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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCACTGGGTCAAACCATTCTCCCTACTCCGGAATCCATGCTGCTAAATTCATCTGCAAACTTCATGCAAGGCTTTGATTTTCATGCGGCACACATGCCTgtaagagtaaacaaaggaaattaaagttggaaataggtgctgtgagatacacaagttgatatgctcttttgtaaaatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g42970.1
intron # 9
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|86487942|gb|CI130575.1|CI130575
EST:     GGCACACATGCCT                         GTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGT
genomic: GGCACACATGCCTgtaagagtaa ... taaaatgcagGTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGT
EST: gi|38481213|gb|CF965302.1|CF965302
EST:     CATCTGCAAACTTCATGCAAGGCTTTGATTTTCATGCGGCACACATGCGT                         GTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGT
genomic: CATCTGCAAACTTCATGCAAGGCTTTGATTTTCATGCGGCACACATGCCTgtaagagtaa ... taaaatgcagGTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGT
EST: gi|218499838|gb|FG962434.1|FG962434
EST:     CATCTGCAAACTTCATGCAAGGCTTTGATTTTCATGCGGCACACATGCCT                         GTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGT
genomic: CATCTGCAAACTTCATGCAAGGCTTTGATTTTCATGCGGCACACATGCCTgtaagagtaa ... taaaatgcagGTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGT
EST: gi|86540396|gb|CI180602.1|CI180602
EST:     CATCTGCAAACTTCATGCAAGGCTTTGATTTTCATGCGGCACACATGCCT                         GTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGT
genomic: CATCTGCAAACTTCATGCAAGGCTTTGATTTTCATGCGGCACACATGCCTgtaagagtaa ... taaaatgcagGTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGT

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: 65 (upstream exon), 54 (downstream exon)
Score: 18

TCCACTGGGTCAAACCATTCTCCCTACTCCGGAATCCATGCTGCTAAATTCATCTGCAAACTTCATGCAAGGCTTTGATTTTCATGCGGCACACATGCCTgtaagagtaa ... taaaatgcagGTTGGACCTGGGCCAGTCACCTATCCCCAGAGGCCTGGAGCAACTGTTTGTGAT




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