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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG

Basic information

species Arabidopsis thaliana
transcript AT1G31360.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 3
gtaagtgactttctgtattttctgatcctaaatatg-attcttgtgtccgcgtt--tgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG
          | ||||     ||   |||| || |  || |        ||  |  ||||   | ||  ||| || || |||   || |  | |      |  | || |||| || || || || ||||  ||||||||||| ||||| || ||||| || ||||| |||||||| || ||||||||||| || ||| | |||| || ||                                               
--------ggtactgttgagcctagccctagatgtacataccacaacttgctatactgcttacagtttcttt-attttgcatccttttaagcatattgcaacct-tccagATAATCAATGCCATCATGAGTGGAAGAGATGTACTGGTCATAATGGCTGCTGGTGGAGGGAAGAGCCTCTGCTATCAACTACCTGCTGTACTTCATGATG-----------------------------------------------

upper sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 3
gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG
   |       || |      |  |  |    |  |  |  |       | | |  || |  ||| | | || || ||    || |   |    ||  |   |  |||| ||||| ||  | ||||  ||||||||||| ||||| || |||||||| ||||| ||||||||||| || || || || |||||| | ||||||| ||                                               
---aactttagtcaggggaaccaaacacccccttcgtattgtacagtttcctcttgtacagtttcctctcattttgcacccattaaacat----attctgcttatagATAATTAATGCAGTCATGAGTGGAAGAGATGTTCTGGTCATAATGGCAGCTGGTGGAGGGAAGAGTCTATGTTACCAGCTCCCAGCTGTACTTCGTGATG-----------------------------------------------

upper sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 2
gtaagtgactttctgtattttctgatcctaaat-atgattcttgtgtccgcgtttgctagaaattcgtttgatgttcca---tttgttgattctttg-aatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG
               || |    |    ||  | |||||| || | |  |  | |    | | |  |  |  ||    |   |||||| |    | | ||||        |||| ||||| || || ||||  ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||||| || ||||| ||| | ||||||| ||                                               
-----------atcataatcaagggctttagtttatgattttttt-ttggtatatatagggattgtgacttttgggtaaaactttgttaacaagtagtaatgtcgatgacagATAATTAATGCCATTATGAGTGGAAGAGATGTTCTGGTGATTATGGCTGCAGGTGGTGGCAAGAGCCTCTGCTACCAGCTTCCTGCTGTTCTTCGTGATG-----------------------------------------------

upper sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 2
---gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG
   || |   | ||| ||| |  | ||| |    | |   ||      |    |||  ||| | | | |||   || |  |       | || || |||  | |  | ||||||| || ||  | ||||  ||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| || || ||||||||||| ||||||| ||                                               
attgttataaaatttatgtttaatttgaac----acactgtttcaaaattt-tgttccctacacaat-gttcattgatttacaaac--aatcattcaat--ttttaccagATTATAAATGCAGTCATGAGTGGAAGGGATGTTCTGGTGATCATGGCTGCAGGTGGTGGTAAGAGCCTTTGTTACCAGCTTCCAGCTATACTTCGTGATG-----------------------------------------------

upper sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S93_66V6.1 (Physcomitrella patens), 3'ss of exon 3
--gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG
  |||| | |  |  |   | |   | | ||  ||||     |||||| |  | || |      |   ||  |  |  |  | ||  ||| ||||  ||   || || ||| || || ||  ||||||  ||||| |||||  | || || |||||||||||||||||||||||||||||||| || || ||||||||| | |||  ||                                               
ttgtaaatcaagtgatagctatcacggtacttgatat-----ttgtgtacttggtttccgcttttaaattaaacttaaccgtggtatattttttggctg---tgcca-gATCATAAATGCAGTAATGAGTGGAAGGGATGTAATCGTAATAATGGCAGCAGGTGGTGGGAAGAGTCTTTGCTACCAGCTCCCAGCTATGTTACGTACTG-----------------------------------------------

upper sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ22718 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG
                                | |  ||||   ||   | |||  |     ||  ||   |||   |||||||      |||  || |   |  ||||| | |||||  | ||||     |   ||||  | ||  | ||||| ||||| || ||||||||||| |||||||| ||||||||| | || || |   |                                              
-------------------------------gtctcgttctccagtttccttttttttt---ttttttgtgtgtgtgatttgtt-----cttgcttgctccttgcagATTGTAAACGCGCTGATGAGTAACAAGAATGTGGTCGTTGTTATGGCGGCAGGAGGAGGGAAGAGTCTGTGCTATCAGCTTCCAGCTCTTCTCCG-GCCAG----------------------------------------------

upper sequence: AT1G31360.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ11578 (Selaginella moellendorffii), 3'ss of exon 1
gtaagtgactttctgtattttctgatcctaaatatgattcttgtgtccgcgtttgctagaaattcgtttgatgttccatttgttgattctttgaatgatatgtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG
                  | ||     | |  |    || || |||     ||| ||     || || || |||   |||||||      |||  || |   |  ||||| | |||||  | ||||     |   ||||  | ||  | ||||| ||||| || ||||||||||| |||||||| ||||||||| | || || |   |                                              
-----------------gtctcgttctccagtttccttttttttgttt---ttttctttccttttgtgtg-tgtgtgatttgtt-----cttgcttgctccttgcagATTGTAAACGCGCTGATGAGTAACAAGAATGTGGTCGTTGTTATGGCGGCAGGAGGGGGGAAGAGTCTGTGCTATCAGCTTCCAGCTCTTCTCCG-GCCAG----------------------------------------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaagattattaacgctataatgacgggaagagatgtcctggtgatcatggcagCAGGTGGTGGGAAGAGTCTTTGCTATCAACTTCCAGCTATGCTTCGTGGTGGGACAACTCTTGTTGTCAGTCCTCTACTTTCACTGATTCAGGATCAG
        tattaac  putative branch site (score: 1)
      attattaa  TA-rich tract