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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGTTGAGCACTTTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattgatcccccttggccttatgaatcaaatatactacgactcttcagaaatagtgcctttgggacgaacttgtctagatgggatgaactcctgg...

Basic information

species Physcomitrella patens
transcript PP1S37_83V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_83V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: Vv05s0020g03430.t01 (Vitis vinifera), 5'ss of exon 6
TTGGTTGAGCACTTTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattgatcccccttggccttat-gaatcaaatatactacgactcttcagaaa-tagtgcctttgggacga--acttgtctagatgggatgaactcctgg
||||| |||||||||||||| ||  ||| ||| |||||||| ||||| || |||||||||||||||| |   ||    |||     |||| | | ||||||    ||  |||   | |   | ||   ||| | | ||  ||   |||  ||   |||  || |   
TTGGTGGAGCACTTTTTCCAGTCTTTGGTGAATACTTCAGGCATGACACTTCACATTCGACAGgtataatgagagtttcctaacatttattgtagcaaata-gtaactcctccaaatattcttgttaatttagaaagaaaacacatctccattcaatggtcttc---
















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|162222109|gb|FC397337.1|FC397337
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|15590622|gb|BI675238.1|BI675238
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|162153154|gb|FC329560.1|FC329560
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|162196839|gb|FC373894.1|FC373894
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|162189058|gb|FC365176.1|FC365176
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|18337884|gb|BJ169908.1|BJ169908
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|162222108|gb|FC397336.1|FC397336
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|15261812|gb|BI437122.1|BI437122
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATTTTT-CCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|208361844|gb|DC950116.1|DC950116
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|162208762|gb|FC384898.1|FC384898
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|162271019|gb|FC447424.1|FC447424
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|19785589|gb|BQ040342.1|BQ040342
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|37838754|gb|BJ596762.1|BJ596762
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|22132850|gb|BQ827398.1|BQ827398
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
EST: gi|162150420|gb|FC326692.1|FC326692
EST:     TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAG                         CTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT
genomic: TTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTT

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), 19 (downstream exon)
Score: 9

TTGGTTGAGCACTTTTTCCAATCCATGGCGAACACTTCAGGAATGACGCTCCACATTCGACAGgtatgaattg ... tgtgatgcagCTTGCAGGGAAGAACTCGCATCACATTATAGAAGCCACATTTAAGGCTTTTGCAAGAGCTCTGCGTCAAGCAACTGAATATGATGCTCGCCGTTTGGGAA




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