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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatattttaatttttgggactcaataagtttgaatgaacataaatgcaaaattcttatacgtgaatgtcttttgcaacttaaacgaattttaatttcagGTGCGTAGGCTTTCAGCCTGTGAAACCATGGGGTCTGCAACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAACGAG

Basic information

species Arabidopsis thaliana
transcript AT4G29900.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM5G892495_T02 (Zea mays), 3'ss of exon 6
gtatgtatattttaatttttgggactcaataagtttgaatgaacataaatgcaaaattcttatacgtgaatgtcttttgcaacttaaacgaattttaatttcagGTGCGTAGGCTTTCAGCCTGTGAAACCATGGGGTCTGCAACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAACGAG
                     | ||  | |      || |  |     ||||   ||||||  | || |     | ||||     || |  ||   |||||||||| || |||||||| ||||||||||| ||||| || || ||||| ||||| ||||| |||||||| || || || |||||| ||
---------------------gtacatatttctccagattagatt---atgctgtattcttcca-gttataacatgttgc----caagc--atgacaatttcagGTTCGGAGGCTTTCTGCCTGTGAAACAATGGGTTCAGCGACAACTATTTGTAGTGACAAGACTGGTACATTAACATTAAACCAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA17G06520.1 (Glycine max), 3'ss of exon 18
gtatgtatattttaatttttgggactcaataagtttgaatgaacataaatgcaaaattcttatacgtgaatgtcttttgcaacttaaacgaattttaatttcagGTGCGTAGGCTTTCAGCCTGTGAAACCATGGGGTCTGCAACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAACGAG
|||||   | |||  ||| ||      |     |||      |  ||  ||  |||| ||           || |  |  |||  |       || |||| |||||| | |||||||| |||||||| || |||||||| || ||||| ||||||||||||||||||||||| |||||  | ||  ||
gtatgccaacttttgtttgtg----ctataggattttggcatatctatttgagaaatgct-----------gtttgatataacaca-------ttgaattgcagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 15
gtatgtatattttaatttttgggactcaataagtttgaatgaacataaatgcaaaattcttatacgtgaatgtcttttgcaacttaaacgaattttaatttcagGTGCGTAGGCTTTCAGCCTGTGAAACCATGGGGTCTGCAACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAACGAG----
|||||   |||||  | |||| |  | |  |  |||| ||  |  ||  ||  |||| ||           || |  |  |||  |       || |||| |||||| | |||||||| |||||||| || |||||||| || ||||| ||||||||||||||||||||||| |||||  | ||  ||    
gtatgccaatttt--tgtttgtgctttaggatttttgcat--atctatttgagaaatgct-----------gtttaatataacaca-------ttgaattacagGTGAGGAGGCTTTCTGCCTGTGAGACAATGGGGTCAGCCACAACCATTTGCAGTGATAAGACTGGAACATTGACTATGAATCAGGTTA

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 15
gtatgtatattttaatttttgggact-caataagtttgaatgaacataaatgcaaaattcttatacgtgaatgtcttttgcaacttaaacgaattttaatttcagGTGCGTAGGCTTTCAGCCTGTGAAACCATGGGGTCTGCAACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAACGAG
|||||   |||   || ||||    |  ||| |||||  |   | ||| |||  ||| | |  |   |  |||||                |  || ||||  ||||  | |||||||| |||||||| |||||||| ||||| ||||| || || |||||||||||||| || |||||| | ||  ||
gtatgccaatt--gatgtttgtacttataatcagttttgacataaatacatgtgaaactttgtttaat--atgtc----------------acattgaattgtagGTAAGGAGGCTTTCTGCCTGTGAGACCATGGGCTCTGCCACAACCATATGTAGTGATAAGACTGGCACATTGACCATGAATCAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA15G18180.1 (Glycine max), 3'ss of exon 15
gtatgtatattttaatttttgggactcaataagtttgaatgaacataaatgcaaaattcttatacgtgaatgtcttttgcaacttaaacgaattttaatttcagGTGCGTAGGCTTTCAGCCTGTGAAACCATGGGGTCTGCAACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAACGAG
|||||   |||    ||| |     | | |  ||||  |   | ||| |||  ||| | |          | | | ||| ||| |         | ||||  ||||  | |||||||| ||||| || |||||||| ||||| ||||| || ||||||||||||||||| || |||||  | ||  ||
gtatgccaattgatgtttgtact-tttagtcggttttgacataaatacatgtgaaacttt---------gtttatattgtaacat---------tgaattgtagGTAAGGAGGCTTTCTGCCTGCGAGACCATGGGCTCTGCCACAACCATATGCAGTGATAAGACTGGTACATTGACTATGAATCAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 18
gtatgtatattttaatttttgggactca------ataagtttgaatgaacataaatgcaaaattcttatacgtga---atgtcttttgcaacttaaacgaattttaatttcagGTGCGTAGGCTTTCAGCCTGTGAAACCATGGGGTCTGCAACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAACGAG
||||||||     |  |||  | ||| |      | ||| ||  ||     ||  ||    ||   |||| || |   |||  |   |    ||||  | | || || | ||||| || |||||||| || ||||| |||||||| ||| | || || ||||||||||||||||| |||||| | || || ||  ||
gtatgtatgacaaatatttctgaactaagcttccacaagattatatatgt-tatgtgggtcatgagtatatgttatatatgcatcgggtggtttaacagcagttgaactgcagGTACGGAGGCTTTCTGCTTGTGAGACCATGGGCTCTTCCACGACTATTTGCAGTGATAAGACAGGAACTCTAACTTTGAATCAG

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 14
gtatgtatattttaatttttgggactcaataagtttgaatgaacataaatgcaaaattcttatacgtgaatgtcttttgcaacttaaacgaattttaatttcagGTGCGTAGGCTTTCAGCCTGTGAAACCATGGGGTCTGCAACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAACGAG
                                                      || ||   || |||  |      |     ||  |   |||||  || ||||| |||    |  | ||||| ||||| ||||| |||||||| || || |||||||||||||| |||||  ||||||| ||| ||
----------------------------------------------------gtaagtcccctaagtgttttgtaagtatggttttgattcatttttgttacagGTCCGTCATTTGGCTGCCTGCGAAACAATGGGATCTGCAACGACTATCTGCAGTGATAAGACCGGAACCCTGACCTTGAACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaaattcttatacgtgaatgtcttttgcaacttaaacgaattttaatttcagGTGCGTAGGCTTTCAGCCTGTGAAACCATGGGGTCTGCAACAACAATTTGCAGTGATAAGACTGGAACTTTGACCTTAAACGAG
                                           ttttaat  putative branch site (score: 3)
                               aacttaaacgaatttt  TA-rich tract