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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacttttataaaattccatcgtaccaatatgaagtctagtgactaattctgaatatttatcaccgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG

Basic information

species Arabidopsis thaliana
transcript AT1G47560.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
gtactacttttataa-aattccatcgtaccaatatgaagtctagtgactaattctgaatatttatcaccgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG
|||    |  | ||  |||| ||   ||   |  |  |  |   | | |  |||| || ||   ||        ||     ||||||||||| ||  |||||||||||||||||||| || ||||||||||||| |||||||| || ||| | ||     | |||
gtaaatttagtctagtaattgcagattatttaactttaaccggatcattt-ttctcaacataattccttttgcttt-----cagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG

upper sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 11
gtactacttttataaaattcc--atcgtaccaatatgaagt-ctagtgact--aattctgaatatttatc---accgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG
||| |   |  ||||| ||    ||  ||    | | ||||  |||  | |  |||  |  || || |        || |  | ||||||| | || ||| |||| ||||| || |||||||||||| ||||||| ||||| |||||||| || ||| || | |||||||||
gtattctctgcataaatttatgaattataaacttttaaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG

upper sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 11
-----gtactacttttataaaattccatcgt-----accaatatgaagtctagtg--actaattctgaatatttatc-accgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG
        |||  || ||    ||  ||  |     |  |   |||  | | | |  |  |||||| | | ||  |  | | | | | |||||||| |||| ||| |||||||||| |||||||||||| | ||||| |||||||| || |||||||| ||| | ||||| ||||||
gtattcccctatcttcatgttgttttattcttgataattatcttgacatttggggctaggaattctaatttttgctggatcacttgtattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG

upper sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ12163 (Selaginella moellendorffii), 3'ss of exon 11
gtactacttttataaaattccatcgtaccaatatgaagtctagtgactaattctgaatatttatcaccgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG
                                  | || ||  |   |  |  ||     ||         |  ||    ||||| || |||||||| ||||| ||||| || ||||| || | |||||| ||||||||||||||| |  |||| || ||||||
----------------------------------gtagccttttcgttt-tgttgttcgcttgctg--attttcttcttgcagAGGGGTCAGCTGAAAAGGCCCGACCACGCAGATTTACGATTCAAATGTAGAACATATGCTCGTTTGCTGCAGCACTTAAAG

upper sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 11
gtactacttttataaaattccatcgtaccaatatgaagtctagtgactaattctgaatatttatcaccgcatcttttaa--acagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG
                                        |||    |   | |   | ||      |  || || |     ||||| || |||||||| ||||| ||||| || ||||| || | |||||| ||||||||||||||| |  |||| || ||||||
---------------------------------------gtagccttttcgttttggtgttcgcttgctgattttcttcttgcagAGGGGTCAGCTGAAAAGGCCCGACCACGCAGATTTACGATTCAAATGTAGAACATATGCTCGTTTGCTGCAGCACTTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatatgaagtctagtgactaattctgaatatttatcaccgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG
                gactaat  putative branch site (score: 2)
                                         catctttt  putative PPT
                   taattctgaatattta  TA-rich tract