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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA

Basic information

species Oryza sativa
transcript LOC_Os01g59340.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
||||   || |   |  ||||   | | |||||||||   |    || ||||||||   |||       ||||||    | |||| | | | ||   |   ||||  | ||         |||     |||        |||  | | |   |||   |||      ||||  ||| |||||||| ||||| ||||||||||| |||||||| || ||||| |||||  ||||||| ||| ||||||||||||||||||||||||| || |||||||||||||
gtaaccccaaatctaaccttctattcttctgttatgctcctagtcctagatatgtt---cag-------gttttc---aataataattaggaca--ctaaggaacctgccatct------attctcacattaagctattcaaaaatgaa---ataattttg------ttctcattcactgcagTTAGAAGGAGAAGCAACTGCACGGGCAATCCGTTTAGCTAAGTTCATCAATACGCCACTGTATGTTGTTCATGTGATGAGCATCGACGCAATGGATGAGA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G18920.1 (Glycine max), 3'ss of exon 6
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                         ||||||       |   || | | | || || |  | | |  |  |||| ||| | |  | | |   |        ||  |  | ||| | |   | |    |  || |||||||||| || ||||||||||| || ||||  |||||  | ||||| || || || || ||||| |||||||| |||||||||||||||||||| || |
-------------------------------------------------------------------------tcttatg------ttgtgtgattcttgtaaagtctaaatatga-aaaatctgtctctgatttatagaagatttccctatttgactttg-gttatgtat--acctatgtagTTGGAAGGAGAGGCAACTGCTCGTGCTATTCATTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                                   |  |   |||  | |  |    |      ||    || |||   | | |         |   |    | || |          |||  |  ||  || |||||||||| || ||||||||||| || ||||| |||||  | ||||| ||||| || || ||||| |||||||| |||||||||||||||||||| || |
----------------------------------------------------------------------------------ctggttttgtcc-tcttatatcttgtgattactgcaaagtttaaatgtctgtctgtgtgattgataggacattcttccatttgactttgttatctgtgtagTTGGAAGGAGAGGCAACTGCTCGTGCCATTCGTTTAGCAGATTTTGTGAATACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                             ||    | |||   |  |||| |||| |       ||    || |||   | | |         |   |    | || |          |||  |  ||  || |||||||||| || ||||||||||| || ||||| |||||  | ||||| ||||| || || ||||| |||||||| ||||||||||| |||||||| || |
----------------------------------------------------------------------------catgttttgttctcttatattttgtgatc-------actgcaaagtttaaatgtctgtctgtgtgatttataggaaattctcccatttgactttgttatctgtgtagTTGGAAGGAGAGGCAACTGCTCGTGCCATTCGCTTAGCAGATTTTGTGAATACTCCTTTATATGTGGTTCATGTAATGAGCATTGACGCAATGGAAGAAA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                                 ||||||   || | | | || || |  | | || |  | || ||| |||  | | |   |        ||  |  | ||| | |   | |    |  || |||||||||| || |||||||| || || ||||| |||||  | ||||| || || || || ||||| |||||||| |||||||||||||||||||| || |
-------------------------------------------------------------------------------ctaatatt-gtgtgattcttgtaaagtctaaatacgaaaatatatgtctatgatttatagaacatttccctatttgactttg-gttatgtat--acctatgtagTTGGAAGGAGAGGCAACTGCCCGTGCTATTCGTTTAGCTGATTTTGTGAACACTCCTTTATATGTGGTTCATGTAATGAGCATTGATGCAATGGAAGAAA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaag--tcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccctg-cagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                               | || ||    |   ||      |||| ||||||    | | ||  |   | |  |   ||| |    |  |    | |||  |  ||   |     | |   |   | ||     || | ||| ||   |  || ||| | || || || || |||||| | |||||||| || ||    ||| | || || ||  | ||||||||||||||||||||  ||||||||||||| ||||
----------------------------------------------gtaatttgcgtcaagcattttccattttattatactgcctcctagattttttcttttctcctatatctgctcttgcctctgtaaagctttgtt-----gaagctactaaaac----aagatccttgtttgacaatgtcagCTCGAGGGAGAGGCCACTGCTAGAGCAATTCGTTTGGCTCGTTTTATTAACACGCCTCTCTATGTTGTTCATGTGATGAGTGTTGATGCAATGGACGAGA

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 5
gtaatttcacactaactcttcgcatttactgttatgcctatttatcttgatatgttggacagatcaagtgttttcttatacaatattcaagtcaatttggtgaactagacacaccatgaaatttgtgtattttctctcacaaggaaggatagataccattgagctgcttcttgttccct--gcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
                                                                            | ||   | ||   ||   | |  |   || ||||   |      |||  || | ||  ||       | |  |  |||  ||    ||  || |||  || |  |||| | ||||| || ||||||||| | || ||||| || ||||  ||||| || || ||  | ||||| ||||||||||||||||||||||| ||||| || |
---------------------------------------------------------------------------ctttattctgtt---gttcttctaattgtct-gacagttc------tttccgtttatttcctggacgtcatgcttttatataatctgtcttttttttggcccttatgcagCTAGAAGGAGAGGCAACTGCTAGAGCTATTCGGTTGGCCAGTTTTGTTAACACGCCTCTCTATGTAGTTCATGTGATGAGCATTGATGCGATGGAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctctcacaaggaaggatagataccattgagctgcttcttgttccctgcagTTGGAAGGGGAAGCAACTGCTCGGGCAATTCGATTAGCCAAGTTTGTCAATACACCATTGTATGTTGTTCATGTGATGAGCATTGATGCAATGGATGAGA
     ctctcac  putative branch site (score: 3)
                                   ctgcttcttgttccct  putative PPT
                    atagata  TA-rich tract