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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggtgccttagtgtagagttgtgtcgtgagaatgagcaggtatttgatgattcatgttgcgtatgaagcagttgtttatggttgaatttggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG

Basic information

species Physcomitrella patens
transcript PP1S505_6V6.2
intron # 11
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|208388484|gb|DC957066.1|DC957066
EST:     GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAG                         GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
genomic: GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
EST: gi|67727357|gb|BJ977616.1|BJ977616
EST:     TCACAAACGCATCAAG                         GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
genomic: TCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
EST: gi|208367883|gb|DC955346.1|DC955346
EST:     GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAG                         GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
genomic: GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
EST: gi|208387195|gb|DC945494.1|DC945494
EST:     GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAG                         GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
genomic: GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
EST: gi|208396976|gb|DC924658.1|DC924658
EST:     CTGACGCGTATAATCC-NGAAACAAGGATCACAAACGCATCCAG                         GAAGAGATTGAACTCGGAAATGGT-TTCCTGACATTCGGTCCACACGTCAG
genomic: CTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
EST: gi|162166440|gb|FC342422.1|FC342422
EST:     GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAG                         GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
genomic: GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
EST: gi|208380622|gb|DC919380.1|DC919380
EST:     GATCACCAACGCATCAAG                         GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
genomic: GATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
EST: gi|208371896|gb|DC951714.1|DC951714
EST:     ATCCTGGAACCANGGNTCNCCAACGCATCAAG                         GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
genomic: ATCCTGGAAACAAGGATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
EST: gi|208354679|gb|DC918705.1|DC918705
EST:     GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAG                         GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
genomic: GCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
EST: gi|67720489|gb|BJ970748.1|BJ970748
EST:     CAAGGATCACAAACGCATCAAG                         GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG
genomic: CAAGGATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAG

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: 22 (upstream exon), 34 (downstream exon)
Score: 12

GATTCGGAGAGTTCTGAAACCTGGGCAACTCTTTGCTGGTTACGAGTGGTGCATAACTGACGCGTATAATCCTGGAAACAAGGATCACAAACGCATCAAGgtattatcct ... ggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgattcatgttgcgtatgaagcagttgtttatggttgaatttggttgcgcagGAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG
 atttgat  putative branch site (score: 12)
                           ttgtttat  TA-rich tract