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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGAGGGGAAGCAGCGGGAGGAGGAGCGGAAGGGGATGGAAGGGTCCGACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACGgtaatcgcggattatctatccccccttggctcccccgctgcgtgacctagatatggctgtcgatttttttttagggggcgttttgtttttttggtttagg...

Basic information

species Oryza sativa
transcript LOC_Os01g10150.2
intron # 1
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|88586277|gb|CI703971.1|CI703971
EST:     ACAAGGGGGGCGCCGGCGAAGACGGGAGCCCCGCGCCGC-CCCGGAGACG                         GTACAAATCGGAAATTCACCAACGTATAAGCTTGAGA
genomic: ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACGgtaatcgcgg ... cttggaccagGTACAAATCGGAAATTCACCAACGTATAAGCTTGAGA
EST: gi|86850166|gb|CI305405.1|CI305405
EST:     ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACG                         GTACAAATCGGAAATTCACCAACGTAT
genomic: ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACGgtaatcgcgg ... cttggaccagGTACAAATCGGAAATTCACCAACGTAT
EST: gi|29688778|gb|CB685053.1|CB685053
EST:     ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACG                         GTACAAATCGGAAATTCACCAACGTATAAGCTTGAGAGGAAGCTTGGAAAG
genomic: ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACGgtaatcgcgg ... cttggaccagGTACAAATCGGAAATTCACCAACGTATAAGCTTGAGAGGAAGCTTGGAAAG
EST: gi|29630440|gb|CB635449.1|CB635449
EST:     ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACG                         GTACAAATCGGAAATTCACCAACGTATAAGCTTGAGAGGAAGCTTGGAAAG
genomic: ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACGgtaatcgcgg ... cttggaccagGTACAAATCGGAAATTCACCAACGTATAAGCTTGAGAGGAAGCTTGGAAAG
EST: gi|29632065|gb|CB637074.1|CB637074
EST:     ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACG                         GTACAAATCGGAAATTCACCAACGTATAAGCTTGAGAGGAAGCTTGGAAAG
genomic: ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACGgtaatcgcgg ... cttggaccagGTACAAATCGGAAATTCACCAACGTATAAGCTTGAGAGGAAGCTTGGAAAG
EST: gi|88696005|gb|CI739580.1|CI739580
EST:     ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACG                         GTACAAATCGGAAATTCACCAACGTATAAG
genomic: ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACGgtaatcgcgg ... cttggaccagGTACAAATCGGAAATTCACCAACGTATAAG
EST: gi|87008715|gb|CI302870.1|CI302870
EST:     ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACG                         GTACAAATCGGAAATTCAC
genomic: ACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACGgtaatcgcgg ... cttggaccagGTACAAATCGGAAATTCAC

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: 75 (upstream exon), 75 (downstream exon)
Score: 51

GCCGGAGGGGAAGCAGCGGGAGGAGGAGCGGAAGGGGATGGAAGGGTCCGACAAGGGGGGCGCCGGCGACGACGGGAGCCCCGCGCCGCTCCCGGAGACGgtaatcgcgg ... cttggaccagGTACAAATCGGAAATTCACCAACGTATAAGCTTGAGAGGAAGCTTGGAAAGGGAGGATTTGGACAAGTATACGTTGGCCGGCGTATTTCCTCTCCTACTC




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