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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCCGATCCCCCTCGCCTCCTTCCCCTTTCCCCCCTCACCTCTCTGCTCTTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtccccgctccatcccgatctggatccgccgcccccccccccccccgacctctgcgtggttttcccccagaatcgaatccctctccgtggcccgtg...

Basic information

species Oryza sativa
transcript LOC_Os01g60410.3
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|88588887|gb|CI706732.1|CI706732
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|58677585|gb|CK066272.1|CK066272
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|58600789|gb|CK011317.1|CK011317
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|88391945|gb|CI683764.1|CI683764
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|58594364|gb|CF992672.1|CF992672
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|58684372|gb|CK073059.1|CK073059
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|58592931|gb|CF991239.1|CF991239
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|38470328|gb|CF954459.1|CF954459
EST:     CGCCCCCTCGCGATCCGACCAGATCGGCGCGA                         GGGCATATCATGGCATTGAAGCGGATCCTCAAGGAACTAAAGGACCTGGAG
genomic: CGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|58600178|gb|CK010706.1|CK010706
EST:     TTCTCCGCCGCACCAATCCGGCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|58683224|gb|CK071911.1|CK071911
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATTGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|112785779|gb|EE591396.1|EE591396
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
EST: gi|33688146|gb|CF316385.1|CF316385
EST:     TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGA                         GGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG
genomic: TTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAG

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: 72 (upstream exon), 74 (downstream exon)
Score: 159

CCCCCGATCCCCCTCGCCTCCTTCCCCTTTCCCCCCTCACCTCTCTGCTCTTCTCCGCCGCACCAATCCGCCCCCTCGCGATTCGACCAGATCGGCGCGAgtaagtcccc ... atttaagcagGGGCATATCATGGCATCGAAGCGGATCCTCAAGGAACTAAAGGACCTGCAGAAAGATCCTCCAACATCATGCAGTGCAG




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