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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACAGGGAGAGGGAGAAGAAAATCCTGAATGGCACAAAGTACTCCCTGCCATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagtgctgaacaatttcagtgttatctgtcagattgggatcccataaacacattgtgtaatttagctttctgtgcatttgcatgatgactgaatggctgtgttgatcatttgggcacag

Basic information

species Oryza sativa
transcript LOC_Os05g02130.1
intron # 7
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|58659990|gb|CK048670.1|CK048670
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTCTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|29637639|gb|CB642648.1|CB642648
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|33812673|gb|CF332225.1|CF332225
EST:     CCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|33677416|gb|CF305655.1|CF305655
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|66918338|gb|CX105186.1|CX105186
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTCTGCTGCATCTGCTTCGACCAGGCTTGCACCNAT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACC-AT
EST: gi|33809660|gb|CF330722.1|CF330722
EST:     CCGATGACGATTTTTGCTCAGAG                         GTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
EST: gi|38473861|gb|CF957993.1|CF957993
EST:     CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAG                         GTGAGCGACACGGAGCTCTGCTGCATCTGCTTCGACCAGGCTTGCACCATT
genomic: CATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATT

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: 60 (upstream exon), 51 (downstream exon)
Score: 8

CAACAGGGAGAGGGAGAAGAAAATCCTGAATGGCACAAAGTACTCCCTGCCATCCCCTTCGCCCGGTGATGACAGTGCCGATGACGATGCATGCTCAGAGgtatttgagt ... ttgggcacagGTGAGCGACACGGAGCTTTGCTGCATCTGCTTCGACCAGGCTTGCACCATTGAGGTGCAAGACTGTGGACATCAAATGTGTGCACCGTGCACGCTGGCAC




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