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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCGCGGCCCTAAACCCTAGCCCAGCGCGCGCCTCTCCTCCTCCTCCTACTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgcttcggtcccctgtctctctgtggttgcgagatttggaggggggtttttctcgccgtggttccgtgctgatctgcaatggcgggggggactgggtgctctctctgcag

Basic information

species Oryza sativa
transcript LOC_Os02g29480.1
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|88722908|gb|CI746418.1|CI746418
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|86850026|gb|CI303479.1|CI303479
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|88390525|gb|CI609150.1|CI609150
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|88372494|gb|CI610817.1|CI610817
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|88420923|gb|CI620241.1|CI620241
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|88400268|gb|CI590958.1|CI590958
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGGGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|87009034|gb|CI304977.1|CI304977
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|88719910|gb|CI741845.1|CI741845
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|88352453|gb|CI615707.1|CI615707
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|86826342|gb|CI311138.1|CI311138
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|88360094|gb|CI610208.1|CI610208
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAAAGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
EST: gi|86888437|gb|CI303719.1|CI303719
EST:     CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTG                         GTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG
genomic: CTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCG

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: 73 (upstream exon), 57 (downstream exon)
Score: 26

CGCCGCGGCCCTAAACCCTAGCCCAGCGCGCGCCTCTCCTCCTCCTCCTACTCCCCCCATGGCCGCGCCGCAGGCTTCCCCGTCGCCCTCCGCGCAAGTGgtaagctgct ... ctctctgcagGTGGGCAACGCGTTCGTGCAGCAGTACTACCAGATCCTGCACCAGTCGCCGGATCTGGTGTACCGGTTCTACCAGGACGCCAGCCGCCTCGGCCGCCCGC




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