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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgtattctcctcttgctacctagctgaagtccttcctgaatcccttcgattgttgtattgttattattatgtgaattttcatgcagaagtaatcttcatgtaaccttgaatttgcgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAATCTGCATCCTTTTTGAGATATGGTTGCCTATCGCGAGAGAATGTAGCCG

Basic information

species Oryza sativa
transcript LOC_Os06g24704.1
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|88234700|gb|CI234549.1|CI234549
EST:     CAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: CAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|88197237|gb|CI197087.1|CI197087
EST:     TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|88967904|gb|CI098146.1|CI098146
EST:     TTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: TTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|29670182|gb|CB666457.1|CB666457
EST:     TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|14571492|gb|BI118860.1|BI118860
EST:     TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|29665964|gb|CB662239.1|CB662239
EST:     TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|86485162|gb|CI127795.1|CI127795
EST:     TGCGAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|89178953|gb|CI043458.1|CI043458
EST:     TTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: TTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|29670227|gb|CB666502.1|CB666502
EST:     TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGAAGAA
genomic: TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|218485341|gb|FG954862.1|FG954862
EST:     TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
EST: gi|86491093|gb|CI133726.1|CI133726
EST:     TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAG                         GATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA
genomic: TGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAA

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: 74 (upstream exon), 42 (downstream exon)
Score: 10

CTACCAACTCGCTGAAGACTTAGCTAGAGCATTTACTGAGCGCACAATTTTGCAAATATTTTTGGAGGATGAGAAGAATATTCCTACTGGTTCTTTAAAGgtatatgtat ... cgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAATCTGCATCCTTTTTGAGATATGGTTGCCTATCGCGAGAGAATGTAGCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaattttcatgcagaagtaatcttcatgtaaccttgaatttgcgttctgcagGATATATTGGGCTTACTAAGGTCTTTATATGTTATGGTTTGCATAGACGAATCTGCATCCTTTTTGAGATATGGTTGCCTATCGCGAGAGAATGTAGCCG
                            atgtaac  putative branch site (score: 10)
     attttcat  TA-rich tract