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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtagtctcaaatgttcattacaaaaacatagatctatacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC

Basic information

species Arabidopsis thaliana
transcript AT1G13000.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G162881_T01 (Zea mays), 3'ss of exon 3
gtacgtagtctcaaatgttcattacaaaaacatagatctatacagtactcttgattccatgtaatattct-tacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
||| | |||  |||   || ||||  |  |  |   | |  | | | || ||  |  |||||||| |  | | ||||||| | || || |||||  | ||||||||||| ||||||||||| || || |||||||||||||||                                 
gtagg-agtg-caatcatttatta-gattattttcttatcgaaatttctgtttttcacatgtaatctgatatgcagGTTTGTTGAAATAATGGCAACTGTATTCTCAAGGGATGCATGGCGCTGTGTATGGCATATGATTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 10
gtacgtagtctcaaatgt-----tcatt-aca------aaaacatagatctatacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
||| ||||   |  ||||     ||||| |||      |    | ||  ||  |    | | |    ||  ||| ||||   | ||||||| | ||||||||||||||||| |||||||||||||||||||| || ||||||||||||||||||                                 
gtaagtagctgctgatgtatttatcatttacattatctagtttacaggactgcatctcattgtgctatcactgttatataaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCAAGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G37770.1 (Glycine max), 3'ss of exon 10
gtacgtagt--ctcaaatgttcattacaaaaacataga-tctat---acagta-ctcttgattcca----tgt-aatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
||| ||||   || |  | || || |  | |  ||| | ||||    || | | ||| |  | | |    ||| ||||    | ||||||| | ||||||||||||||||| |||||  ||||||||||||| || ||||||||||||||||||                                 
gtaagtagctgcttatgtatttatcattacattatatagtctacaagactgcatctcattgtgctagcactgttaatacaaatgcagGTTTGTTGAGATTATGGCTCCAGTGTTCTCGCGAGATGCATGGCGCTGTGTGTGGCATATGATTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G14040.1 (Glycine max), 3'ss of exon 10
gtacgtagtc-tcaaatgttcattacaaaaacatagatctatacagtactcttgattccat-gtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
||| | |    |  ||   | |||     |  ||  | | ||||   ||| |  || | ||  |  ||| | | ||| ||| | ||||||||||||||||| || ||| |||||||||||||||| || |||||||||||||||                                 
gtaagcatcagttgaagcattatttttgtattatccacccataccaaactgt--atccaattatgttatgcatgcagATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCGTTGTGTCTGGCATATGATTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 10
gtacgtagtc-tcaaatgttcattacaaaaacatagatctatacagtactcttgattccat-gtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
||| | |    |  ||   | |||        ||  | | ||||   ||| |  || | ||  |  |||   | ||| ||| | ||||||||||||||||| || ||| |||||||||||| ||| ||||||||||||||||||                                 
gtaagcatcagttgaagcattatttttgtcttatctacccataccaaactgt--atccaattatgttatgtatgcagATTTGTTGAGATTATGGCTCCAGTGTTTTCACGAGATGCATGGCATTGTGTGTGGCATATGATTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G14050.1 (Glycine max), 3'ss of exon 8
gtacgta---gtctcaaatgttcattacaaaaacatagatctatacagtactcttgattccatg----taatattct------tacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
||| |||   ||  || || ||  ||         || |    |     |   ||  ||   ||     |  |||||      | ||||||| | ||||||||||||||||| || ||| || |||||||||| || ||||||||||||||||||                                 
gtaagtaactgttacagatttttttttgggggggttacaatattttcccatctttagttagctgattccaccattctgtaacatgcagGTTTGTTGAGATTATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA05G30850.1 (Glycine max), 3'ss of exon 8
-----------gtacgtagtctcaaatgttcatta-caaaaacatagatctatacagtactc------ttgattccat-gtaatatt-cttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
            ||   | | |  | | ||  ||  ||     | |    | | |  |  |        ||||||||   |  | |  | | ||||||| | ||||| ||||||||||| || ||| || |||||||||| || ||||||||||||||||||                                 
gtaagtaactgttaaagaatttttatttttttttggcaggggtacaatattttcccatctttaatgagctgattccaccattctgtaacatgcagGTTTGTTGAGATAATGGCTCCAGTGTTTTCACGAAATGCATGGCGCTGTGTGTGGCATATGATTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------gtacgtagtctcaaatgttcattacaaaaacatagatct-atacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
                          |    | || ||    | |||      |  || |||   | |||  | | ||  ||     |  |     | ||||||| | ||||| |||||||| ||||| || |||||||||||||| || |||||||||||| |||||                                 
ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttt-ccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------------gtacgtagtctcaaatgttcattacaaaaacatagatct-atacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
                                      |    | || ||    | |||      |  || |||   | |||  | | ||  ||     |  |     | ||||||| | ||||| |||||||| ||||| || |||||||||||||| || |||||||||||| |||||                                 
gtatgaaaagctttgagcaatactattgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttt-ccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
-------------------------------------gtacgtagtctcaaatgttcattacaaaaacatagatct-atacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
                                     ||    | || ||    | |||      |  || |||   | |||  | | ||  ||   | |  |     | ||||||| | ||||| |||||||| ||||| || |||||||||||||| || |||||||||||| |||||                                 
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttt-tcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG---------------------------------

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ06933 (Selaginella moellendorffii), 3'ss of exon 9
gtacgtagtctcaaatgttcattacaaaaacatagatctatacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
    |||          |||| |      |||||||| | ||      ||||  |    |      ||||  ||| ||| | ||||| |||||||| || || || ||  |||| ||| | ||||||||||||||||| || ||||||||||| ||||||||||| || || |||
----gtaagtcttggctttcact---tggacatagatttctat----ttcttagtggtgt------ttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC

upper sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ09147 (Selaginella moellendorffii), 3'ss of exon 6
gtacgtagtctcaaatgttcattacaaaaacatagatctatacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
    |||          |||| |      |||||||| | ||      ||||  |    |      ||||  ||| ||| | ||||| |||||||| || || || ||  |||| ||| | ||||||||||||||||| || ||||||||||| ||||||||||| || || |||
----gtaagtcttggctttcact---tggacatagatttctat----ttcttagtgttgt------ttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacaaaaacatagatctatacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC
                            tcttgat  putative branch site (score: 4)
                                            tattctt  putative PPT
                                      atgtaatattctta  TA-rich tract