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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtagtctgtgacctctcacacgctctcacacacatatgtagcctttggtacataagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g54020.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 12
gtctgtagtctgtgacctctcacacgctctcacacacatatgtagcctttggtacataagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
|| | |    | |  | |||    ||||||| |  || | | |   | ||  ||     |||||||||||  |||| ||  ||  ||||||  |||| |||||||||||||||||||| |||||||  ||||||||||| || ||||||||||| || | ||| ||||| |||
gtttctctcttctcgcttct---gcgctctctc-tacctctcttttcattattat---ggaaactcattccattgaactcata--tttcagTATGGAGTTTGACAACCCAGAGAGGCCGGAATGCAGAAATCTTCTCTCTATATACCAGATTATCACTGAGAAGACTAAGGAG

upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA04G09130.1 (Glycine max), 3'ss of exon 12
------------------------------------------gtctgtagtctgtgacct-ctcacacgctctcacacaca-tatgtagcctttggtacat----aagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
                                           ||  |  |   | |  | ||      || | |  |    | | | |  |||||||  |    ||   |||  | || || |      | ||| ||| ||||||||||||||| | |||||||||||||| ||||||||||| || || |||||| ||                     
tgattgatgatcttagtcctcagaggtttagtctataaatgcttccatttttcataattttcttgttttctataaatctttctttttggtgtttggtaagTTCTCAAATTACTTGTGCACTTTATGACAAATCTTACAGTTTGGAATTTGACAACTCTGAGAGGCCTGAATGTAACAATCTTCTTTCCATATACCAGCTT---------------------

upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA06G09240.1 (Glycine max), 3'ss of exon 12
------------------------------------------------------------gtctgtagtctgtgacctctcacacgctctc-----acacacatatgtagccttt----ggtacataagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
                                                            |  || | |   | | |  | ||  | | ||     |      | | | |  |||     || |  ||   |||  | || || |        ||| ||||||||||||||||||| | |||||||||||||| ||||||||| | || || |||||| ||||| |||| || || ||||||
gttagtacttgtaatattaccatatgatgatcttagtcctcagaggtttagtctataaatgcttgcatttgttcatcatttacttgttttctataaatctttctttttggtgtttcgctagttctcaaattacttgtgcactttatgacaattcttacagCTTGGAATTTGACAACTCTGAGAGGCCTGAATGTAACAATCTTGTTTCCATATACCAGCTTATTTCAGGAAAGACGAAAGAG

upper sequence: LOC_Os01g54020.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G25840.1 (Arabidopsis thaliana), 3'ss of exon 10
-------------------------------------------gtctgtagtctgtgacctctcacacgctctcacacacatatgtagcctttggtacataaga---aactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
                                              | |  | | |  ||| |  |  | |  ||      | |  |   |  | ||  |||     ||  | |    ||    |||| ||     ||||| ||||||||||  | ||||| ||||||||||||||||| ||||| || || |||||| || |||| || |  ||||||
gtgagcgctacttatgtcgctaaaaaatttcttgcaatgcacaaagttttttttttttcctttttcttgttaccatttcagttttcaaattgagatatctaatgttgaaagcttctgcttcttgttgttccaacagGCTTG-AATTTGACAATGCTGAGAGACCTGAATGCAACAATCTCCTCTCAATATATCAGATTGTTTCAGGCAAGAAAAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgtagcctttggtacataagaaactcattcatttgaccttgtacctttcagCTTGGAATTTGACAACCCAGAGAGGCCTGAATGCAACAATCTTCTCTCGATCTACCAGATTATTACAGGGAAAACTAAAGAG
                                  atttgac  putative branch site (score: 4)
                                             tacctttc  putative PPT
                   ataagaaa  TA-rich tract