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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctgcttgatttagggtctgcattctagagtttctgtagagtttctgtgtcaatttatttgactttcgagtgtcaaatttgatgttaatgtgttgcatggttacgaactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTGCGCTCTGGCACTACATCTGCTACTGCTTAGACGTACTGGTTACTGTTGA

Basic information

species Physcomitrella patens
transcript PP1S22_76V6.1
intron # 6
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|162262297|gb|FC437624.1|FC437624
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|67694098|gb|BJ954331.1|BJ954331
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162270731|gb|FC446344.1|FC446344
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162224836|gb|FC400836.1|FC400836
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162227758|gb|FC402686.1|FC402686
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|15728661|gb|BI740905.1|BI740905
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|37841928|gb|BJ599936.1|BJ599936
EST:     GCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162262298|gb|FC437625.1|FC437625
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|19781574|gb|BQ039741.1|BQ039741
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGG
EST: gi|162267059|gb|FC443290.1|FC443290
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|37830037|gb|BJ588049.1|BJ588049
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|37841076|gb|BJ599084.1|BJ599084
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162273803|gb|FC449734.1|FC449734
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162267060|gb|FC443291.1|FC443291
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|18363914|gb|BJ195986.1|BJ195986
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGT
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGT
EST: gi|37842317|gb|BJ600325.1|BJ600325
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|37845725|gb|BJ603733.1|BJ603733
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162224837|gb|FC400837.1|FC400837
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|67692927|gb|BJ953160.1|BJ953160
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162205889|gb|FC381335.1|FC381335
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162270730|gb|FC446343.1|FC446343
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162272796|gb|FC447978.1|FC447978
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|37834233|gb|BJ592245.1|BJ592245
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162205890|gb|FC381336.1|FC381336
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|37845346|gb|BJ603354.1|BJ603354
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|15728104|gb|BI740621.1|BI740621
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|67571863|gb|BJ944687.1|BJ944687
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|37824207|gb|BJ582273.1|BJ582273
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|67569660|gb|BJ942484.1|BJ942484
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162273804|gb|FC449735.1|FC449735
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
EST: gi|162227744|gb|FC402685.1|FC402685
EST:     GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAG                         GTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG
genomic: GCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTG

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), 35 (downstream exon)
Score: 38

CTTACATGTCCTCTCCTTGCCACATTGAATTGATTCTTTCTGAGAAGGAGGCGCCAGTGAAAAAAGAGgtaatgctgc ... aactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTGCGCTCTGGCACTACATCTGCTACTGCTTAGACGTACTGGTTACTGTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactttcgagtgtcaaatttgatgttaatgtgttgcatggttacgaactttgcagGTTGAAGAGGTTTCTGCACCACGGTCAAACAAGAGAGACCAAGGACGCCTGCGCTCTGGCACTACATCTGCTACTGCTTAGACGTACTGGTTACTGTTGA
                      tgttaat  putative branch site (score: 38)
              aaatttgatgttaat  TA-rich tract