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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggaagttaagattgatatctcaattttgtagttaggcagaaccaaagcatgcataggtttgatgtttagtctgttatatagtattgttattttattgattcatttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG

Basic information

species Glycine max
transcript GLYMA17G32170.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
gtgaggaagttaagattgatatctcaattttgtagttaggcagaaccaaagcatgcataggtttgatgtttagtctgttatatagtattgttattttattgattcatttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG
|| |      ||| ||| |  | |  |||    | | |    || |    |  | ||    |   |    |||| || |   ||  | ||||| |   |    || | | | |  ||  | |||||  | |||||||| || |||||  |||| |||||||| ||||| || ||| |||| || || ||||||||||||||||| ||||||||||||||  | |
gtaatttc-ctaatatttacctgttcattaaa-attcatagggatcatttgatttcaaccatacaagcagtagtttgattgcta--aatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG

upper sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G882708_T03 (Zea mays), 3'ss of exon 3
---------------------------gtgaggaagttaagattgatatctcaat----tttgtagtt-aggcagaaccaaagcatgc----ataggtttgatgtttagtctgttatatagta--ttgttatttta--ttgattcatttttctgttgtttt---------cagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG
                               || | |  | ||    |||| |||    |||||   | |   |  ||  |   |||       | |  |    || | ||    |   | ||  ||| || || |   | | |||||||||| || |  |         |||||| |||| ||||| || |||||  |||| |||||||| ||||| |||||  | || || |||||||||||||||||||| |||||||||||  |  | |
gtaaactttgcatgttaatttgtaattcctggggactagaaatgttcatctgaataacatttgtttctcaaaaactactgacatatgttcctgaaagcctagatttcaatcataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G882708_T01 (Zea mays), 3'ss of exon 1
gtgaggaagttaagattgatatctcaattttgtagttaggcagaaccaaagcatgcataggtttgatgtttagtctgttatatagtattgttattttattgattcatttttctgt-tgttttcagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG
           |  | ||| ||    || ||   |  || |   |    |     ||||      ||  || |   |||| |       | ||  | |||  |   || | |||  ||  | |||||| |||| ||||| || |||||  |||| |||||||| ||||| |||||  | || || |||||||||||||||||||| |||||||||||  |  | |
-----------actactgacat----atgttcctgaaagcctagatttcaat---cataaaagcaatactttgatagttaaa-------ggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
---------------------------------------------gtgaggaagttaagattgatatctca----attttgtagttaggcagaaccaaagcatgcat----aggtttgatgtttagtctgttatatagta--ttgttatttta--ttgattcatttttctgttgtttt---------cagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG
                                              |    | ||| |  |  ||| ||      ||||  |  | |   |  ||  |   |||  |    | |  | |  || | ||    |   | ||  ||| ||  | |   | | |||||||||| ||    |         |||||| |||| ||||| || |||||  |||| |||||||| ||||| || ||| | || || |||||||| ||||||||||| |||||||||||  |  | |
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgaggaagttaagattgatatctcaattttgtagttaggcagaaccaaagcatgcataggtttgatgtttagtctgttatatagtattgttattttattgattcatttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG
    |  | ||    |||||||     || | | |||  |  |       || || |   ||    | || |  ||      | |||||| |||    ||| ||  | ||| || || |  |||||||| || |||||||| ||||| || |||||||| |||||||| || ||||| || || || || ||||| || ||||| |||||||||||  || |||
----gtgaattttctttgatatgctcgttgtattgttttgatgg--tggtgcctgaaagtgtcctcttttaaacct------tggtattgatat----ttgtttgctgtttttgatgata-cagTATCTGTCCAATGCTGCTCTTGCTCGTACAAGTGTGGCAAGTACTACTGTATTGTCTTCAACCTCGGGACTGTTTACTCTGTTCATTGGTGTATTTTTGG

upper sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
gtgaggaagttaagattgatatctcaattttgtagttaggcagaaccaaagcatgcataggtttgatgtttagtctgttatatagtattgttattttattgattcatttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG
                ||   | |     || || ||   ||     |   || |   | ||   ||||  ||    | | | ||      || || ||||      |||||| || ||| |||||| | ||||||||||| ||||| || ||||||||||| |||||||| ||  |||| || |||||||||||||||||||| ||||||||||  ||| |||
----------------tgtcttttagggattcta-ttttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagag----tacttgattg---tgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtctgttatatagtattgttattttattgattcatttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG
                           tattgat  putative branch site (score: 3)
                                     tttttctgttgttttc  putative PPT
      tgttatatagtattgt  TA-rich tract