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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcactgtcttgttattatcggggtttggtttcgcaaactaatatttacttgagatagctattaacttgcattttcatgattgtggcagATTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCA

Basic information

species Arabidopsis thaliana
transcript AT2G42810.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 10
-------------------------------gttagttcactgtcttgttattatcggg-gtttg-----gtttcgcaaactaat---atttacttgagatagctattaacttgc---attttcatgat--tgtggcagATTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCA
                               ||| |       ||||   |  ||| |   ||||     || ||   | ||  |    ||  ||||  | |    || ||||     |||| | ||||  |||  ||||  |  | || || || |||||||| ||||||||||| |||||  |||||||||| || || || ||||| || |||||||| || ||||| || || ||
gtatgaagtaaaatttgttaaaaagtttccggttggaattggatctttcaaacatctgttatttgtaatagtgtcaagagcttgttttgttcccttggaaaattatttcacttatttgatttgcctgatgatgttccagACCTTGTTGTTCGATCCCATGAAGTGAAAGATGAAGGCTATGAAATTGAACATGATGGAAAGCTTATAACGGTGTTCTCTGCTCCCAATTATTGCGACCA

upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 9
gttagttcactgtcttgttattatcggggtttggtttcgcaaactaatatttacttgaga-tagctattaacttgcattttcatgattg--tggcagATTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCA
              |   |||| | ||   |   || |   ||  |  ||||||  | || |   | | | |||   ||||| | ||    || ||||| |  | |||||||| ||||||||||| ||||||||  ||||  |||||||||| || || || ||||| |||||||||||||| ||||||||||| ||
-------------gtaaatattgtgggatctcaattac-tgaaggagaatttacacgtgaatttttttcatcttttgttttcttaatgagttgccagATCTTATTGTCCGGTCTCATGAAGTAAAGGATGAAGGCCATGAAATTGAACATGATGGAAAGCTTATAACAGTCTTCTCTGCGCCTAATTACTGTGACCA

upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 10
gttagttcactgtcttgttattatcggggtttggtttcgcaaactaatatttacttgagatagcta-ttaacttgcattttcatgattgtggcagATTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCA
          ||| |||   |  || |   ||  ||    || || || | | ||| |   ||    || || |  |||  ||  |||    |||||||  | ||  | || || |||||||| ||||| ||||||||| |||||||||| ||||||||||||||||| || ||||| |||||||||||||| ||
-------gtatgttttgcattagtctgatgtt--ttattaaagcttatttgttctttaatcagtggcttcacataaattacca--attt--acagATTTAGTTGTGAGATCTCACGAAGTAAAGGATGAGGGTTATGAGATTGAACATGAGGGTAAACTCATAACTGTGTTTTCTGCTCCAAATTACTGTGACCA

upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 10
gttagttcactgtcttgttattatcggggtttggtttcgcaaactaatatttacttgagatagcta-ttaacttgcattttcatgattgtggcagATTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCA-
          ||| |||   |  || |   ||  ||    |  || || | | ||| |   ||    || || |  |||  ||  |||    |||||||  | || || || ||||||||||| || || ||||||||| |||||||||| ||||||||||||||||| || ||||| |||||||||||||| || 
--------tatgttttgcattagtctgatgtt--ttattaatgcttatttgttctttaatcagtggcttcacataaattacca--attt--acagaTTTAGTTGTGCGATCTCATGAAGTAAAGGACGAGGGTTATGAGATTGAACATGATGGTAAACTCATAACTGTGTTTTCTGCTCCAAATTACTGTGACCAG

upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 4
gttagttcactgtcttgttattatcggggtttggtttcgcaaactaatatttacttgagatagctattaacttgcattttcatgattgtggcagATTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCA
        |||    |  ||  ||  |  | |  |||   |   | ||||||  ||||  |  || |   | ||||  |   |  || || |||||||  | || || || ||||||||||| |||||||| |||||| |||||||||| || || || || ||||| || ||||| ||||| || ||||||||
------gtacttctctacta--atttgtatattattt---atggtcatattttgttgaagtcactctcttcatgcacatggcttgtt-tgacagATTTAGTTGTGCGATCTCATGAAGTAAAGGATGAAGGCTATGAGATTGAACATGATGGCAAGCTTATTACTGTGTTTTCTGCTCCAAACTATTGTGATCA

upper sequence: AT2G42810.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: PP1S87_139V6.2 (Physcomitrella patens), 3'ss of exon 10
-------gttagttcactgtcttgttattatcggggtttggtttcgcaaactaatatttacttgagatagctattaacttgcattttcatgattgtggcagATTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCA
        | | ||   ||   |  | | |||  ||| |   || | ||   ||||| |   |     |  |  |    ||  |   | |   |||  ||||  |  |||| ||||| ||||| || || ||||| || ||||| || || |||| ||| |||||||| |||||||||||||| |||||||||||||||||
gcatagcatcaattttatgaaatcgt-tgatcatggtgtcaatttgaaaggcaatatgttggttttccatgttgtgtgatggttgaacctttctgtaacagAGCTAGTGGTGCGGTCCCATGAGGTCAAGGATGAGGGCTATGAAGTGGACCATGGCGGCAAACTCATTACTGTCTTCTCTGCACCAAATTACTGTGATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaactaatatttacttgagatagctattaacttgcattttcatgattgtggcagATTTGTTGGTCCGGTCACATGAAGTAAAAGATGAAGGTTATGAGGTTGAACATGACGGTAAACTCATAACTGTCTTCTCTGCGCCAAATTACTGTGATCA
                         tattaac  putative branch site (score: 1)
     taatatttacttga  TA-rich tract