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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtctactacatcaaatatagaaacatgtgatcttctacattatccttcatctttatgcttttctaatcaataaactctgtttactcttccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG

Basic information

species Arabidopsis thaliana
transcript AT3G21180.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
gttagtctactacatcaaatatagaaacatgtgatcttctacattatccttcatctttatgcttttctaatcaataaactctgtttactcttccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG
             |   ||  | ||      | |||||  ||| |       |  || |    |  || | || | | |  | | ||   ||| |||| || || ||||| ||||| || ||||| || || || || || || ||||||||||||||||| |||||||| || |||||||||||||| || || |
----------gttagggaagttggagcttaataatcttacacaat------taatttaacaaatgccttaacatttatccatatgtaacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 27
--gttagtctactacatcaaatatagaaacatgtgatcttctacattatccttcatctttatgc--ttttctaatcaataaactctgtttactct-tccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG
   || | || | |  |   ||  ||| | |  |    |||      |  |  ||     || |       ||    | |      ||| ||| | |  |||||||||| |||||||||||||| ||||| || ||||||||||| || || |||||||| ||||| ||||| || || ||| |||| |||||||| || |
gattttggcttc-atcttggattaagagataaatttatttcatggagacacaacacgagcattcagcagattatctgagatgtgtagttcactttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAGCTCACTGTTAATGTAGCTGCTCTTGTAATAAATGTTGTGGCCG

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
-----gttagtctactacatcaaatatagaaacatgtgatcttct---acattatcctt-catctttatgcttttctaatcaataaactctgtttactcttccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG
      ||  |||  |  ||  |  | ||| | || |  |        |||  |  |   |||   || | || |||||    |  | |   | |  |  |  |||||||||| |||||||||||||| ||||| || ||||||||||| || || ||||| || ||||| |||||||| || ||| |||| ||||| || ||||
cacggattgatct--tggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagt---tctctttgtgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 28
----gttagtctactacatcaaatatagaaacatgtgatcttctacatt-atccttcatctttatgcttttctaatcaataaactctgtttactcttccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG
     || |  ||       |  |||   | || |  |  |     ||  ||   ||| | |     || | |||    |  | |   ||   |  |  ||||||| || |||||||| ||||| ||||| || ||||||||||| || || ||||||||||| || |||||||| || ||| |||| |||||||| ||||
gggttttggcttaaggagagatttatttcaccaagacacgtgtcctatggattgctcaacctgtaatttgtgtaagatttctatttcattc-tttgtgtagGTTGTCCGCTGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTCCAGCTTACAGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 25
--gttagtctac-------tacatcaaatatagaaacatgtgatcttctacattatccttcatctttatgcttttctaatcaataaactctgtttactcttccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG
   || |  ||        |  ||   |   ||| |||||| ||| | |  |||     |||||||     || ||| |    |  | |   ||   |  |  ||||||| || |||||||| ||||| ||||| || ||||||||||| || || || ||||| || || |||||||| || ||| |||| |||||||| ||||
gttttggcttaaggagagatttatttcaccaagacacatgt-atcctatggattgc---tcatcttgtaatttgtctgagatgtctatttcattc-tttgtgtagGTTGTCCGATGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTCACGGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: PP1S8_288V6.1 (Physcomitrella patens), 3'ss of exon 27
--------------------------------------------------------------------------gttagtctactacatcaaatatagaaacatgtgatcttctacattatccttcatctttatgcttttctaat-caataaactctg-----tttactctt----ccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG
                                                                          ||     |   || ||   ||  |||     | |  || ||  | ||  ||  |   | | || |    ||  | | |  ||||     | |  |||     | ||||||| || ||||| || || || ||||| ||||||||||| ||||||||||| || || ||||| |||||| | || ||||  |||||| |||| ||| 
gttcgattcgatcagtcattcctctaatctagagttcctcatgttcagctttgtaacccaatcgcatagccgttgtatactttgcacgtccgttagtgaaggtacttactttttagttaatagttagtaggttttctctggggatgtacttatgtctgacgtttctgttctgatcgctagGTTGTGCGCTGGGGACGATCCGTCTATGCCAACATTCAGAAGTTCATACAATTTCAACTGACTGTCAATGTTACGGCTCTTACCATCAATTTTGTCGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatccttcatctttatgcttttctaatcaataaactctgtttactcttccagGTTGTTCGTTGGGGCCGTTCTGTGTATGCTAACATTCAGAAATTCATACAATTCCAGCTTACTGTGAATGTTGCCGCACTTATAATCAATGTTGTAGCAG
                       ttctaat  putative branch site (score: 2)
                                     ctctgtttactcttcc  putative PPT
                     ttttctaatcaataaa  TA-rich tract