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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgatgtttcatgttttatacaatatatcctgatagctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG

Basic information

species Arabidopsis thaliana
transcript AT2G43020.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
--------------------------gtttgtgatgtttcatgttttata--caatatatcctgatagctgattttg-atatctctttctcacggtgtggttct----tggtgttt----agGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
                            |||| ||| |  | |||  ||   |  |  |     ||  |  || |||   |  |||| | ||| | ||  ||||    |||| | |    ||||| |  | || || || |||||||| || |||||  || |||||||||||||||| ||||| |||||||||||||| || ||||| ||
gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaagtgcatttcaaatgttgtgaaattcttccccactg-gttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG

upper sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G000052_T01 (Zea mays), 3'ss of exon 3
-------------------------------------gtttgtgatgtttcatgttttatacaatatatcctgatagctgattttgatat-ctctttctca-cggtgtggttcttggtg------tttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
                                     ||| |||   | | |    ||| |   | |||     | ||  |  |   ||  | |||| | | |  | |   | |  |||      |  |||||||  ||||||| |||||||| || ||||||||  ||||||||||||| ||||| ||||| ||||| || ||| | || ||||| ||
gtgattttcggtgttattttttttgtcatgtttcggtgttggtgtaatgttacaacttacaacctgtatttatttggcgaaaatgagtagaccctttgtgatccttttcaatttgtgtgacacattccagGTTATTCTACTGGAATCCCGTGATAGGATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCGGTCGATTTGGGAGCATCTTG

upper sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G396856_T02 (Zea mays), 3'ss of exon 3
-----------------------------------gtttgtgatgtt-tcatgttttatacaatatatcctgatagctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
                                   ||| ||||||   |||| ||| ||   | | |    || || |  |||||  ||   ||||    | | || | | |    || |||||||  | ||||| || ||||| |||||||||||  ||||||||||||| ||||| ||||| ||||| || ||| | || ||||| ||
gtatttttcagtgttacttcttgtcatgtttgtgtgttggtgatgcaatcatattt-atttgagaaaaatggaaagatccttttgtgatgcatttcggttgctctgatgcat----ttcagGTTATTCTTCTGGAATCTCGTGATAGAATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCAGTCGATTTGGGAGCATCTTG

upper sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G14620.1 (Glycine max), 3'ss of exon 2
-----------gtttgtgatgttt-----catgttttatacaat---atatcctgatagctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
            |   || ||||      ||  | |||| ||||     ||    | || |||       |    || ||     | |  || |||||    ||||| |  |  | |||||  | || ||||||||||| ||| |||||||||||||||||||||||||||||||||| || || ||||||| 
gaaacttgaacctacatgttgttcgaagccaattattatgcaattatgcatttccagagttgagggactaaatggttcctttgtttataatttttggt---caGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT-

upper sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G45140.1 (Glycine max), 3'ss of exon 2
--------gtttgtgatgtttcatgttttataca-atatatcctgata-gctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
        |||| || | |  | | ||  | | | ||| || ||  |   ||  ||    ||| | |||       |     | ||  |  | |||||||  | || || || || || |||  |||||| ||| |||||||||||||||||||||| ||||||||||| ||||||||||| ||
gtattaaagtttttgttttcccctcttgaacatacatacatacttttgtacttgttaatttatttatttgcataaattgtacttttatttgtcagGTTATTCTTCTAGAATCACGGGAAAGACCTGGTGGCCGAATTCACACTGATTACTCATTTGGCTTTCCTGTTGACCTTGGTGCATCGTG

upper sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G41570.3 (Glycine max), 3'ss of exon 2
-----------gtttgtgatgtttcatgtt------ttatacaatatatcctg-atagctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
           | ||||| ||||   || |      || || | |  | | |  || ||     ||  ||  |  | |  | | | |  || |||||    ||||| |  |  | |||||  | || ||||||||||| ||| ||||||||||||||||||||||||||||||| ||  | || ||||||||
taactttcaaggattgtggtgttgtgtgctgcttaattgtaaacttgaacttacatggcctcaattattaaatggtgcctatgttttaatttttggt---cagGTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATG

upper sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G03610.2 (Glycine max), 3'ss of exon 2
--------gtttgtgatgtttcatgttttataca-atatatcctgatagctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
        |||| |    ||||   | ||  ||| | |||   |  ||  || |  |  ||| | ||| |     |     | ||  |  | |||||||  | || || || || || ||| ||||||| ||| |||||||||| ||||||||||| ||||||||||| || |||||||| ||
gtattaaagtttttttgttttcccctcttgaacatacatacttttgtacttgttaatt-tatttatttgtataaattgtacttttatttgtcagGTTATTCTTCTAGAATCACGAGAAAGACTTGGTGGCCGAATTCACACTGACTACTCATTTGGCTTTCCTGTTGACCTGGGTGCATCGTG

upper sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
------------gtttgtgatgtttcatgttttatacaatatatcctgat---agctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
              |  || | | |  |||||  ||   |   |  ||||   |  |   |||| ||| |   |  |         ||  |  | |||||||| |  |  |||| || ||||| |||||||||||||| ||||| ||||||||||||||||||||||||||||| || || ||||||||
tagccatagataaatattgctctgttctgtttgctattttcgtttttgatcagatttctgtttgctatattcctaactatacacactttatcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctgatagctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATG
                           ttctcac  putative branch site (score: 2)
                                         ttctt  putative PPT
             attttgatat  TA-rich tract