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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattttttactctttggtgtattctgtttcctcttattccattccactcgcatactcatcctgattcttgtcctcacatctaaacagGTTGATATTGCGATCCCAGAAGTCTTCATTGGAGGGTTATTAGGTGCCATGCTTATATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTG

Basic information

species Arabidopsis thaliana
transcript AT1G16780.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 11
gtacattttttactctttggtgtattctgtttcctcttattccattccactcgcatactcatcctgattcttgtcctcacatctaaacagGTTGATATTGCGATCCCAGAAGTCTTCATTGGAGGGTTATTAGGTGCCATGCTTATATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTG
|||  ||| |||||       | |   |  || || |   | | |   ||    ||| |  || ||  |  ||   |          |||||||| || || |||||||| || ||  |||| || ||| | ||| | |||||||||||||||||||| || ||||||||| | || |||||  ||||||
gtat-tttattacttagacacgcaaaatacttactttctgtgcttataacatatataatggtcttgtgtaatggatt---------gcagGTTGACATAGCAATCCCAGAGGTTTTTGTTGGTGGTTTACTTGGTTCAATGCTTATATTCCTGTTTAGTGCATGGGCTTGTTCTGCTGTTGGCAGAACTG

upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 11
gtacattttttactctttggtgtattctgtttcctcttattccattccactcgcatactcatcctgattc-ttgtcctcacatctaaacagGTTGATATTGCGATCCCAGAAGTCTTCATTGGAGGGTTATTAGGTGCCATGCTTATATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTG
        | | |  |  | ||| | || |  ||   |     | |  |||    | |||||  | | |  | || | || ||     |||||||| || ||  |||| ||  | ||  |||| || ||||||||  | |||||||||||||||||||| || ||||||||| ||||||||||   |||||
-------gtatgcagtacg-tgt-tgctatgcccatgtggaatactgaacttttgtgctcatattcagtgatcgtacaca-attgttgcagGTTGACATAGCAGTCCCGGAGATTTTTGTTGGTGGTTTATTAGGCTCGATGCTTATATTCCTGTTTAGTGCATGGGCTTGTTCAGCAGTTGGCAAAACTG

upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
-----gtacattttttactctttggtgtattctg---tttcctcttattccattccactcgcatactcatcctgattcttgtcctcacatctaa--acagGTTGATATTGCGATCCCAGAAGTCTTCATTGGAGGGTTATTAGGTGCCATGCTTATATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTG
       |||| ||| | ||     | ||  | |   | |  |  | |  |||   | |    |  |  | || | |     | |   ||  ||   |||||||||||||| || || ||||| ||| |||| |||||  ||||| |||||||||||||  | ||||| |||||||| ||| | || |||||  ||||||
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG

upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 11
--gtacattttttactctttggtgta-ttctgtttcctcttattccattccactcgcatac-----tcatcctgattcttgtcctcacatctaa--acagGTTGATATTGCGATCCCAGAAGTCTTCATTGGAGGGTTATTAGGTGCCATGCTTATATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTG
    |||| ||| | ||  |    || || |  || || |||||   |  ||   |  | |     |  | || | |     | |   ||  |    |||||||||||||| || || ||||| ||| |||| ||| |  ||||| |||||||||||||  | ||||| |||||||| ||||| || |||||  ||||||
ctaaacatatttaagtcactcccctaattattattactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgagttgcagGTTGATATTGCTATTCCCGAAGTTTTCGTTGGTGGGCTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTGCTGCTGTTGGCAGAACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattccattccactcgcatactcatcctgattcttgtcctcacatctaaacagGTTGATATTGCGATCCCAGAAGTCTTCATTGGAGGGTTATTAGGTGCCATGCTTATATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTG
                                      tcctcac  putative branch site (score: 2)
                                             atctaaa  TA-rich tract