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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtgaaactaaaatcctctctagttacatataaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG

Basic information

species Arabidopsis thaliana
transcript AT1G25350.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 12
----gcaagtgaaactaaaatcctctctagttacatataaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG
    |||| || |||| || |    | |  ||   |||             |  ||  |   | |    || ||    | ||   |  | |||||| | ||||||||  | |||||||| |||||||| |||||||| || ||||| ||||| |||||||  || |||||||||||||| || || ||||||
gtaagcaa-tgcaactgaattgtgttttgcttgtctat-------------ttcctgataaatacacaactcacactctgatg-accatacagTTCACTCCTCATCCACATGCTGGTGATAAGTGGTGCATCTATCCAAGCTATGACTATGCTCACTGCATGGTGGATTCTCTTGAGAACATTACACATTCG

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G048012_T01 (Zea mays), 3'ss of exon 11
gcaagtgaaactaaaatcctctctagttacatataaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG
| |||||| | |      ||   || | |  |  | ||  ||            |    ||    || | ||||| ||   | |  |||||| | ||||||||  | |||||||| || ||||||||||||||||| ||||| ||||| || ||||  || ||||||||||| || || |||||||||
gtaagtgacattgctcaactgattattaattttcacaatata------------taacatcagaactaa-ttgtttatgcacat-acagTTCACCCCTCATCCACATGCTGGTGATAATTGGTGTATCTATCCGAGCTATGACTATGCTCATTGCATGGTGGATTCTCTTGAAAACATCACGCATTCG

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 12
gcaagtgaaactaaaatcctctctagttacatataaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG
| |||||| | |        ||| | | | |    ||    | | | | |  | ||    |       | ||||| |||  | |  |||||| | || |||||  | ||||| |||||||||||| |||||||||| ||||| || || || ||||  || ||||||||||| || || || ||||||
gtaagtgacagtg-------ctcaactgataatctaatttcatgatatataacatcagaact------aattgtttatacacat-acagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 13
gcaagtga--aactaaaatcctct-ctagttacatataaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG
| ||||    ||||  | |  | |  |  | | || |     | ||    |   |  | | ||      ||| |  ||  | ||| |   ||||  | || || ||| | ||||| ||||| |||||||||||||| |||||||||||||| ||||||| ||| |||||||| |||||||| || ||||| 
gtaagtactcaactgcatttttttattgctcaaatttctttgggagataataatttatttcttatgacgtgaatgctt--tctgcatcttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACACTGCATTGTGGATTCTCTAGAGAATATCACACATTCA

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
gcaagtga--aactaaaatcctctctagttacatataaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG
||||||    ||||| | |  | | | | |  |  |   | | ||    |   |  | | ||    | ||| |  ||  | ||| ||  ||||  | || || ||| | ||||| ||||| |||||||||||||| |||||||||||||| || |||| ||| |||||||| |||||||| || ||||| 
gcaagtactcaactacatttttttattgctcaaatttctaggaagataatgattgatttcttatgatgtgaatgctt--tctgcattttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------gcaagtgaaactaaaatcctctctag-ttacatataaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG
                           | | |  |||   | |  |  |||  |||| ||| ||||  |      |     |  || |   |     |   |  | |  | | |||||  | ||||| ||  | ||||| |||||||||||| | ||||| ||||| |||||||| || |||| ||| |||||||||||||| || || ||||| 
gcaagtctgtactcatagacatcttaactatttcaacatgagtagttactaaattacctatcaaaaaaaaaaaaacatgagtagttactaattgatttcact--tcttttgtccagTTTACTCCTCACCCACATGCTGGAGACAAGTGGTGTGTTTATCCAAGTTACGATTATGCTCATTGCATTGTAGATTCTCTTGAGAACATCACTCATTCA

upper sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 13
gcaagtgaaactaaaatcctctctagttacatataaaaagtaggctctctctcttcttttcctg-tctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG
|||||||   ||||  |     |  |||  |  | | |   | | |    |||||  ||    | | |||| | ||  |      | |||||  | ||||||||  |  | || |||||||||||||| ||||| |||||||||||| | || |||| ||| ||||||||||| ||||| || ||||||
gcaagtg---ctaacctttgaacatgttgtagctcacattcaaggtactactctttattcaagggtttgacatttttgttattcgtccagTTTACCCCTCATCCACATTCAGGGGACAAGTGGTGTATTTATCCAAGTTATGATTATTCTCATTGCATTGTGGATTCTCTTGAAAATATTACACATTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG
                                     tgttaat  putative branch site (score: 3)
                                    ttgttaatat  TA-rich tract