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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttttcatcatctgtttctaattaagcttaattttgtttttgagtatagtcaccttttctcattgctgtatttactatagTTTCAGATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGG

Basic information

species Arabidopsis thaliana
transcript AT2G02560.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 2
----gtcttttcatcatctgtttctaa----ttaagcttaattttgtttttgagt-----atagtcaccttttctcatt-gctgtatttactatagTTTCAGATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGG------
    |  |||   | |||||  | | |    | || || ||||||| | || | |     ||  |    | ||  |||  | ||| |  | | |  ||||||||||| || |||||||| || |||||||| |||||||| || ||||||||||  || ||||| || ||   ||| |||   ||||  ||| | |      
gtatgggtttcactgatctgcatgtgaactgtaaacctgaattttgctctttatttttctatgatttgatcttaacatccgttgtgtaaaattttctttcagATGACAGGGAAAGATAAGGACTACAGATATATGGCAACTTCAGATTTGCTTAGCGAATTGAACAAAGAGGGCTTCAAAGCTGACCAAGACATCGAGCCAA

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g07340.1 (Oryza sativa), 3'ss of exon 2
---------------gtcttttcatcatctgtttctaattaagcttaattttgtttttgagtatagtcaccttttctcattgctgtatttactatagTTTCAGATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGG-------
                |||     | | |||| |  |  | |  ||   | | | |||   |||  |    ||||  ||| |  || |  | | |  ||||||||||| || |||||||| || |||||||| |||||||| ||  |||||||||  || ||||| || ||   ||| |||   ||||  ||| | |       
gtatgggtttcactgatctgcatgtgaactgtat--acctgaattttgctctttatttatctatgatttgattttaacatcgtcgtgtaaaatttgctttcagATGACAGGGAAAGATAAGGACTACAGATATATGGCAACTTCAAATTTGCTTAGCGA-TTGAACAAAGAGGGCTTCAAAGCTGACCAAGACATTGAGCCAAA

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G168629_T05 (Zea mays), 3'ss of exon 2
gtcttttcatcatctgtttctaattaagcttaattttgtttttgagtatagtcaccttttctcattgctgtatttactatagTTTCAGATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGG------
||     | | | ||  |    || ||  |   ||    | |  |   |  | || |||    |   || | || | |       |||||||| || ||||||||||| |||||||| |||||||| || ||| |||||| ||| |||||||| ||   ||| |||   || |  ||| | |      
gtaacccc-taaactaatgtacatgaaattgggttcaactatgcatcgttttgacttttaa--agcactttgttaaatgcctgcacagATGACAGGGAAAGATAAAGACTACAGATATATGGCAACATCAGATCTGCTTAGTGAATTGAATAAAGAAAGCTTCAAAGCTGATCAAGACCTTGAGCCAA

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 1
gtcttttcatcatctgtttctaattaagcttaattttgtttttgagtatagtcaccttttctcattgctgtatttactatagTTTCAGATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGG------
   | | |||   |    ||| ||     || || ||| | |  | | | |       |  | | || | |      | | |   |||||||| || || || |||||||||||||| ||||| || ||||||||||| ||||||||||  ||     | |||||   |||    || ||||      
--gtatgcatacacatgctctgatg----ttcatgttgatatgcattgtggctgttcatgatgaatggttttcgatttcttggcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTGAATGAGTTGAGCAAAACAACGTTTAAGGCCGATGCTGATTTGGAGGTCA

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G40230.1 (Glycine max), 3'ss of exon 2
gtcttttcatcatctgtttctaattaagcttaattttgtttttgagtatagtcaccttttctcattgctgtatttactatagTTTC----AGATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGG------
               || | ||   |    |  |  ||||  |  | || ||  |  ||  | ||   ||  ||| | ||   |||    ||||||| || || || |||||||||||||| ||||| || ||||||||||| ||||||||||  || |   | |||||   |||    ||  |||      
---------------gtatgtatacacatgttctgatgttcatatgcattgtggctgttcatgatgaatg-gttttcgatttcttcgcgcagATGACTGGGAAGGACAAAGATTACAGATATATGGCCACATCTGATTTGCTCAATGAGTTGAGCAAAGCAACGTTTAAGGCCGATGCTGATCTGGAGGTCA

upper sequence: AT2G02560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------gtcttttcatcatctgtttctaattaagcttaattttgttt-------------ttgagtatagtcaccttttctcattgctgtatttactatagTTT-CAGATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGG------
                                                             | |||| ||  |||| |        || ||  |||| |||             || ||  | || |   |      |||   | |||    | |||| ||||||||||||||||||||||| || ||||| |||||||| ||||||||  | |||||||| || || ||    |||| |   ||    || ||||      
gtatgttttttatttttgtatttttttgtgggcttattttttcaaaagaagatttttaattttttttaattttctgctatcttggcagtttccttttctttgatggtgaagagttttaggctggtaattatcgtcttttggcttgtttgggtttgtttgcagATGACGGGTAAAGATAAAGACTATAGATATATGGCAACTTCTGATTTATTAAATGAGTTAAACAAAGAAGGATTTAGAGCTGATGCTGATTTGGAGATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttaattttgtttttgagtatagtcaccttttctcattgctgtatttactatagTTTCAGATGACGGGTAAAGATAAAGATTACAGATACATGGCAACCTCTGATTTGCTTAATGAGTTGAATAAGGATTCCTTTAAAATCGACCTGGACTTGG
 gcttaat  putative branch site (score: 4)
     attttgttttt  TA-rich tract