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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCACCGCAAGAAGCAAGTAGAGCCTCCAATTTCATGAGAGCATCCAAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATGgtatgtactttccttttgtgattttgttctgaatttttctttagccatacgtttgttctggtttaaatagctgagagtccatattcactgttcgttatttatcatcag

Basic information

species Oryza sativa
transcript LOC_Os06g01630.5
intron # 5
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|58675328|gb|CK064015.1|CK064015
EST:     AAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATG                         TGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG
genomic: AAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATGgtatgtactt ... ttatcatcagTGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG
EST: gi|58683216|gb|CK071903.1|CK071903
EST:     AAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATG                         TGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG
genomic: AAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATGgtatgtactt ... ttatcatcagTGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG
EST: gi|88299497|gb|CI574610.1|CI574610
EST:     AAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATG                         TGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG
genomic: AAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATGgtatgtactt ... ttatcatcagTGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG
EST: gi|33659417|gb|CF282030.1|CF282030
EST:     AAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATG                         TGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG
genomic: AAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATGgtatgtactt ... ttatcatcagTGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG
EST: gi|58610517|gb|CK038229.1|CK038229
EST:     AAATATGGAATGCCAATTACTGCTAATGGGATACATAGTTTGTTCTCATG                         TGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG
genomic: AAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATGgtatgtactt ... ttatcatcagTGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG

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: 67 (upstream exon), 61 (downstream exon)
Score: 25

GTCTCACCGCAAGAAGCAAGTAGAGCCTCCAATTTCATGAGAGCATCCAAATATGGAATGCCAATTACTGCTAATGGGGTACATAGTTTGTTCTCATGgtatgtactt ... ttatcatcagTGGGCAGGTAGTACCGTCTAGGTGTTTTTCAAGTGGAGCAG




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