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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcctttatatatgtttatttgagactgttttatcttgcatacataatttgctaacatatttccctttttcttgggaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT

Basic information

species Arabidopsis thaliana
transcript AT3G15980.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
gtacgttcctttatatatgtttatttgaga---ctgttttatcttgcatacataatttgctaacatatttccctttttcttgg--gaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT
               |||||||  | || |    || ||  | |    |  |  || || |||  | | |  ||      | |     | ||||||||| || || ||  | || || ||  ||||||| |||||||| ||||||||||| || |||||||||   || ||  |||||||| |  | || || 
--------------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
gtacgttcctttatatatgtttatttgaga---ctgttttatcttgcatacataatttgctaacatatttccctttttcttgg--gaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT
               |||||||  | || |    || ||  | |    |  |  || || |||  | | |  ||      | |     | ||||||||| || || ||  | || || ||  ||||||| |||||||| ||||||||||| || |||||||||   || ||  |||||||| |  | || |||
--------------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagcttggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 5
gtacgttcctttatatatgtttatttgagactgttttatcttgcatacataatttgctaacatatttccctttttcttgggaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT
||| |||   |   | |   |  ||     || |  | | | ||||  || | || ||  |  | |  |   |  |||||   | ||||||||| || || ||  | || || ||  ||||||| |||||||| ||||||||||| || |||||||||   || ||  |||||||| |  | || || 
gtatgttttctcgaaaacaatgcttc----ctttcctttgtagcatctattaatttct--ctgactaacaaatagcttgg---tacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
gtacgttcctttata-tatgtttatttgagactgttttatcttgcatacataatttgctaacatatttccctttttcttgggaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT
||| ||   |  ||  | ||  |  || | | | | | |      || ||  | |    |  || |||    | || |     |  |||||| || ||||| || || ||  | ||  |||||||||||||||| ||||| ||||| || |||||||| || |||||| ||||| ||||  ||||||||
gtaagtggatcaatggtttgcattattcaaaatatctca------atgcagtaatcctgattattttttaactgtttt-----actcagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
gtacgttc--ctttatatatgtttatttgagactgttttatcttgca--tacataatttgctaacatatttccctttttcttgggaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT
||| ||    |||    |  | |||||  |    ||||||  |||||   |  |    | ||    | |||  |  ||| ||       |||||| || ||||| || |||||  | ||| ||||||| |||||||| ||||||||||| || |||||||| || |||||| ||||| ||||  |||| || 
gtaagtgaaacttctgcttggattattcaaa---gttttaaattgcagtaatcttgactacttttctgtttatcaatttttttt---ctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 5
gtacgttcctttata-tatgt-ttatttgagactgttttatcttgcatacataatttgctaacatatttccctttttcttgggaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT
||| ||   |  ||  | ||  |||||  | |    |  ||   |    | | ||||  |  | | |||   |||  ||  |  |  ||||||  | ||||| || || ||  | ||  |||||||||||||||| || || ||||| || |||||||| || |||||| ||||| ||||  ||||||||
gtaagtggatcaatggtttgcattattcaaaatctctcaatgcagtggtcctgattttttttcttcttt---tttaactgtgttactcagTGTTGTGGGATACACACTACTTTTAAGTTTGATTGAATACAAGACACTAGTCATGCGCGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
gtacgttc--ctttatatatgtttatttgagactgttttatcttgcatacataatttgctaacatatttccctttttc--ttgggaatg-cagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT
||| ||    |||    |  | |||||  |    ||||||  |||||   ||||| |   |  || ||||  ||| ||  |||    |  |||||| || ||||| || |||||  | ||| ||||||| |||||||| ||||||||||| || |||||||| || |||||| | ||| | ||  |||| || 
gtaagtgaaacttctgcttggattattcaaa---gttttaaattgca---ataatct-tgactatttttctgtttatcaattgtttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
----gtacgttcctt-tatatatgtttatttgagactgttt--tatcttgcatacataatttgctaacatatttccctttttcttgggaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT
    ||    |  |   | | | |   | | |||  || ||  | | ||||  ||||  |||  ||  | | ||   |||| |||   ||||||||||||| ||||| ||  | || || ||  ||||||| |||||||||||||||||||| || ||  ||||  | |||||| || |||||||| ||||||| 
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatc-tttattatta-agttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatcttgcatacataatttgctaacatatttccctttttcttgggaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT
                     tgctaac  putative branch site (score: 1)
                             tatttccctttttctt  CT-rich tract
           atacataattt  TA-rich tract