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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAACGACGAACAACAACATCTCGCCACGAAGAGGAGGGCGAGAGCCTGCACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctctctcagatctctgtgcttggcggtgcggatcggttttttgtcatcagttgtcctgatttttgttccggggtgtctaatttgggcccgatccgatcag

Basic information

species Oryza sativa
transcript LOC_Os11g03380.1
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|4715628|gb|AU056744.1|AU056744
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|33658304|gb|CF280918.1|CF280918
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|33658126|gb|CF280740.1|CF280740
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|33690612|gb|CF318851.1|CF318851
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|14714076|gb|AU198016.1|AU198016
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCAGGCTGCCTGGGCAGGCAGGTGGTGGCCGTGATGCTCCTCCTTGCG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGC-GGCTGCCTGGGC-GGC-GGTGGTGGCCGTGATGCTCCTCCTTGCG
EST: gi|88312635|gb|CI587543.1|CI587543
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCTGTGATGCTCCTCCTTGCGCA
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCC-GTGATGCTCCTCCTTGCGCA
EST: gi|29663528|gb|CB659803.1|CB659803
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|33679537|gb|CF307776.1|CF307776
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|29658170|gb|CB654445.1|CB654445
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCCCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|88316617|gb|CI622863.1|CI622863
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCC-AG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|58664366|gb|CK053052.1|CK053052
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|58677950|gb|CK066637.1|CK066637
EST:     CACGAGTCCGAAATCCCCAAGCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|88332593|gb|CI651753.1|CI651753
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|29678424|gb|CB674699.1|CB674699
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|33822526|gb|CF337070.1|CF337070
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|86906721|gb|CI291169.1|CI291169
EST:     ACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: ACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|33658022|gb|CF280636.1|CF280636
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|58598104|gb|CK008632.1|CK008632
EST:     GCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCT-CT-CTTGCGCAG
genomic: GCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|88728556|gb|CI752066.1|CI752066
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|88445308|gb|CI587202.1|CI587202
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|88696206|gb|CI739781.1|CI739781
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|29624905|gb|CB629916.1|CB629916
EST:     ACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: ACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|2428191|gb|C72654.1|C72654
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
EST: gi|58694105|gb|CK082792.1|CK082792
EST:     CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAG                         ATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG
genomic: CACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAG

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), 73 (downstream exon)
Score: 73

CACAACGACGAACAACAACATCTCGCCACGAAGAGGAGGGCGAGAGCCTGCACGAGTCCGAAATCCCCAATCCGGGTTCCCTGCTTCTCTTCGCGCCAAGgtaagatctc ... atccgatcagATGGCGGCTGCCTGGGCGGCGGTGGTGGCCGTGATGCTCCTCCTTGCGCAGGTGTCAGCCGCGGCTCCGGTGATGGGGCCTGCCTTCCTCTGGGCGCCCA




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