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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAAGTCGCGCGCCGCCGCGGCGCCGACCCCCATTGGCAATCCTTTCAGCGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctggtgtatccgaccgaacgacgtttcacctgttgccgcgccagatgcagtgttgctaatgtttaccatggcggatttgcttgcttatag

Basic information

species Oryza sativa
transcript LOC_Os07g48410.1
intron # 5
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|58597206|gb|CK007734.1|CK007734
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCA
EST: gi|86253323|gb|CI058248.1|CI058248
EST:     ACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: ACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|58603862|gb|CK014390.1|CK014390
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|58657427|gb|CK046107.1|CK046107
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|58676590|gb|CK065277.1|CK065277
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|58607975|gb|CK036008.1|CK036008
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|29666734|gb|CB663009.1|CB663009
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|58673342|gb|CK062028.1|CK062028
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|86257029|gb|CI061792.1|CI061792
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|58599584|gb|CK010112.1|CK010112
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAA
EST: gi|58659889|gb|CK048569.1|CK048569
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|88221815|gb|CI221771.1|CI221771
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|58612737|gb|CK040449.1|CK040449
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
EST: gi|29681057|gb|CB677332.1|CB677332
EST:     CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCG                         GGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA
genomic: CGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCA

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), 69 (downstream exon)
Score: 44

TTCAAGTCGCGCGCCGCCGCGGCGCCGACCCCCATTGGCAATCCTTTCAGCGCTTCTCAGACCGCCGCCAACGCGACCGGCGAGTCGCCTCCCGATTCCGgtaggacctg ... ttgcttatagGGGAGCTCGGTAAGGGAAGCGGCTTCCTTCTTGCTCACAAGAAGGCGGTCAACGGAGCCGATAAGGAGGAATCCACCGGAGAGTCCTCCAGCCCTAACAC




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