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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatctatatatagagacaaccaaaagttttgaattttaacactctttctgtgtgtatttattcctttctctttgcgtcggtgacttgtcttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCACTCGCAGTCTTTGCCCTACGGGAAATCAATCTTACCAAG

Basic information

species Physcomitrella patens
transcript PP1S84_76V6.1
intron # 7
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|37851942|gb|BJ609950.1|BJ609950
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|208360945|gb|DC946634.1|DC946634
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|18339266|gb|BJ171293.1|BJ171293
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|162258880|gb|FC434887.1|FC434887
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTTTCGTGTTCCCATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|208372438|gb|DC952282.1|DC952282
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|37847781|gb|BJ605789.1|BJ605789
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|208375291|gb|DC945018.1|DC945018
EST:     TAACGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|18334585|gb|BJ166602.1|BJ166602
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|208365784|gb|DC951047.1|DC951047
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|18334591|gb|BJ166608.1|BJ166608
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|18334132|gb|BJ166148.1|BJ166148
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|208372580|gb|DC952357.1|DC952357
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|18340558|gb|BJ172586.1|BJ172586
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|15320383|gb|BI488392.1|BI488392
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|162182472|gb|FC357447.1|FC357447
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|162196646|gb|FC374936.1|FC374936
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|208367467|gb|DC955675.1|DC955675
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
EST: gi|37842276|gb|BJ600284.1|BJ600284
EST:     TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG                         ACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA
genomic: TAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCA

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), 22 (downstream exon)
Score: 8

GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAGgtgaattttt ... cttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCACTCGCAGTCTTTGCCCTACGGGAAATCAATCTTACCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttctgtgtgtatttattcctttctctttgcgtcggtgacttgtcttgatgcagACCAGTATCGTGTTCACATTAGAGGAAGGACCAGGTGTTCTGTTCAAGGCACTCGCAGTCTTTGCCCTACGGGAAATCAATCTTACCAAG
                                            tcttgat  putative branch site (score: 8)
                                        cttgtctt  CT-rich tract
         tgtatttatt  TA-rich tract