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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGATGCTGCAATCGTACGGATCATGAAAACACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatatttcatacctcgaattattatccagaatttcggattcacttctgcaagtcatcgatgatgtgtagtgctgttattgaaattctgtatttcaagtgttttttttgttgttaaacgcatgtgatgttaaattgcag

Basic information

species Physcomitrella patens
transcript PP1S70_181V6.1
intron # 15
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|162178398|gb|FC354122.1|FC354122
EST:     CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
genomic: CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatattt ... taaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
EST: gi|162176873|gb|FC352848.1|FC352848
EST:     CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
genomic: CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatattt ... taaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
EST: gi|162257954|gb|FC433840.1|FC433840
EST:     CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
genomic: CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatattt ... taaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
EST: gi|162162041|gb|FC338832.1|FC338832
EST:     CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
genomic: CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatattt ... taaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
EST: gi|162178399|gb|FC354123.1|FC354123
EST:     CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAG                         CTGAAATTTC-AATTAAACCAGCTGACTTGAAGAA
genomic: CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatattt ... taaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAA
EST: gi|162175711|gb|FC351298.1|FC351298
EST:     CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
genomic: CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatattt ... taaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
EST: gi|208364364|gb|DC950665.1|DC950665
EST:     CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAG                         CNGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
genomic: CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatattt ... taaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
EST: gi|37835143|gb|BJ593155.1|BJ593155
EST:     CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAG                         CTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG
genomic: CACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatattt ... taaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTG

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

ATCGATGCTGCAATCGTACGGATCATGAAAACACGCAAGGTGTTAAGTCACACATTGTTAATAACTGAACTATTTCAGCAGgtgaatattt ... taaattgcagCTGAAATTTCCAATTAAACCAGCTGACTTGAAGAAAAGAATCGAGAGCTTGATTGACCGGGAGTACCTTGAAAGGGACAAAGCCAATCCTCAGATCTACA




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