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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCCgtaagttgttttccctagaatacataaatatatagcagcaatgccactatgacacatctgaaatgtttttttttcctgaatgcag

Basic information

species Oryza sativa
transcript LOC_Os06g46310.3
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g46310.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G069198_T02 (Zea mays), 5'ss of exon 13
ATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCCgtaagttgttttccc-tagaatacataaatatatagcagcaatgccactatgacacatctgaaatgtttttttttcctgaatgcag
||||||||||||||||| || ||||||||| ||||||||||||| |||||||| |||||||  ||||| ||||||||||| |||||||||| |  ||| |||  ||||  |  |||||  | |   ||      | | |  ||     || ||||| |  || || |        |||||||
ATGATACTGTCATTTGAACTCCCTTTTGCTTTAGTTCCACTCCTTAAATTCACCAGCAGCAAAACAAAGATGGGGCAGCATACAAATTCAATATTCgtgagtcattttgtcacagaatcgacagtaattaccttgaatttgcatagcaactcatctaacttgattgtc------aaatgcag

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA15G00590.1 (Glycine max), 5'ss of exon 12
ATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCCgtaagttgttttccctagaatacataaatatatagcag--caatgccactatgacacatctgaaatgtttttttttcctgaat--gcag---------------
|||||  | ||||||||||||||||||||| | ||||||||||| || || ||||||||||  || || ||||||   ||    || || |     |||| || ||||   ||  ||    |||| | |||  |  || ||| || |      |  |  | |   | |||  |   |||  | ||               
ATGATCTTATCATTTGAGCTTCCTTTTGCTTTGGTTCCACTCCTCAAGTTTACAAGCAGCAAAACCAAGATGGGGACACATGTCAACTCTACCATGgtaaatt-tttttggtaacatg---aaatttgtagttgtgcattgcaaccaaatagtaaattgattacatatttgacaaaaatcagtagagaggtgctgttaga

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA07G02680.1 (Glycine max), 5'ss of exon 11
ATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCCgtaagttgttt--tccctagaatacataaatatat----agcagcaatgccactatgacacatctgaaatgttttttt--ttcctgaatgcag--------
|||||  | ||||||||||||||||||||| |  |||||||||| || ||||| |||||||  |  || |||||  | ||    || ||||   | |||| || |||  |  |  ||| |   |||  | |    |  || ||    | |   | || ||  ||||||| |     |   |  |  ||         
ATGATCTTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCTCGgtaatttttttggtgacatgaaaattgaaacttgttacaaatagtaaattgattgcca-acttcacaaatgttgtcaaaatatttagaatcattgtctgac

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA13G44710.1 (Glycine max), 5'ss of exon 11
ATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCCgtaagttgttttccctagaatacataaatatatagcagcaatgccactatgacacatctgaaatgtttttttttcctgaat--gcag---------------
|||||  | ||||||||||||||||||||| | ||||||||||| || || ||||||||||  || |||||||||   ||    || || | |   |||| || ||||   ||  ||  | |  ||||   | ||| ||| || |      |  |  | |   | |||  |   |||  | ||               
ATGATCTTATCATTTGAGCTTCCTTTTGCTTTGGTTCCACTCCTCAAGTTTACAAGCAGCAAAACCAAAATGGGGACACATGTCAACTCTACAATGgtaaatt-tttttggtaacatgaa-acttatagttctgcattgcaaccaaatagtaaattgattacatgtttgacaaaaatcagtagagaggtgctgttaga

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA08G23320.1 (Glycine max), 5'ss of exon 13
ATGATACTGTCATTTGAGCTTCCTTTTGCTCTAGTTCCACTCCTAAAATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCCgtaagttgttttccctagaatacataaatatatagcagcaatgccactatgacacatctgaaatgtttttttttcctgaatgcag-----------------
||||| || ||||||||||||||||||||| |  |||||||||| || ||||| |||||||  |  || |||||  | ||    || ||||   | |||| || ||||         | ||  | |  | |||   ||   |  || |    ||||| || |  | |||    | | | |                  
ATGATCCTATCATTTGAGCTTCCTTTTGCTTTGATTCCACTCCTCAAGTTCACTAGCAGCAAAATCAAGATGGGAGAACATGTCAACTCAATCACGgtaattttttttgtgacatgaaaattgaaacgttgcaaatat-ttagaatcatg-gtctgacatatgctatttgaaagcaagaaagacacatgtactattca

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|27921051|gb|CB096859.1|CB096859
EST:     GGGGCAGCACACAAATTCAAAAGCC                         ATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACC
genomic: GGGGCAGCACACAAATTCAAAAGCCgtaagttgtt ... ctgaatgcagATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACC
EST: gi|218490953|gb|FG953072.1|FG953072
EST:     AATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCC                         ATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACC
genomic: AATTCACAAGCAGCAGGACAAAAATGGGGCAGCACACAAATTCAAAAGCCgtaagttgtt ... ctgaatgcagATTTCTGTGATAACATGGGGAATTGGTTCGTTTATCGTTGTCATCAACACC