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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctaaatgatcttttattcttctaaaaaatatatgtttgcctagagatcaaacaaacaaaagatattattttctgaaacaaaacaggtaaaaaaatatgttccgtactccagaatgcaaattgtctgatactagaaagaattaacacttgtcacttcaatgaccgctgcagGCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCCGAACTTCGTTTCCTCTGTTGAGCCACTCTTGCTTAACCACAAG

Basic information

species Oryza sativa
transcript LOC_Os01g58640.1
intron # 9
splice site 3'
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|29681233|gb|CB677508.1|CB677508
EST:     GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGG                         GCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC
genomic: GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGGgtaagctaaa ... accgctgcagGCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC
EST: gi|58593137|gb|CF991445.1|CF991445
EST:     GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGG                         GCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC
genomic: GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGGgtaagctaaa ... accgctgcagGCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC
EST: gi|87015622|gb|CI277580.1|CI277580
EST:     GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATTTTCATTGG                         GCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC
genomic: GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGGgtaagctaaa ... accgctgcagGCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC
EST: gi|66915919|gb|CX102767.1|CX102767
EST:     GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGG                         GCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC
genomic: GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGGgtaagctaaa ... accgctgcagGCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC
EST: gi|29668284|gb|CB664559.1|CB664559
EST:     GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGG                         GCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC
genomic: GATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGGgtaagctaaa ... accgctgcagGCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCC

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: 39 (upstream exon), 66 (downstream exon)
Score: 4

TACAATTGGATGGAAATGGATTTGTCATCGGTTGATAGATCAAGAACACCATGGGTGATCTTCATTGGgtaagctaaa ... accgctgcagGCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCCGAACTTCGTTTCCTCTGTTGAGCCACTCTTGCTTAACCACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaattgtctgatactagaaagaattaacacttgtcacttcaatgaccgctgcagGCATAGACCAATGTATTCATCCAGCAGCGGTATTCCGCCCAGCGTTGATCCGAACTTCGTTTCCTCTGTTGAGCCACTCTTGCTTAACCACAAG
                      aattaac  putative branch site (score: 4)
                  aaagaattaa  TA-rich tract