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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctcgtagaatatttgttctgatgctttcacttcatatcacattttggattagtaaaaaaaaaattacttgatacatttgttgttgctctacacacag

Basic information

species Oryza sativa
transcript LOC_Os03g10940.1
intron # 7
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|89171248|gb|CI109772.1|CI109772
EST:     AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAG                         GCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
genomic: AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
EST: gi|15852784|gb|BI805580.1|BI805580
EST:     AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAG                         GCATA-CAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
genomic: AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
EST: gi|87016659|gb|CI275661.1|CI275661
EST:     AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAG                         GCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
genomic: AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
EST: gi|66923472|gb|CX110320.1|CX110320
EST:     AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAG                         GCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAAAAAATAGGCATCT
genomic: AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
EST: gi|88490510|gb|CI427782.1|CI427782
EST:     GCTTGAGGCTCTGATTGGGAG                         GCATACCAGNAAACCTTGGTCTAANTTTATAAATCCAGAGAATAGGCATCT
genomic: GCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
EST: gi|25806912|gb|CA762873.1|CA762873
EST:     AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAG                         GCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
genomic: AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
EST: gi|86261473|gb|CI017215.1|CI017215
EST:     AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAG                         GCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
genomic: AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
EST: gi|12623221|gb|AU173434.1|AU173434
EST:     AATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAG                         GCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
genomic: AATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
EST: gi|86425593|gb|CI070690.1|CI070690
EST:     AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAG                         GCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT
genomic: AATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCT

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: 62 (upstream exon), 74 (downstream exon)
Score: 26

GTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAGgtattacctc ... ctacacacagGCATACCAGGAAACCTTGGTCTAAGTTTATAAATCCAGAAAATAGGCATCTTGTCTCTCCAGAG




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