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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGAAGGCTGGGGCTTCAAAGAAGAGGAAAGCACTTACTGATGCAGCTGCAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAGgtaagcatgcaggtgctcttaccgatgggacaacaaagtgttctctaggcactgaattttactatgaaatatcttcttaatgctccaattaatctgataa...

Basic information

species Oryza sativa
transcript LOC_Os07g08729.1
intron # 18
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|88907734|gb|CI091132.1|CI091132
EST:     AGTAGTAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAG                         CTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
genomic: AG-AGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAGgtaagcatgc ... taatttgcagCTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
EST: gi|88256684|gb|CI359072.1|CI359072
EST:     CAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAG                         CTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
genomic: CAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAGgtaagcatgc ... taatttgcagCTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
EST: gi|58687994|gb|CK076681.1|CK076681
EST:     CAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAG                         CTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
genomic: CAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAGgtaagcatgc ... taatttgcagCTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
EST: gi|88959987|gb|CI381865.1|CI381865
EST:     CAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAG                         CTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
genomic: CAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAGgtaagcatgc ... taatttgcagCTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
EST: gi|568027|gb|D38862.1|D38862
EST:     CAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAG                         CTGAAGGACATGACGGTGGTGGNCTTGAAATCTTACCTGAGTGCACATGGC
genomic: CAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAGgtaagcatgc ... taatttgcagCTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
EST: gi|88268594|gb|CI378529.1|CI378529
EST:     CAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAG                         CTGAAGGACATGACGTTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC
genomic: CAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAGgtaagcatgc ... taatttgcagCTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGC

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), 70 (downstream exon)
Score: 10

AGCGAAGGCTGGGGCTTCAAAGAAGAGGAAAGCACTTACTGATGCAGCTGCAGAGAAAAGTGCAGCACATAATTGGGCAGAACTTGCGGATACTGGAAAGgtaagcatgc ... taatttgcagCTGAAGGACATGACGGTGGTGGACTTGAAATCTTACCTGAGTGCACATGGCCTCCCAGTTTCTGGAAAGAAAGAGGCACTCGTCAGCAGAATCTTGACTC




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