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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCTgttagtaccttaacttttatatgcacttccccattctgctcttttcaaagacgagttaaactgagtagtagttatttttccag

Basic information

species Oryza sativa
transcript LOC_Os04g45190.2
intron # 6
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|300215748|gb|HO088374.1|HO088374
EST:     ACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT                         GCTACAAGAGCACACAAGGATGCAGAAGATGTAACATCTGATTCTGAG
genomic: ACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCTgttagtacct ... atttttccagGCTACAAGAGCACACAAGGATGCAGAAGATGTAACATCTGATTCTGAG
EST: gi|27547307|gb|CA765509.2|CA765509
EST:     AC--A-AC---TCGGGAATCTGATGAGCCACCATTGCTATCT                         GCTACAAGAGCACACAAGGATGCAGAAGATGTAACATCTGATTCTGAG
genomic: ACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCTgttagtacct ... atttttccagGCTACAAGAGCACACAAGGATGCAGAAGATGTAACATCTGATTCTGAG
EST: gi|117238779|gb|CT842528.1|CT842528
EST:     ACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCT                         GCTACAAGAGCACACAAGGATGCAGAAGATGTAACATCTGATTCTGAG
genomic: ACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCTgttagtacct ... atttttccagGCTACAAGAGCACACAAGGATGCAGAAGATGTAACATCTGATTCTGAG

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: 64 (upstream exon), 51 (downstream exon)
Score: 3

ACGCAGACAACTCGGGAATCTGATGAGCCACCATTGCTATCTgttagtacct ... atttttccagGCTACAAGAGCACACAAGGATGCAGAAGATGTAACATCTGATTCTGAG




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