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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag

Basic information

species Oryza sativa
transcript LOC_Os03g17120.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G044237_T02 (Zea mays), 5'ss of exon 12
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
||||||||| ||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| || ||         ||  ||    ||||    |          |||| |  ||  || |       | |  ||| ||| |||| |||  |||||||  || |     | |  | | |  |  ||||  |  | | |    || |||| |   | ||||| ||   | ||| |||||  |   || || ||
GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgcataa--------tcctttgatgccattttga---------acattataattgggctt------ctaagttttaataaacaatttggcttatctgaaaagt-taaaactttagtctgtactatat--agctccttcctatattttcatgaatatgacataa-tgtttaatgtgcct-tcttctgtgcag

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA10G05090.1 (Glycine max), 5'ss of exon 12
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgact-tgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
||||||||||||||||| ||||| ||||| |||||||| || ||||||||||| ||  |||||||            ||||  ||    ||  |  || || ||| | |||  |||     || |      ||| | ||   ||| |||  | |||     |      ||  |  ||                                                                                    
GTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAGgt------------atttt-tttgtgtca-aggataaggatatt-tgcatcatgactgttgatttatgtgattgtgttcttttataatccaatattaatcctccacagttcttgt-----------------------------------------------------------------------------------

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA13G19450.1 (Glycine max), 5'ss of exon 13
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
||||||||||||||||| ||||| ||||| |||||||| || || |||||||| ||  |||||||            ||||  ||    ||  |  || || ||| | |||  |||     || |      ||||| |  |||| |||| | |||     |      ||     ||                                                                                    
GTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAGgt------------atttt-tttgtgtca-aggataaggatatt-tgcatcatgactgttgatttatgtgact-gttgttttatattccaatattaatcctccacagtccttgtgc---------------------------------------------------------------------------------

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT2G37500.2 (Arabidopsis thaliana), 5'ss of exon 13
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
|| |||||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||| || |||||| |     ||  | |    | | | |  ||| |  |  |   |       ||  |   || ||  |  | |  ||                                                                                                                        
GTGATGCAAGGACTTGCTAAATCAATAGCTTGGGATGGTGAAGGTGCTACATGTCTCATCGAGgttcacaaaataaaacta---ttattcccaaccctttgattgaaaacaaatcttaaccaataacacaaata-tcaacag----------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 5'ss of exon 13
GTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgtttgatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtag
|||||||| |||||||||||||| |||||||||||||| || || |||||||| ||||||||||| | | |  |  ||||  |  ||    |||   | |    ||  |    || | | |   |   |||  | ||  |       || ||||   | | |     ||| |                                                                                        
GTAATGCAGGGTCTTGCAAAATCAATAGCATGGGATGGAGAAGGAGCAACATGCCTAATTGAGgt-atgagtcttacattaaaagcat---gcatacttaatg-agcctaacccaatat-tgcaaatttgaccatttttc--caatcatgcaaaccaaat-agtgaacaaat----------------------------------------------------------------------------------------

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|27546388|gb|CA767223.2|CA767223
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG                         GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgct ... ccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
EST: gi|86494844|gb|CI137477.1|CI137477
EST:     AAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG                         GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
genomic: AAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgct ... ccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
EST: gi|86499008|gb|CI141641.1|CI141641
EST:     AAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG                         GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
genomic: AAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgct ... ccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
EST: gi|29613227|gb|CB618240.1|CB618240
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG                         GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgct ... ccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
EST: gi|29670993|gb|CB667268.1|CB667268
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG                         GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgct ... ccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
EST: gi|87012910|gb|CI297137.1|CI297137
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG                         GTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAGgttaagcgct ... ccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGT