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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtttcgatttccatttagtttttttgagggatttctttttatgtcattcgctctgtttttttttcgctgtgttgataatttctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG

Basic information

species Arabidopsis thaliana
transcript AT1G52360.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------gtattgtttcgatttccatttagtttttttgagggatttctttttatgtcat------tcgctctgtttt-----tttttcgctgtgttga-taatttctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG
                                                        || ||| || | ||| ||   |  |||| || |   | | ||| | ||  |       | ||   |||||     ||||| || |  |  | | |||| ||| |||  | ||||   ||| ||||  | |||||||| || |||||||| || ||||||||||| ||||| |||||||||||
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgt-ttgattagcttttcagcgaccttttatgtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaa-cagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------gtattgtttcgatttccatttagtttttttgagggatttctttttatgtcattc-----------gctctgtttttttttcgctgtgttgataatttctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG
                                                       |  ||| ||   ||  ||   || |||| || |   |   ||| | || ||              | | | |   ||| | ||||     |    || ||| |||  | ||||   ||| ||||  | || ||||| || |||||||| || ||||||||||| ||||| |||||||||||
gtactcttcttctgtcatttgatttgaggtttattttggtttggttgctgagaatggtttgattaccttgtcagcgagattttatgtgatttagatttctctgccaccaagcatggcagagttttataactttctggctgctcgaactgattgttttcgtaatatttgaa-cagCGAAAGCTTGCCCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 2
------gtattgtttcgatttccatttagtttttttgagggatttctttttatgtcattcgctctgtttttttttcgctgtgttgata--attt--ctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG
       | ||  |||  |||  ||| | || | |  |  ||||   | |    |  ||   |  ||||  |  | |  || |||||   ||||  |||   ||   |||||| |||||| ||| | |||||||| || |||||||| |||||||||||||| |||||  | || |||||
gtacgcttgtttattccctttgaattgatttctatgtacagattagatctcgatttgtttaat--gtttaatagttgaagtattgatgtcattttgcttctggtaaattttggatcagAGGAAACTCGCGCAAAGATCAGAGAGAGTAAAATCTGTGGATCTGCATCCATCTGAGCCATG

upper sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
gtattgtttcgatttccat-ttagtttttttgagggatttctttttatgtcattcgctctgtttttttttcgctgtgttgataatttctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG
  ||||  |   | ||    | ||   | |||  |  | |    |  ||   ||    |||      |||   |||| ||||| |        | | || ||  ||||| | ||| | ||||||||||||||| ||||||| | ||||||||||||||| ||||| |||||
-aattgaattcttctcatcatcagcagtgttgcagagtgtgaagtggtgattttatgcctgcacaggttt---tgtgctgatagtgct-----gattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctctgtttttttttcgctgtgttgataatttctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG
                     tgttgat  putative branch site (score: 4)
                                        ttgttttt  putative PPT
                       ttgataatttcttt  TA-rich tract