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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttttttgtttttagtgttgatactttcgcaagtttgtttgttttctttgattctttgtttcattatgttatctttatggaactttttagTGTGTCGAGGGAGAAGAGTGATAAGGAGATCATGAGGGAGATTCAAGCTATTATGAGACAGGTTGCTTCAAGTGTTACTTACTTGCCTTGTCTTGATGAA

Basic information

species Arabidopsis thaliana
transcript AT3G25980.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G047143_T03 (Zea mays), 3'ss of exon 4
-----------------------gtcagttttttgtttttagtgttgatactttcgcaagt-----ttgtttgttttctttgatt--ctttgtttcattatgttatc-----tttatggaactttttagTGTGTCGAGGGAGAAGAGTGATAAGGAGATCATGAGGGAGATTCAAGCTATTATGAGACAGGTTGCTTCAAGTGTTACTTACTTGCCTTGTCTTGATGAA
                         ||  ||  ||            |  |  || |||||      ||    || | |  |  |  | | | || |   || || |      || ||    |  | || |     | ||||||||| || |||||||||||||||||||| || || || ||| | ||| | || ||  |  | || ||| | || || || || || 
gtgcgccacacactatcttatcccccatcttcctgcgcgcgacccataaccaatcccaagtagacgctgcgcattgtgtcagcctgccatggcttgacattgatagcgtcgtcttctgatgttcgtcagGGCCATCAAGGAGAAGAGCGACAAGGAGATCATGAGGGAGATCCAGGCCATCATGCGCCAGATCGCGTCTTGCATCACCTACCTCCCCTGCCTCGACGAG

upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G37380.1 (Glycine max), 3'ss of exon 4
-------gtcagttttttgtttttagtgttgatactttcgc---aagtttgtttgttttctttgattctttgtttcattatgttatctttatggaactttttagTGTGTCGAGGGAGAAGAGTGATAAGGAGATCATGAGGGAGATTCAAGCTATTATGAGACAGGTTGCTTCAAGTGTTACTTACTTGCCTTGTCTTGATGAA
         ||||   |  |        |   ||  |||     ||  |   ||| ||| |    ||| || |||   | || | | ||||    |  ||| ||||| |||||||| |||||||| |||||||||||||| ||||| ||||| |||||||| ||| ||||||||||| | ||||| ||||| || || ||||||
ttattcaaacagtgcctaatcccagacttaattatcttcctttaaaactcccttggtttatgcttttcatttttttcatttgcttttttta----atctttcagTGTCTCGAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCCATTATGAGGCAGATTGCTTCAAGTATCACTTATTTGCCATGCCTGGATGAA

upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G01350.1 (Glycine max), 3'ss of exon 4
-gtcagttttttgtttttagtgttga-----tactttcgcaagtttgtttgtt--ttctttgattctttgtttcattatgttatctttatggaactttttagTGTGTCGAGGGAGAAGAGTGATAAGGAGATCATGAGGGAGATTCAAGCTATTATGAGACAGGTTGCTTCAAGTGTTACTTACTTGCCTTGTCTTGATGAA
   ||||   |   |   ||  |  |     | | |||  ||  |  |   ||  |  ||   || ||  ||   |||| |  ||||| |  ||  ||| || || || ||||| |||||||| |||||||||||||| ||||| ||||| |||||||| ||| ||||||||||| | ||||| ||||| || || ||||||
aaacagtgcatgaatcccagactaaattatcttccttcataaactcctcccttggtgtttaagtttttcattcttttatttgttcttttt--aatctttcagAGTCTCAAGGGAAAAGAGTGACAAGGAGATCATGAGAGAGATACAAGCGATTATGAGGCAGATTGCTTCAAGTATCACTTATTTGCCATGCCTGGATGAA

upper sequence: AT3G25980.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0010g02430.t01 (Vitis vinifera), 3'ss of exon 4
--------------------gtcagttttttgtttttagtgttgatactttcgcaagtttgtttgttttctttgattctttgtttcattatgttatctttatggaactttttagTGTGTCGAGGGAGAAGAGTGATAAGGAGATCATGAGGGAGATTCAAGCTATTATGAGACAGGTTGCTTCAAGTGTTACTTACTTGCCTTGTCTTGATGAA
                     | |  |   | ||   | | |  | ||  ||| ||| ||  | ||||||||    | ||||||||||| || | | |||||        | || ||||| |||||||||||||| || ||||| ||||| ||||| ||||| || ||| ||||| ||||||| ||  | ||||| ||||| ||  | ||||||
gtaatattattatctggttttttatctccattttccaaatctcaaaaccctcgaaaggtttctggttttcttca--tgtttgtttcatt-tggtttgtttat--------tcagGGTGTCAAGGGAGAAGAGTGACAAAGAGATTATGAGAGAGATACAAGCAATCATGCGACAGATTGCTTCCAGCATCACTTATTTGCCATGCATCGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgttttctttgattctttgtttcattatgttatctttatggaactttttagTGTGTCGAGGGAGAAGAGTGATAAGGAGATCATGAGGGAGATTCAAGCTATTATGAGACAGGTTGCTTCAAGTGTTACTTACTTGCCTTGTCTTGATGAA
          ctttgat  putative branch site (score: 5)
                                               cttttt  putative PPT
                           attatgttatctttat  TA-rich tract