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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCGGTATGTAATGAAATACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTGgtgcgttttattctctgtaattactctctttggaccctgtgagctgcgttgatttggttgccagagctcgctgtctcttaatttccttacttattgagtt...

Basic information

species Physcomitrella patens
transcript PP1S79_221V6.1
intron # 2
splice site 5'
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|162224606|gb|FC400502.1|FC400502
EST:     ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTG                         TGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
genomic: ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTGgtgcgtttta ... ggttttgcagTGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
EST: gi|162266195|gb|FC441932.1|FC441932
EST:     ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTG                         TGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
genomic: ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTGgtgcgtttta ... ggttttgcagTGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
EST: gi|162224605|gb|FC400501.1|FC400501
EST:     ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTG                         TGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
genomic: ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTGgtgcgtttta ... ggttttgcagTGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
EST: gi|67573415|gb|BJ946239.1|BJ946239
EST:     ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTG                         TGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
genomic: ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTGgtgcgtttta ... ggttttgcagTGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
EST: gi|67696796|gb|BJ957029.1|BJ957029
EST:     ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTG                         TGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
genomic: ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTGgtgcgtttta ... ggttttgcagTGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
EST: gi|18328787|gb|BJ160792.1|BJ160792
EST:     ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTG                         TGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
genomic: ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTGgtgcgtttta ... ggttttgcagTGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
EST: gi|162266209|gb|FC441933.1|FC441933
EST:     ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTG                         TGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG
genomic: ACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTGgtgcgtttta ... ggttttgcagTGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAG

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: 11 (upstream exon), 26 (downstream exon)
Score: 2

ACGCGGTATGTAATGAAATACAGGCATTGTGATGGCAAACTTGTTCTCAAAGTCACTGATGACAAAGTGgtgcgtttta ... ggttttgcagTGTCTGAAGTTCAAGACAGATCAAGCTCAGGACATAAGGAAGATGGAGAAGCTGAATAATACATTTTTTAGTATGATGGCCCGAGGACCAGATG




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