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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGCAAGGCGCTCAACACCTGGGCTAGATGGGTCGACGCCAACCTCCTCCAGACCAACACCAGAGTCTTCTTCCAGGGCATCTCCCCCTCTCACTACAGgttaaacatctgattctgcaatgaactctgcgacaaattgtcatgcagtagtaacatactcctagctaagaccttgtttagatccaactctaaaactttt...

Basic information

species Oryza sativa
transcript LOC_Os01g11810.2
intron # 4
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|87009911|gb|CI277412.1|CI277412
EST:     CAGACCAACACCAGAGTCTTCTTCCAGGGCATCTCCCCCTCTCACTACAG                         GGGCCAAGATTGGGGCGACACGGCGAGTGCGACGTGCATGGGGCAGACGCG
genomic: CAGACCAACACCAGAGTCTTCTTCCAGGGCATCTCCCCCTCTCACTACAGgttaaacatc ... tgcaatgcagGGGCCAAGATTGGGGCGACACGGCGAGTGCGACGTGCATGGGGCAGACGCG
EST: gi|88985679|gb|CI016388.1|CI016388
EST:     CACCAGAGTCTTCTTCCAGGGCATCTCCCCCTCTCACTACAG                         GGGCCAAGATTGGGGCGACACGGCGAGTGCGACGTGCATGGGGCAGACGCG
genomic: CACCAGAGTCTTCTTCCAGGGCATCTCCCCCTCTCACTACAGgttaaacatc ... tgcaatgcagGGGCCAAGATTGGGGCGACACGGCGAGTGCGACGTGCATGGGGCAGACGCG
EST: gi|29673718|gb|CB669993.1|CB669993
EST:     CAGACCAACACCAGAGTCTTCTTCCAGGGCATCTCCCCCTCTCACTACAG                         GGGCCAAGATTGGGGCGACACGGCGAGTGCGACGTGCATGGGGCAGACGCG
genomic: CAGACCAACACCAGAGTCTTCTTCCAGGGCATCTCCCCCTCTCACTACAGgttaaacatc ... tgcaatgcagGGGCCAAGATTGGGGCGACACGGCGAGTGCGACGTGCATGGGGCAGACGCG

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: 53 (upstream exon), 62 (downstream exon)
Score: 2

TCAGCAAGGCGCTCAACACCTGGGCTAGATGGGTCGACGCCAACCTCCTCCAGACCAACACCAGAGTCTTCTTCCAGGGCATCTCCCCCTCTCACTACAGgttaaacatc ... tgcaatgcagGGGCCAAGATTGGGGCGACACGGCGAGTGCGACGTGCATGGGGCAGACGCGGCCGGTGAACGGCACGGCGTACCCCGGGGGGCCGATCCCGCAGCAGGCG




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