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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATGAAGAGCCAAATTACGGCAAGCTTGTTCTACTCTTCGATTCTATCTTAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattctatgatcttcttttacttagtttttcctgttcctacacagaggattctttttttcaacctactctttatttgatcatcatattaataaagtctatcgtttccag

Basic information

species Physcomitrella patens
transcript PP1S131_16V6.1
intron # 10
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|162165498|gb|FC340609.1|FC340609
EST:     TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAG                         TGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
genomic: TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattcta ... tcgtttccagTGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
EST: gi|162252531|gb|FC427340.1|FC427340
EST:     TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAG                         TGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGA
genomic: TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattcta ... tcgtttccagTGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGA
EST: gi|162191374|gb|FC367130.1|FC367130
EST:     TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAG                         TGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
genomic: TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattcta ... tcgtttccagTGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
EST: gi|162185156|gb|FC362290.1|FC362290
EST:     TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAG                         TGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
genomic: TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattcta ... tcgtttccagTGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
EST: gi|162176694|gb|FC352539.1|FC352539
EST:     TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAG                         TGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
genomic: TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattcta ... tcgtttccagTGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
EST: gi|162228110|gb|FC405692.1|FC405692
EST:     TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAG                         TGTTCCATACA
genomic: TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattcta ... tcgtttccagTGTTCCATACA
EST: gi|162184061|gb|FC358807.1|FC358807
EST:     TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAG                         TGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
genomic: TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattcta ... tcgtttccagTGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
EST: gi|162163687|gb|FC340286.1|FC340286
EST:     TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAG                         TGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT
genomic: TAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattcta ... tcgtttccagTGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGAT

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), 32 (downstream exon)
Score: 14

CGATGAAGAGCCAAATTACGGCAAGCTTGTTCTACTCTTCGATTCTATCTTAGGTCCTAATCCTGCTGTGCGACCCATAAACACAGACGGTGCTCAAAAGgtgcattcta ... tcgtttccagTGTTCCATACAGGTTGGTCAGAAGAGAGGGCGAATTAGTGTTGAAGAAGATGAGGATGACCAACCTAAGAAAAAGATCCGGTTAGGAATGCCTGCAACTC




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