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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactttaaattttcttgcattcttgttatgagtttttctttcgttagtctctatgcaaaatatatttcagtatgtaaaatatcttctcttctccttggtatattgatcggcagTGCTCAGCATATACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTGCTCTTGCTACAATCGTTGGGTCAG

Basic information

species Arabidopsis thaliana
transcript AT5G01460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 3
gtaatactttaaattttcttgcattcttgttatgagtttttctttcgttagtctctatgc------aaaatatatttcagtatgtaaaatatcttctcttctccttggtatattgatcgg--cagTGCTCAGCATATACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTGCTCTTGCTACAATCGTTGGGTCAG
             | || ||     || ||| | | ||||   || | |||| |   ||       |    ||||||  |  |||     ||  ||  || | |     ||  |  ||    |||||||||||||   | |||| | || | || || || |||||| ||||||||||||| |||||||||||||||||||| ||||||||||| ||||| || |
------------gtctttttctgcactagttgttatttttctgttggctagttttgttgttttcagaggtaatatttttgc-tgttgctcatactccttttttccccacattgtcctcaaaccagTGCTCAGCATTCTCTGCTAGTCCTTCATCAGAGAAAACATGGACCATGCGTACTACCTTTCCAGAATATGTTGTTGCACTTGCTACAATTGTTGGATCTG

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G18160.1 (Glycine max), 3'ss of exon 3
gtaatactttaaattt-tcttgcattcttgttatgagtttttctttcgttagtctctatgcaaaatatatttcagtatgtaaaatatcttctcttctccttggtatattgatcggcagTGCTCAGCATATACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTGCTCTTGCTACAATCGTTGGGTCAG
||  |  | |  | |  | ||   || || || ||  |  || | | |||       |   | ||||| |||     ||   | | || | | ||| ||        |  | |  ||||| |||||||   | |||| | || | || || || |||||| ||||||||||||| |||||||||||||||||||| |||||||| || ||||| || |
gtgtttttctgcactagttttttgtttttcttttggctagttttgttgttg----tcagagataatatttttgctgttgctcattctccttttttcccccattgtcctcaaac--cagTGTTCAGCATTCTCTGCTAGTCCTTCATCAGAGAAAACATGGACCATGCGTACTACCTTTCCAGAATATGTTGTTGCACTTGCTACTATTGTTGGATCTG

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 3
--------gtaatactttaaattt-tcttgcattcttgttatgagtt----tttctttcgttagtctctatgc-----aaaatat---atttcagtatgtaaaatatcttctcttct----ccttggtatattgatc-----ggcagTGCTCAGCATATACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTGCTCTTGCTACAATCGTTGGGTCAG
        ||    || |   | | |||  |  |||    |  |||     ||| ||| |  ||| |   |||      || |||   ||||   | | |    | | |    ||||      ||  ||  ||  ||       ||||| || ||||  || || | | || | || || || |||||| ||||||||||||| |||||||||||||||||||||||||| || || ||||| || |
gtctgtttgtttctctctctctctctctctctctctcaccaacagtccatattttttttgccagttttgttgctcttagaagtattttatttttatttttttgctgtttctcattctggtttttttttacctttgtcctaaaatcagTGTTCTGCATTCACTGCCAGTCCTTCATCAGAGAAAACATGGACCATGCGTACTACCTTTCCAGAATATGTTGTTGCTCTTGCCACTATTGTTGGATCTG

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 3
gtaatactttaaattttcttgcattcttgttatgagttt---ttctttcgttagtctctatgc---aaaatatatttcagtatgtaaaatatc-ttctcttctccttggtatattg-atcggcagTGCTCAGCATATACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTGCTCTTGCTACAATCGTTGGGTCAG
        |     |||||  || ||||   |  |||     || ||  |  ||| |   ||     | |   |||||| | |      | || ||||  | |  |   | | |   |    ||||| || ||||  || || | | || | || ||||| |||||| ||||||||||||| ||||| |||||||| ||||||||||| || || ||||| || |
-----gtctgcttgtttctctcactcttaccaacagtccatatttttatgccagttttgttgttcttagaagcatttcatttttctgtttctcattctggttttttacctttgtcctaatatcagTGTTCTGCATTCACTGCCAGTCCTTCATCAGAAAAAACATGGACCATGCGTACTACCTTTCCTGAATATGTCGTTGCTCTTGCCACTATTGTTGGATCTG

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 2
gtaatactttaaattttcttgcattcttgttatgagtttttctttcgttagtctctatgcaaaatatatttcagtatgtaaaatatcttctcttctccttggtatattgatcggcagTGCTCAGCATATACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTT-GTTGCTCTTGCTACAATCGTTGGGTCAG
                                                              ||||| |||     ||   | | || | | ||| ||        |  | |  |||||||||||||   | |||| | || | || || || |||||| ||||||||||||| ||||||||||||||| ||||| |||||||| || ||||| ||  
------------------------------------------------------------gtaatatttttgctgttgctcattctccttttttcccccattgtcctcaaac--cagTGCTCAGCATTCTCTGCTAGTCCTTCATCAGAGAAAACATGGACCATGCGTACTACCTTTCCAGAATATGTTTGTTGCACTTGCTACTATTGTTGGATCT-

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------gtaatactttaaat---tttcttgcattcttgttatgagtttttctttcgtta-gtctctatgcaaaatatatttcagtatgtaaaatatcttctcttctccttggtatattgatcggcagTGCTCAGCATATACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTGCTCTTGCTACAATCGTTGGGTCAG
                                                   |||||||||   |   |   |   |||    || |||| || ||| | | ||  | | |   ||  | | || | | |||    | |    |  ||| || |   | | ||      |||||||| |||||| | || | |||| | ||||| || |||||| | ||||| ||||| ||||||||||||||||||||||||||||| || || || || |
gttctatttccattcatttgattatctctgaagttccattgttgcaggagataatactttctgtacctcgttcttatttcccttttgagattatctcttgctatatttttggtcatcacaaatataaatatcctta-tcctgtgccttttcttctctttttt------cagTGCTCTGCATATTCTGCAAGTGCTTCATCTGAGAAAACATGGACTATGCGCACTACTTTTCCAGAATATGTTGTTGCTCTTGCTACCATTGTCGGATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatatttcagtatgtaaaatatcttctcttctccttggtatattgatcggcagTGCTCAGCATATACAGCTAATGCTGCGTCTGAAAAGACATGGTCCATGCGTACTACGTTTCCAGAATATGTTGTTGCTCTTGCTACAATCGTTGGGTCAG
                                          tattgat  putative branch site (score: 3)
            tatgtaaaatatctt  TA-rich tract