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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGACAGCTCTGAGGTGCATCGATTTGAATGCTGAGAAGAGACCAAGGATGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAGgtttgattcgtttcaaaaataaatgtgcatacatatatatcatatagctgtgtgcatatcagatgcaaaggctgtagctctaaactcttcctttacctaa...

Basic information

species Oryza sativa
transcript LOC_Os11g01740.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01740.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G162702_T01 (Zea mays), 5'ss of exon 6
TTTGACAGCTCTGAGGTGCATCGATTTGAATGCTGAGAAGAGACCAAGGATGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAGgtttgattcgtttcaaaaataaatgtgcatacatatatatcatatagctgtgtgcatatcagatgcaaaggctgtagctct--aaactcttcctttacctaa
|||||| ||||||||||| ||||||||||||||||||||||| || || |||||||||||||||||||||||||| |||||||||| ||| || |||||||||||| |   || |   |      || | |  | |  ||  | ||| | | |      | |  |    ||||   ||  |  | ||   ||   |  ||| 
TTTGACTGCTCTGAGGTGTATCGATTTGAATGCTGAGAAGAGGCCTAGCATGGACCAGGTGGTCCGGATGTTGGATTCTAATGAACTCATACCGCAAGAGgtttgaatttgtttatttaattccatgtagaactgt-catagtctaggtttattgggtacgggggaggtggctagggccatggagaccactcgcatggcta-
















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|44675040|gb|CR288474.1|CR288474
EST:     TGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAG                         GAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
genomic: TGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAGgtttgattcg ... tgatttgcagGAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
EST: gi|15008978|gb|AU223366.1|AU223366
EST:     TGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAG                         GAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAAACCGAGCCA
genomic: TGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAGgtttgattcg ... tgatttgcagGAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
EST: gi|58031067|gb|CX728610.1|CX728610
EST:     ATTCCTCAAGAG                         GAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
genomic: ATTCCTCAAGAGgtttgattcg ... tgatttgcagGAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
EST: gi|89186565|gb|CI048237.1|CI048237
EST:     TGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAG                         GAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
genomic: TGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAGgtttgattcg ... tgatttgcagGAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
EST: gi|29624053|gb|CB629064.1|CB629064
EST:     TGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAG                         GAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
genomic: TGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAGgtttgattcg ... tgatttgcagGAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
EST: gi|88961525|gb|CI096806.1|CI096806
EST:     AGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAG                         GAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA
genomic: AGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAGgtttgattcg ... tgatttgcagGAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCA

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: 66 (upstream exon), 21 (downstream exon)
Score: 3

TTTGACAGCTCTGAGGTGCATCGATTTGAATGCTGAGAAGAGACCAAGGATGGACCAGGTGGTCCGGATGTTGGACTCTAATGAACCCATTCCTCAAGAGgtttgattcg ... tgatttgcagGAAAGAAGACAACGACAGAACCACATCTCTAATAATTCAGAGACCGAGCCATTAAGAGGCAAGAGCAGCAGCGGCAAGAGTGATGCCCCTGAAAATGAGA




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