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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaatttacacattgagttattcatgggaactatacttcgcttttctttatgtacctaagacttttgagttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA

Basic information

species Oryza sativa
transcript LOC_Os03g63020.3
intron # 12
splice site 3'
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|29613120|gb|CB618133.1|CB618133
EST:     CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
EST: gi|29644979|gb|CB649986.1|CB649986
EST:     CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
EST: gi|29663527|gb|CB659802.1|CB659802
EST:     ACGAAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: ACG-AAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
EST: gi|34996388|gb|CF569133.1|CF569133
EST:     CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
EST: gi|29666009|gb|CB662284.1|CB662284
EST:     ACGAAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: ACG-AAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
EST: gi|29666008|gb|CB662283.1|CB662283
EST:     CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
EST: gi|29638287|gb|CB643296.1|CB643296
EST:     ACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: ACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
EST: gi|29656192|gb|CB652467.1|CB652467
EST:     CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
EST: gi|33381337|gb|CF196680.1|CF196680
EST:     CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
EST: gi|218497584|gb|FG955131.1|FG955131
EST:     CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAAT                         GTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT
genomic: CACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATT

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: 69 (upstream exon), 56 (downstream exon)
Score: 18

CAACTTTGTTCCTGGGATCCACGAAGAAGGCCAACTGCTGAGCAATCACTACAGCATCCGTTCTTTAATgtactaattt ... agttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgggaactatacttcgcttttctttatgtacctaagacttttgagttgtctagGTGGGCAACTGGGTACCAAGGCCACTCCATGCCTCTCACACAAAGACAATTGAAACTA
                   ttttctttat  TA-rich tract