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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATTCCGCTTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttctaccctccaaacttttgatttattgttatttccgtttttttacagtaaatgaataattgatcacaatcttatgaccttcaatgggtagttat...

Basic information

species Oryza sativa
transcript LOC_Os01g24880.2
intron # 3
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|38469794|gb|CF953925.1|CF953925
EST:     TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGA                         TGAAGGAGAGTCAGCACCACCCGTAACCT
genomic: TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttcta ... tcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT
EST: gi|58608025|gb|CK036058.1|CK036058
EST:     TTCCAATGGTGTCCTATNGGCCGCTGAGCCCAACTTCCATCTGTATTTGA                         TGAAGGAGAGTCAGCACCACCCGTAACCT
genomic: TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttcta ... tcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT
EST: gi|29656889|gb|CB653164.1|CB653164
EST:     TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGA                         TGAAGGAGAGTCAGCACCACCCGTAACCT
genomic: TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttcta ... tcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT
EST: gi|29615731|gb|CB620743.1|CB620743
EST:     TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGA                         TGAAGGAGAGTCAGCACCACCCGTAACCT
genomic: TTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttcta ... tcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT

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: 59 (upstream exon), 29 (downstream exon)
Score: 104

CCATTCCGCTTCCAATGGTGTCCTATTGGCCGCTTAGCCCAACTTCCATCTGTATTTGAgtatgttcta ... tcttttccagTGAAGGAGAGTCAGCACCACCCGTAACCT




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