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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctagcttcttgtctcctttctcatctgttctttaatcagctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG

Basic information

species Arabidopsis thaliana
transcript AT3G13870.2
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 20
------------------tttctagcttcttgtctcctttctcatctgttctttaatcag-ctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggattt--------cagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG-----
                  | | ||  || | || |  |   | |    || |  | |  |  | ||     |   |  || ||| || | | | |      |      ||   |||        ||||| || ||     |||| ||||||||||||||||||||||||||| |    ||  ||| | | |||||||| || || || |||||  | ||||      
gtatcctgttaattgaaatctttaattt-tcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 20
------------------tttctagcttcttgtctcctttctcatctgttctttaatcag-ctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggattt--------cagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
                  | | ||  || | || |  |   | |    || |  | |  |  | ||     |   |  || ||| || | | | |      |      ||   |||        ||||| || ||     |||| ||||||||||||||||||||||||||| |    ||  ||| | | |||||||| || || || |||||  | |||| 
gtatcctgttaattgaaatctttaattt-tcgtttggtacttgaaacattgtggagtgggattgacctattgggtataaaatgatgtatgattgtatgcctaactgttttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 20
tttctagcttcttgtctcctttctcatctgttctttaatcagctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
      || |  ||  |   || |||       || |||    |        | |||| | || |       || | |||| | |||  ||   |||||||| || |||   || || ||||||||| | || || |||||||||||  ||||  ||||| |||| |||||||||||||||||||| ||  ||||
------gcatgatgcataagttatcaag-acatttgaatttcttgtt-----ggaaaacattttactaactgatgt-aatatattctttttat-tttcagGAGGCCAACAAGCGCAACAACAACTGGTTACCTCCCCCATGGGCAATAGTTGCTTTGGTTATTCTGGGATTTAATGAATTTATGACACTTCTAAG

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 20
--tttctagcttcttgtctcctttctcatctgttctttaatcagctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
   |  | | | | | | |   |   ||| || | | |  |||   | ||  |     | ||| |     ||     |||   |  |    ||  |||||||||||| |||   || |  | ||||||| | || ||||||||||| ||  | ||  || || ||||||||||||||||||||||||| || |||||
acatcatggatgcatat-tatgtaggcatttgatttctg-tcactgatcaaacattttactaacttttacttattgatgatgtagtttatttttaatttcagGAAGCCAACAATCGTAGCAGCAACTGGTTACCTCCTCCATGGGCGATTGTGGCTTTGATTATTCTTGGATTTAATGAATTTATGACACTTTTAAG

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 21
tttctagcttcttgtctcctttctcatctgttctttaatcagctaacaccc--ggaaaaataattgaggtttcaatctgaata------aagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
            | || | |||   |  | ||    ||  ||  | | |    || |||| |    |  |||   | |  ||       || |    ||  |||||||||||| |||   || |  |   ||||| | || || |||||||| ||  | ||  || || ||||||||||||||||||||||||| || |||||
-------aaatctatcccatttggtaatt-ttgaaaaaaaagtcatcccttttggtaaaaaagccaacttttacttattgatggtgtgtaatttctttttaatttcagGAAGCCAACAATCGTAGCAGGCACTGGTTACCTCCACCATGGGCGATTGTGGCTTTGCTTATTCTTGGATTTAATGAATTTATGACACTTTTAAG

upper sequence: AT3G13870.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 20
tttctagcttcttgtctcctttctcatctgttctttaatcagctaacacccggaaaaataattgaggtttcaatctgaataaagtctccttggatt-tcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
    ||  |||||          |       | ||| |  | | |   |||   |   | | ||   | | | | |    |    ||| ||  ||| ||||||||| |||   || |||||||||||| | |||||||||||||||||  ||||  |||| || || ||||| |||||||||||||| ||  ||||
-caatattttctttgagaaacagtatcaaaatatttcactaaccatgccccattaccgtcaatggtatctaattgttttcacttcctctttcaattatcagGAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTTGCTATGGTCGTCCTGGGATTCAATGAATTTATGACACTTCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acacccggaaaaataattgaggtttcaatctgaataaagtctccttggatttcagGAAGCTAACCGACGGAATAACAACTGGCTGCCACCTCCATGGGCAATCCTTGCCCTGGTTGTTCTTGGATTTAATGAATTTATGACTCTCTTAAG
 agctaac  putative branch site (score: 2)
                                       tctcctt  putative PPT
        aaaaataattga  TA-rich tract