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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCACTCTCCCTCGCGTCGGCGGCCGCGCGCAACTTTCCCTGAAGCCCCGGATCCACTCAACCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccgtcgtcccgcttctgcggtagccttagatctcgctttcttccttccctttgttgcctgtatggcggcggatctgtgggctgtcggttgtag...

Basic information

species Oryza sativa
transcript LOC_Os11g21990.1
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|33796511|gb|CF324122.1|CF324122
EST:     TCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: TCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|58676820|gb|CK065507.1|CK065507
EST:     GATCCACTCAA-CCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: GATCCACTCAACCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|8594697|gb|AU093235.1|AU093235
EST:     TCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: TCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|29665731|gb|CB662006.1|CB662006
EST:     GATCCACTCAANNNNNNNNNNNNTCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: GATCCACTCAACCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|58689644|gb|CK078331.1|CK078331
EST:     TCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: TCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|701897|gb|D48188.1|D48188
EST:     TCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: TCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|33801526|gb|CF326635.1|CF326635
EST:     GATCCACTCAANNNNNNNNNNNNTCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: GATCCACTCAACCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|58607968|gb|CK036001.1|CK036001
EST:     GATCCACTCAANCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: GATCCACTCAACCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|5004597|gb|AU069772.1|AU069772
EST:     TCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: TCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|117231433|gb|CT842219.1|CT842219
EST:     GATCCACTCAANNNNNNNNNNNNTCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: GATCCACTCAACCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|88729881|gb|CI753102.1|CI753102
EST:     GATCCACTCAANCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: GATCCACTCAACCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG
EST: gi|58601558|gb|CK012086.1|CK012086
EST:     GATCCACTCAA-CCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAG                         CTCGAAGGAGAAGCCCACTCTTGG
genomic: GATCCACTCAACCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG

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: 302

CTCACTCTCCCTCGCGTCGGCGGCCGCGCGCAACTTTCCCTGAAGCCCCGGATCCACTCAACCCCCCTCCCCCTCCGCGCCAGATCGTTGTGTTTATGAGgtacttgccg ... ttgtctgcagCTCGAAGGAGAAGCCCACTCTTGG




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