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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATGGCAGTGAATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgcagaatctattttgttgtctgctcactgttcaatacttcaacctgttctgttgctaaatgcatcaaacaaataccag

Basic information

species Oryza sativa
transcript LOC_Os08g06480.1
intron # 17
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|58606002|gb|CK034035.1|CK034035
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|58664660|gb|CK053346.1|CK053346
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|66913224|gb|CX100072.1|CX100072
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAATGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|58681187|gb|CK069874.1|CK069874
EST:     TTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAAGTGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: TTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAA-TGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|113930872|gb|DQ883977.1|DQ883977
EST:     TCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGA
genomic: TCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGA
EST: gi|33675906|gb|CF304145.1|CF304145
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|29616634|gb|CB621646.1|CB621646
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|163929084|gb|EG710965.1|EG710965
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|29624933|gb|CB629944.1|CB629944
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCCAGATGTTAAGCCAAG
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCC-AGATGTTAAGCCAAG
EST: gi|300216043|gb|HO088669.1|HO088669
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|33675039|gb|CF303278.1|CF303278
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|88316475|gb|CI621714.1|CI621714
EST:     GCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: GCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
EST: gi|33678958|gb|CF307197.1|CF307197
EST:     ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTG                         GCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT
genomic: ATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGAT

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: 71 (upstream exon), 75 (downstream exon)
Score: 37

TGTCAACACCCTTGGTTCTGTTTCCAATGTGTCTAGTCCTATGGCAGTGAATTCGGAGAGACCTGATCGGGCATTGCCCACAGTGTCAATGAGTGGCCTGgtgagtttgc ... caaataccagGCGCCCATGGATGTTAGCAGAACCCCAGATGTTAAGCCAAGAATTACAGATGAATCTGAAAAGGTTAAAACCTGGAAGTTGGCAGACATTGGTGACTCAG




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