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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT

Basic information

species Glycine max
transcript GLYMA20G16100.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g36950.3 (Oryza sativa), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacct-ttagcagctatggtctaattaaaggcaataataa-tgattaaatgtttggtggggttt-gttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
                                                                             |  || ||| |    |  |   || | |  |||    ||    | |   | | |||    | | || |   | |||| ||  ||  |    |||  |||||||||| || ||||| ||| | || || ||||| ||||| |||||||||||||||||||| || || || || |||||||| ||||||    | ||||   
---------------------------------------------------------------------------atatttctagcaac---tctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAGGTACCATTGATCTTCA

upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g36950.2 (Oryza sativa), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacct-ttagcagctatggtctaattaaaggcaataataa-tgattaaatgtttggtggggttt-gttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
                                                                             |  || ||| |    |  |   || | |  |||    ||    | |   | | |||    | | || |   | |||| ||  ||  |    |||  |||||||||| || ||||| ||| | || || ||||| ||||| |||||||||||||||||||| || || || || |||||||| |||                
---------------------------------------------------------------------------atatttctagcaac---tctgataatttttactactcgctaattacgagtttattattttgtgaattattgcctaattacatacttatttctttttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAGAAGTGCCCCGGCGAGTCGCGCTTCCCTGCACAG----------------

upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G860590_T01 (Zea mays), 3'ss of exon 2
------------gtatgtgtgcgtatattttcttttttttagtctgttgttg-catcactttaatttgatgaa---aatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
             |||   | | | || | |  | ||||  || | |  |   ||||| | | | | ||| |     |||| | || ||       |  |||      ||   |  ||  |  | | | | |   |||   | |||  ||||        |||   | |  || |  ||||       ||||||||||| || ||||||||||| || |||||| | ||||||||||||||||||||||| || || || || ||||||||||||                
gtgaggtccaaactatacctac-tctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatc---tttatctttcaatcatgcttgtggttacta-aatataaaaaaagaagggggaaatttctcatcgtcta-tgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG----------------

upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G860590_T02 (Zea mays), 3'ss of exon 2
-------gtatgtgtgcgtatattttcttttttttagtctgttgttg-catcactttaatttgatgaa---aatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
        |||   | | | || | |  | ||||  || | |  |   ||||| | | | | ||| |     |||| | || ||       |  |||      ||   |  ||  |  | | | | |   |||   | |||  ||||        |||   | |  || |  ||||       ||||||||||| || ||||||||||| || |||||| | ||||||||||||||||||||||| || || || || ||||||||||||                
gtccaaactatacctac-tctactctactcttttgtgtttatcatcatcatcattattactcgatcagtcgtatgcatatgattccatcatttcagcatc---tttatctttcaatcatgcttgtggttacta-aatataaaaaaagaagggggaaatttctcatcgtcta-tgggacgaacgcagGCTGCAAGCTTCGGAGGATCCAACATCGATCCAGCAGCTTGGGAGGACAAGAAGTGCCCCGGCGAGTCCCGCTTCCCTGCTCAG----------------

upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagct-atggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
                        |||   | | ||  |      | | || |       ||| | | | || ||     |   | | |     |     |   ||  |  || ||||  | ||| | |   | | |      |  || |   ||||||      | | ||||||||||||||| ||||||||| | || ||||||||||| |||||||||||||||||||||||||| ||||| || ||||||||||||                
-----------------------gtttgtatttctttctaagaatcataaactctgcagtaattcatgtattcttt----tggggttttctcaaaaatattagattcaatattcagcacttcatgttttggattatgc-----accattacctaatgttatacttg-tatgttcagGCTGCAAGCTTTGGAGGAACAAACATTGATCCAACTGCTTGGGAGGACAAGAAGTGCCCTGGCGAATCACGCTTCCCTGCTCAG----------------

upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: PP1S6_446V6.1 (Physcomitrella patens), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
                                                                       |  |  |   ||    |    |||   ||| |  |   |  || | |  ||  |   ||    |    || |||   ||   |||       | || || | |||||||||| |||||||| ||||| || |||||||| |||||||| |||||||||||||  || |||||  | || ||||| |||                
-----------------------------------------------------------------------tgatacatgacagagcagtagttaccgcatttgctacgcgcttcgaatgtaaag---aagatgaaattatgata-caatctcatgagaaacagtgtctgattagGCTGCAAGCTTTGGAGGCTCCAACATAGATCCAACAGCTTGGGAAGACAAGAAGTGCCGCGGAGAATCAAGATTTCCTGCACAG----------------

upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ35508 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
                                                                                                    |   | ||||  |||   |||    |    ||     |  | | | |   ||||   |   |        | |||||  ||||||||||||| ||||| || ||| |||| || |||||||||||||||||||  || || ||  | ||||| ||||||                
---------------------------------------------------------------------------------------------------gtacgtattacacttaagtgcttctttgccgttgtcctctttgaaact--ctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG----------------

upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ22023 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
                                                                                            | | || | |||| |  |    || |  | ||     | | | |   ||    |   |  ||  ||| | | |  |  | |||||||| |||||||| || || || || ||||| || || ||||| ||||||||||| | ||| |||||||| |||||||| |||                
-------------------------------------------------------------------------------------------gtaaagctacctctctcgc----aggatttgtgac---actcatgttgatggcga--gtccaaacttttgcgtgactc-tacagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG----------------

upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ18285 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
                                                                                            | | || | ||||    |  | || |  | ||       | | |   ||    |  ||  ||  ||| | | |  |  | |||||||| |||||||| || || || || ||||| || || ||||| ||||||||||| | ||| |||||||| |||||||| |||                
-------------------------------------------------------------------------------------------gtaaagctacctct----ctctcaggatttgtgactc---tcatgttgatggcga--atccaaacttttgcgtgactc-tacagGCTGCGAGTTTTGGGGGCTCAAACATAGATCCTACTGCGTGGGAAGACAAGAAGTGTCGTGGAGAATCTCGGTTCCCTGCACAG----------------

upper sequence: GLYMA20G16100.3 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24245 (Selaginella moellendorffii), 3'ss of exon 2
gtatgtgtgcgtatattttcttttttttagtctgttgttgcatcactttaatttgatgaaaatgcttttgtttttggacatcaagctatggattaggccatctcttttacctttagcagctatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
                                                                                                    |   | ||||  |||    ||    |    ||     |  |   | |   ||||   |   |        | |||||  ||||||||||||| ||||| || ||| |||| || |||||||||||||||||||  || || ||  | ||||| ||||||                
---------------------------------------------------------------------------------------------------gtacgtattacacttaagttcttctttgccgttgtcctctttggaact--ctaaagaatctatcaatccaatccagGCAACAAGTTTTGGAGGCTCCAACATCGATGCAACTGCGTGGGAGGACAAGAAGTGCCGCGGAGAGTCGAGATTCCCAGCTCAG----------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggtctaattaaaggcaataataatgattaaatgtttggtggggtttgttcagGCTGCAAGTTTTGGAGGATCCAATATTGATCCAACGGCTTGGGAGGACAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGGTATATATCATCTCAT
    gtctaat  putative branch site (score: 3)
                                              tttgttc  putative PPT
       taattaaaggcaataa  TA-rich tract