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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAGGATTGCTCGGATTTTTAACACATATGGTCCTCGCATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAGgtagccgtcacttgcatcttcctcttttggctcccgaatttacagatggtttgattgttcctttgatactgacatcttgtttctgcaattatggttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g21320.1
intron # 4
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|300216208|gb|HO087993.1|HO087993
EST:     CTCGCATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAG                         GCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
genomic: CTCGCATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAGgtagccgtca ... tggttttcagGCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
EST: gi|29656946|gb|CB653221.1|CB653221
EST:     CATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAG                         GCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
genomic: CATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAGgtagccgtca ... tggttttcagGCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
EST: gi|29678441|gb|CB674716.1|CB674716
EST:     ATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAG                         GCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
genomic: ATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAGgtagccgtca ... tggttttcagGCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
EST: gi|86907161|gb|CI292784.1|CI292784
EST:     CTCGCATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAG                         GCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
genomic: CTCGCATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAGgtagccgtca ... tggttttcagGCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
EST: gi|86493952|gb|CI136585.1|CI136585
EST:     CTCGCATGTGCATTGATGATGNCCGTGTTGTCAGCAACTTTGTTGCTCAG                         GCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
genomic: CTCGCATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAGgtagccgtca ... tggttttcagGCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
EST: gi|29656945|gb|CB653220.1|CB653220
EST:     CTCGCATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAG                         GCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
genomic: CTCGCATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAGgtagccgtca ... tggttttcagGCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
EST: gi|29670681|gb|CB666956.1|CB666956
EST:     TGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAG                         GCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG
genomic: TGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAGgtagccgtca ... tggttttcagGCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGG

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: 50

GTGAGGATTGCTCGGATTTTTAACACATATGGTCCTCGCATGTGCATTGATGATGGCCGTGTTGTCAGCAACTTTGTTGCTCAGgtagccgtca ... tggttttcagGCACTGAGGAAGGAACCTTTGACTGTCTATGGTGATGGCAAGCAGACTAGGAGCTTTCAATATGTCTCTGATTTG




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