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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGACCTCCGTCCTCCTCCACCACCGCTCCGCCCTCACCCGCCGCTCCCCGGCGATCGGCGGCGGCGTCCTTCCCCGTGCTCTCTTCTTCTCCACGCTCGgtaacattccctcccgaactccggcccgatcccggcaggtggtgaggcggcgatttgacggggcggtctgtctgtctgtctgtctctgtcccgcgcag

Basic information

species Oryza sativa
transcript LOC_Os06g05080.1
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|86854015|gb|CI252006.1|CI252006
EST:     GCGATCGNCGNCGGCGTCCTTTCCCCGTGCTCTCTTCTTCTCCACGCTCG                         ATGCGGCGCAGGCGAGGACGAGGGTGGAGGACGTGATGCCGATCGCCACCG
genomic: GCGATCGGCGGCGGCGTCC-TTCCCCGTGCTCTCTTCTTCTCCACGCTCGgtaacattcc ... tcccgcgcagATGCGGCGCAGGCGAGGACGAGGGTGGAGGACGTGATGCCGATCGCCACCG
EST: gi|58600462|gb|CK010990.1|CK010990
EST:     GGCGATCGGCGGCGGCGTTCTTCCCCGTGCTCTCTTCTTCTCCACGCTCG                         ATGCGGCGCAGGCGAGGACGAGGGTGGAGGACGTGATGCCGATCGCCACCG
genomic: GGCGATCGGCGGCGGCGTCCTTCCCCGTGCTCTCTTCTTCTCCACGCTCGgtaacattcc ... tcccgcgcagATGCGGCGCAGGCGAGGACGAGGGTGGAGGACGTGATGCCGATCGCCACCG
EST: gi|86822729|gb|CI251809.1|CI251809
EST:     GGCGATCGGCGGCGGCGTCCTTCCCCGTGCTCTCTTCTTCTCCACGCCCG                         ATGCGGCGCAGGCGAGGACGAGGGTGGAGGACGTGATGCCGATCGCCACCG
genomic: GGCGATCGGCGGCGGCGTCCTTCCCCGTGCTCTCTTCTTCTCCACGCTCGgtaacattcc ... tcccgcgcagATGCGGCGCAGGCGAGGACGAGGGTGGAGGACGTGATGCCGATCGCCACCG

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: 75 (upstream exon), 75 (downstream exon)
Score: 74

GCGACCTCCGTCCTCCTCCACCACCGCTCCGCCCTCACCCGCCGCTCCCCGGCGATCGGCGGCGGCGTCCTTCCCCGTGCTCTCTTCTTCTCCACGCTCGgtaacattcc ... tcccgcgcagATGCGGCGCAGGCGAGGACGAGGGTGGAGGACGTGATGCCGATCGCCACCGGGCTCGAGCGCGAGGAGATCGCCGCCGAGCTCCAG




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