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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggccccacattttttgaatgatcatgaatggaaaacacggtgtagacagggagatgtcttgttcaggtaaaatcttgatgtgttaaaatgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTGGCCCGTCATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGA

Basic information

species Physcomitrella patens
transcript PP1S234_46V6.1
intron # 2
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|67574713|gb|BJ947537.1|BJ947537
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCNACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|100439014|gb|BY961917.1|BY961917
EST:     GCATGGATTTTACTGACCCAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|67570256|gb|BJ943080.1|BJ943080
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|208391184|gb|DC938158.1|DC938158
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|208397563|gb|DC912181.1|DC912181
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATNACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|100399143|gb|BY954221.1|BY954221
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|67718764|gb|BJ969023.1|BJ969023
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|208363866|gb|DC943323.1|DC943323
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|208363993|gb|DC939586.1|DC939586
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|208389733|gb|DC938309.1|DC938309
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
EST: gi|100356295|gb|BY946293.1|BY946293
EST:     GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAG                         GTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG
genomic: GCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTG

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: 27 (upstream exon), 23 (downstream exon)
Score: 5

GTCCGGGAGCTTGCAAATAAGACAGGCATGGATTTTACTGACCAAATTGCCGAGCTCGAAGAGAGATATGACCAGgtttgtattc ... tgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTGGCCCGTCATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacagggagatgtcttgttcaggtaaaatcttgatgtgttaaaatgctaagcagGTGCGTAGAGAACTGTATGGGCAACTTACACCAATGCAGCGCCTTAGTGTGGCCCGTCATCCTAACCGGCCAACTTTCTTGGACCACGTCATGAATATGA
                             tcttgat  putative branch site (score: 5)
                        taaaatctt  TA-rich tract