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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCGCCGCGGCGCGGCGCCAGGGCGTCGACGGCGTCGGCGAGGATCACGATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGGgtgagccagccagccagccgctctgcctctgccactgcctcgccgcggccgcgtcgaacgactcgatctcgtcttgttctgcttgatgctgtgcaaaatttggtgacgactttgtgctcgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os11g32500.1
intron # 1
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|27576865|gb|CA999559.1|CA999559
EST:     CGCGACTGCGG                         GTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
genomic: CGCGACTGCGGgtgagccagc ... tcgtttgcagGTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
EST: gi|38477358|gb|CF961491.1|CF961491
EST:     ATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGG                         GTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
genomic: ATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGGgtgagccagc ... tcgtttgcagGTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
EST: gi|86599734|gb|CI253719.1|CI253719
EST:     GCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGG                         GTACATCTACAGCGGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACT
genomic: GCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGGgtgagccagc ... tcgtttgcagGTACATCTACAGC-GACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACT
EST: gi|15854402|gb|BI807198.1|BI807198
EST:     ATGCGCTTCGGC-TCGCGTCCAAGCAGGCCTACATCTGCCGCGACT-CGG                         GTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
genomic: ATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGGgtgagccagc ... tcgtttgcagGTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
EST: gi|27576230|gb|CA998924.1|CA998924
EST:     CGCGACTGCGG                         GTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
genomic: CGCGACTGCGGgtgagccagc ... tcgtttgcagGTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
EST: gi|87016907|gb|CI284241.1|CI284241
EST:     ATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGG                         GTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
genomic: ATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGGgtgagccagc ... tcgtttgcagGTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
EST: gi|86261567|gb|CI017309.1|CI017309
EST:     ATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGG                         GTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
genomic: ATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGGgtgagccagc ... tcgtttgcagGTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
EST: gi|38480409|gb|CF964498.1|CF964498
EST:     ATGCGCTTGGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGG                         GTACATGTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT
genomic: ATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGGgtgagccagc ... tcgtttgcagGTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTT

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: 74 (upstream exon), 63 (downstream exon)
Score: 38

CGCCGCCGCGGCGCGGCGCCAGGGCGTCGACGGCGTCGGCGAGGATCACGATGCGCTTCGGCGTCGCGTCCAAGCAGGCCTACATCTGCCGCGACTGCGGgtgagccagc ... tcgtttgcagGTACATCTACAGCGACAGGACCCCCTTCGACAAGCTTCCCGACAAGTACTTCTGCCCCG




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