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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGTGATGGCTGTATTATTCGTCGTTTGTAACCTCACAATTTCGGATGTTTTTGCTAGTATTCTTGGGTTCATGCCTACTGGTTGGTGCATTCTTCTGgtgagtgaaacccttctgcaccacttatttgtttttttttgtaagcataaaacttaattccaagaacaaatataaaaccctgtccattttctcaataaaaagataaattttagcgttcatcgtaatctggacccaaatgatttgtatgatcttgtcattcatccacag

Basic information

species Oryza sativa
transcript LOC_Os01g34880.1
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|163928804|gb|EG711916.1|EG711916
EST:     TTTTTTCTAGTATTCTTGGGTTCATGCCTACTGGTTGGTGCATTCTTCTG                         ATTGGGCAGGCATGTTCGCCGTTGGTGAAGAAGGCAATGCTGTGGGATTCC
genomic: TTTTTGCTAGTATTCTTGGGTTCATGCCTACTGGTTGGTGCATTCTTCTGgtgagtgaaa ... tcatccacagATTGGGCAGGCATGTTCGCCGTTGGTGAAGAAGGCAATGCTGTGGGATTCC
EST: gi|88842424|gb|CI081680.1|CI081680
EST:     TTTTTGCTAGTATTCTTGGGTTCATGCCTACTGGTTGGTGCATTCTTCTG                         ATTGGGCAGGCATGTTCGCCGTTGGTGAAGAAGGCAATGCTGTGGGATTCC
genomic: TTTTTGCTAGTATTCTTGGGTTCATGCCTACTGGTTGGTGCATTCTTCTGgtgagtgaaa ... tcatccacagATTGGGCAGGCATGTTCGCCGTTGGTGAAGAAGGCAATGCTGTGGGATTCC
EST: gi|89194773|gb|CI003237.1|CI003237
EST:     TTTTTGCTAGTATTCTTGGGTTCATGCCTACTGGTTGGTGCATTCTTCTG                         ATTGGGCAGGCATGTTCGCCGTTGGTGAAGAAGGCAATGCTGTGGGATTCC
genomic: TTTTTGCTAGTATTCTTGGGTTCATGCCTACTGGTTGGTGCATTCTTCTGgtgagtgaaa ... tcatccacagATTGGGCAGGCATGTTCGCCGTTGGTGAAGAAGGCAATGCTGTGGGATTCC
EST: gi|87016737|gb|CI275739.1|CI275739
EST:     TGGGTTCATGCCTACTGGTTGGTGCATTCTTCTG                         ATTGGGCAGGCATGTTCGCCGTTGGTGAAGAAGGCAATGCTGTGGGATTCC
genomic: TGGGTTCATGCCTACTGGTTGGTGCATTCTTCTGgtgagtgaaa ... tcatccacagATTGGGCAGGCATGTTCGCCGTTGGTGAAGAAGGCAATGCTGTGGGATTCC

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: 45 (upstream exon), 62 (downstream exon)
Score: 5

CTCTGTGATGGCTGTATTATTCGTCGTTTGTAACCTCACAATTTCGGATGTTTTTGCTAGTATTCTTGGGTTCATGCCTACTGGTTGGTGCATTCTTCTGgtgagtgaaa ... tcatccacagATTGGGCAGGCATGTTCGCCGTTGGTGAAGAAGGCAATGCTGTGGGATTCCATCATGGAGCTCGGGAGGTCGTACGAGAACCTGATGGGACTCGTCCTCT




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