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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatgcatctctctctatctctatctctctttccaacaattacggtcaaagtttaggttttcaggcatacttagtgagtctgctcgaggctcttgtgtcttctttcggcttttgattagtcatggttttgctgtttcagGCCATAGCATACATGGGGGACGATTTTATGTTTCAGCTGTATGGGAAGTACCAGGATATGGCTTTAGCAGTTAAAAACCCATGCCATCTTAACATAGCAG

Basic information

species Arabidopsis thaliana
transcript AT3G21640.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G21640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 5
gttatgcatctctctctatctctatctctctttccaacaattacggtcaaagtttaggttttcaggcatacttagtga-gtctgctcgaggctcttgtgtcttctttcggcttttgattagtcatggttttgctgtttcagGCCATAGCATACATGGGGGACGATTTTATGTTTCAGCTGTATGGGAAGTACCAGGATATGGCTTTAGCAGTTAAAAACCCATGCCATCTTAACATAGCAG
                                                             | ||   |   || ||| |||        ||| ||||    |  |    | |        |    ||| | || || ||||| || |||||||||||||| ||||| ||||||||  ||| ||||||||||   || ||||| ||||| || ||||| || |||||||| ||||| || |
------------------------------------------------------------gttagttgt--ctactgatgtcattcttcagctattgtaagatgctcaatcataatccccctagctgttcttct-ttacagGCAATTGCATACATGGGGGATGATTTCATGTTTCAATTGTTTGGGAAGTACAGAGACATGGCCTTAGCTGTGAAAAATCCCTGCCATCTCAACATGGCCG

upper sequence: AT3G21640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA09G36250.1 (Glycine max), 3'ss of exon 6
gttatgcatctctctctatctctatctctctttccaacaattacggtcaaagtttaggttttcaggcatacttagtgagtctgctcgaggctcttgtgtcttctttcggcttttgattagtcatggttttgctgtttcagGCCATAGCATACATGGGGGACGATTTTATGTTTCAGCTGTATGGGAAGTACCAGGATATGGCTTTAGCAGTTAAAAACCCATGCCATCTTAACATAGCAG
||||  ||  | |     | |||    |||||    | ||||           |||      || | | | ||  |   |||  |  |   | ||| ||  | |  |   |||    | ||| ||||| |    | ||||||||||||||| ||||| || || || ||||| ||| ||| |||||||||    ||||||||| | || || || || ||||||||||||||||| ||||
gttacacacttat----gtttcttgtgctcttctacataatt----------cttaa---cccatggaaatttctttcttctctt--attattttgggttgtttgacaaatttgtggttgtcttggttct----tgtcagGCCATAGCATATATGGGAGATGACTTCATGTTCCAGTTGTTTGGGAAGTATAGAGATATGGCTCTGGCTGTAAAGAATCCATGCCATCTTAACATGGCAG

upper sequence: AT3G21640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA12G01080.1 (Glycine max), 3'ss of exon 5
gttatgcatctctctctatctctatctctctttccaacaattacggtcaaagtttaggttttcaggcatacttagtgagtctgctcgaggctcttgtgtcttctttcggcttttgattagtcatggttttgctgtttcagGCCATAGCATACATGGGGGACGATTTTATGTTTCAGCTGTATGGGAAGTACCAGGATATGGCTTTAGCAGTTAAAAACCCATGCCATCTTAACATAGCAG
||||  ||  | |     | |||    |||||   || ||||     |     |||  |     |  |||  |  |   | |  |   || | || || |          || ||||| ||| ||||| |    | ||||||||| ||||| ||||| || || || ||||| ||| ||| |||||||||    ||||||||| | ||||| || || ||||||||||||||||| ||||
gttacacacttat----gtttcttgtgctcttcttaataattcttcgctgttcttaa-tccatggaaatatcttctctttttattttgggttatt-tgaca------aatttgtgatt-gtcttggttct----tgtcagGCCATTGCATATATGGGAGATGACTTCATGTTCCAGTTGTTTGGGAAGTATAGAGATATGGCTCTGGCAGTAAAGAATCCATGCCATCTTAACATGGCAG

upper sequence: AT3G21640.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv13s0064g00580.t01 (Vitis vinifera), 3'ss of exon 6
gttatgcatctctctctatctctatctctctttccaacaattacggtcaaagtttaggttttcaggcatacttagtgagtctgctcgaggctcttgtgtcttctttcggcttttgattagtcatggttttgctgtttcagGCCATAGCATACATGGGGGACGATTTTATGTTTCAGCTGTATGGGAAGTACCAGGATATGGCTTTAGCAGTTAAAAACCCATGCCATCTTAACATAGCAG
                                             || | |   | | |  |||| ||   || |||       | |||  | |   |  ||  |||  |||||||  |    |   |||  |    |||||||||||||| ||||| || || || ||||| ||| ||| |||||||||||  || |||||||| || || || || |||||||| |||||||| ||||
---------------------------------------------gttacatacttgctcctcagtcaatattggtg-----ttttgagtttatgcagattttcttcctcttttgacaaa--gtccctttttttaaccagGCCATAGCATATATGGGAGATGACTTCATGTTCCAGTTGTTTGGGAAGTACCGTGACATGGCTTTGGCTGTGAAGAATCCATGCCACCTTAACATGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaggctcttgtgtcttctttcggcttttgattagtcatggttttgctgtttcagGCCATAGCATACATGGGGGACGATTTTATGTTTCAGCTGTATGGGAAGTACCAGGATATGGCTTTAGCAGTTAAAAACCCATGCCATCTTAACATAGCAG
                         ttttgat  putative branch site (score: 4)
                                         ttttgct  putative PPT
                         ttttgatta  TA-rich tract