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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCGTGATGATAGTTTAGCAGCTCAAGCTTCCACAGTGGCTTATGATGACAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactgatcctttgcatgttggtgcctcaaaggataaaccattgtaaatttatgaatagtgtattggatacag

Basic information

species Oryza sativa
transcript LOC_Os06g28060.1
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|29642488|gb|CB647495.1|CB647495
EST:     CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|66920553|gb|CX107401.1|CX107401
EST:     CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|86437904|gb|CI119824.1|CI119824
EST:     TCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: TCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|29687744|gb|CB684019.1|CB684019
EST:     CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|86892642|gb|CI312037.1|CI312037
EST:     CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|86597685|gb|CI274676.1|CI274676
EST:     CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|58665464|gb|CK054150.1|CK054150
EST:     CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|86482331|gb|CI124964.1|CI124964
EST:     TCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: TCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|86596961|gb|CI270757.1|CI270757
EST:     CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|29626226|gb|CB631237.1|CB631237
EST:     CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
EST: gi|29687745|gb|CB684020.1|CB684020
EST:     CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAG                         AGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA
genomic: CAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAA

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: 68 (upstream exon), 68 (downstream exon)
Score: 6

GCTCGTGATGATAGTTTAGCAGCTCAAGCTTCCACAGTGGCTTATGATGACAATTCAAGAGCCAGAGAATCTGTATTGTTTGACATGTCTTCCAATGGAGgtaactactg ... ttggatacagAGTCATCCAAAAGAAGAAATTCATGCTCAGTGATTCATTGGAGGGCTCAAAAAAGGCAGCACATCAATGATTACGCTAATCAACCTCCAGACGTCAATGC




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