698|gb|FC454808.1|FC454808
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100361319|gb|BY965781.1|BY965781
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|18356191|gb|BJ188250.1|BJ188250
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|208385252|gb|DC915052.1|DC915052
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|208361425|gb|DC935112.1|DC935112
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100386104|gb|BY970043.1|BY970043
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|18331507|gb|BJ163518.1|BJ163518
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100363976|gb|BY966264.1|BY966264
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|208375453|gb|DC936996.1|DC936996
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|162225064|gb|FC401688.1|FC401688
EST:     CGTAGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100378191|gb|BY949726.1|BY949726
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|18360912|gb|BJ192976.1|BJ192976
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100365162|gb|BY966841.1|BY966841
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTACGCTGTAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|18364385|gb|BJ196458.1|BJ196458
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100448660|gb|CJ972959.1|CJ972959
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|162178358|gb|FC355180.1|FC355180
EST:     AGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: AGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100375395|gb|BY948855.1|BY948855
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|18359114|gb|BJ191174.1|BJ191174
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|162237033|gb|FC413192.1|FC413192
EST:     CGTAGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|18349313|gb|BJ181362.1|BJ181362
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100406861|gb|BY955754.1|BY955754
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100444932|gb|BY982760.1|BY982760
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100388010|gb|BY988483.1|BY988483
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAGGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100385258|gb|BY950850.1|BY950850
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|100418007|gb|BY993291.1|BY993291
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|18369448|gb|BJ201535.1|BJ201535
EST:     CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
EST: gi|162158960|gb|FC334820.1|FC334820
EST:     CGTAGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAG                         GTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA
genomic: CGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATA

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: 34 (upstream exon), 32 (downstream exon)
Score: 21

CTCCTGCTAGGCTTCCAGGCTTTCATGTGTGCGTGGGGAGTGGAGGAGAGAAGCAATTACCGGATTGGTATGCTGAAAAAGgtaagtgctc ... tgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATAAGACCTTGACAACTAATAAGGGCGATATTTACGAGTATGGGACTCTGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacgtgaaggatacatgcagttatagcatcaacaatgtgtattctgactttcagGTATTGAACTTAAATTGGAGACTGAGATCGTGAAAGCGGACGTGGAGAATAAGACCTTGACAACTAATAAGGGCGATATTTACGAGTATGGGACTCTGAT
                                          ttctgac  putative branch site (score: 21)
                                                ctttc  CT-rich tract
                   agttata  TA-rich tract