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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGTTGGAACGGATAAGAGAAAACCATCTAAAAATGGTATCTTACAGTTTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAGgtaaaaggatagaatttgatactcttttatgtgttataatatcttcctattctaattatatctactctctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g05530.1
intron # 9
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|86831264|gb|CI297533.1|CI297533
EST:     TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAG                         GATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC
genomic: TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAGgtaaaaggat ... ctctctgcagGATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC
EST: gi|89185066|gb|CI049612.1|CI049612
EST:     TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAG                         GATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC
genomic: TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAGgtaaaaggat ... ctctctgcagGATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC
EST: gi|29628348|gb|CB633359.1|CB633359
EST:     TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAG                         GATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC
genomic: TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAGgtaaaaggat ... ctctctgcagGATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC
EST: gi|88292005|gb|CI532597.1|CI532597
EST:     TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAG                         GATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC
genomic: TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAGgtaaaaggat ... ctctctgcagGATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC
EST: gi|89177341|gb|CI250790.1|CI250790
EST:     TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAG                         GATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC
genomic: TTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAGgtaaaaggat ... ctctctgcagGATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCC

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: 43 (upstream exon), 73 (downstream exon)
Score: 12

CAAGGTTGGAACGGATAAGAGAAAACCATCTAAAAATGGTATCTTACAGTTTGATTTTATGAGGAATTCCGATGTTCATATACCTGAAAAGGCATTAAAGgtaaaaggat ... ctctctgcagGATGGTATCACCCCCTTTCGTTTGTCATGGACAGATTATATTTTAACTTCCCGCTACCCAACGTACTTGCGTGCCATTCAAAAAAGTTTGGAACCATACA




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