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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttctcaacggtagaatggggatttcacatagtttttttactctctttgtccttcagcgctaacctgttctctggcttttattctatttcctttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT

Basic information

species Oryza sativa
transcript LOC_Os01g66730.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G173989_T02 (Zea mays), 3'ss of exon 4
atcttctcaacggtagaatggggatttcaca--tagtttttttactctctttgtccttcagcgctaacctgt------tctctggcttttattctatttcctttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT-------------------------------------------
           || ||| || ||||     |    |||  |      |  | ||  ||||||  | | | ||      |   ||    |  |  | |||  ||| |||||||||||||||||||||||||| ||||||||| ||||||| ||||||||||||||                                            
--------cgtgggagactgcggatagtgtagtctgttcctccctatttatcgtgattcagcagtgatcagtcacttattcatgttcatggtcttcttttttttacagTATATACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGACGTAAGTATACATTTATATTCAGGAGTATGTGAGTTGATACTTG

upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 2
----atcttctcaacggtagaatggggatttcacatagtttttttactctctttgtccttcagcgctaacctgttctctggcttttattctatttcctttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGT--TGACACCA-AACCAGAT
    | ||       || ||| || ||||    |     | ||  || ||||| ||| |   | | |        | ||   | || |||| | |  ||||||||||||||||| ||||||||||||||||||||||  |||  |  ||       ||||| | 
tcttaactgtaacgtgggagactgtggatagtgctagtctgttccaccctcttggtcat---gtgttttagcagccacttattcttgttct-tcttttttgcagTATATACCTTATGTAGAAGATACAGTTCTTGGTACTGTCATACTGTGGTTGGAACCAAAC

upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 4
atcttctcaacggtagaatggggatttcaca--tagtttttttactctctttgtccttcagcgctaacctgt------tctctggcttttattctatttcctttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT
           || ||| || ||||     |    |||  |      |  | ||  ||||||  | | | ||      |   ||    |  |  | |||  ||| |||||||||||||||||||||||||| ||||||||| ||||||| |||||||||||||| 
--------cgtgggagactgcggatagtgtagtctgttcctccctatttatcgtgattcagcagtgatcagtcacttattcatgttcatggtcttcttttttttacagTATATACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC

upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 4
atcttctcaacggtagaatggggatttcaca--tagtttttttactctctttgtccttcagcgctaacctgttctctg-----gcttttattctatttcctttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT
           || ||| |  ||||     |    |||  |      |  ||||  ||||||  | | | ||    |      | |  |  |||  ||  |||  |||||| |||||||||||||||||| ||||||||| ||||||| |||||||||||||| 
-------acgtgggagactccggatagtgtagtctgttcctccctctttattgtgtttcagcagtgatcagtcacttattcatgttcatggtcttctttttttatagTATAAACCTTCTGTAGAAGATACCGTTCTTGGTATTGTGGTCGACACCAAACCAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgtccttcagcgctaacctgttctctggcttttattctatttcctttgcagTATATACCTTCTGTAGAAGATACAGTTCTTGGTGTTGTGGTTGACACCAAACCAGAT
              cgctaac  putative branch site (score: 2)
                        ttctctggcttttatt  putative PPT
                                 ttttattctattt  TA-rich tract