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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG

Basic information

species Oryza sativa
transcript LOC_Os01g59340.2
intron # 11
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 11
lower sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 8
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcaca--tggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                                                                    | | ||    |     |  |   || |   ||||    || |   | || |         || | |   |||| |  |  || |  | |||||||  |||  |     ||||||||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||||||||  | |||||||| |||||||| ||||
--------------------------------------------------------------------ttaattgctgagaggcaatgttacattacctgct-atggagaaggaaactt-------atgttgcatttttcatagttacataaacacctaactgtactttgt-----tgcagCTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATG

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 8
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                                                          | |||    |     ||  |  | |||      | |||| ||||  ||   | || |   || |||||     ||  | || ||   |   ||  | || |  |  ||||          ||| |||||||||||||||||  |||| || ||||| ||||||||| | ||   |||||| ||| | || |||||||||||||| ||||
----------------------------------------------------------tgtttctgagctctgtattatctaata------ccctgtgtgct--caattaattcttttttactaag--actgattatttgaccaagggtaccgttta-caacctttca----------gCTGGTAGGAACTGATCATTGTGCCTTTAATTCCACCCAGAAAGCTCTTGGAATTGATGACTTCCGGAAAATTCCTAATGGTGTCAATG

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                                                                   ||   ||  |    | |  |     |||      |||||  | | | || | | | ||  | ||  |   |  | |    |   | ||    |  |       ||| |||||||||||||||||||||| ||||| ||||| || ||||| |||||| | ||   |||||||||| | |  || ||||||||||||||||
-------------------------------------------------------------------gtttctttcctcgctgt--gcataaactagagaattgcatga-cctgtagcat-caaaatgttaagatcttctaaacacctttttctccttttattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                                                                             | |||  |||       || |          ||  |  |  ||| ||      ||  | |||   ||   |  || ||  |     | |      | ||||||||||||| |||||||||||  ||||||| ||||||||||||||||| ||   |||||||||| |||| |||||||||||||| ||||
--------------------------------------------------------------------------tctacattg-aggataatgttgatcctaaagcataatcttgatattgttacttaa-agtgatctttgaat---tttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                            atctaac  putative branch site (score: 2)
                                  ctgctcttcatttct  CT-rich tract
                                           atttctat  TA-rich tract