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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGCTGACACAACGCAAGCATTGAAGCAAGTTAAATGCCAGAGAAGAATTGCCTTAACTGGCTCACCCCTTCAAAACAATCTCATGGAGTATTATTGTgtaagttactgagggaactatataaaattgtgacctaattttttcttatctccagtatctttagctatgtctgtactgcaacag

Basic information

species Arabidopsis thaliana
transcript AT1G08600.4
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08600.2 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: GLYMA20G37100.1 (Glycine max), 5'ss of exon 21
CAAGGCTGACACAACGCAAGCATTGAAGCAAGTTAAATGCCAGAGAAGAATTGCCTTAACTGGCTCACCCCTTCAAAACAATCTCATGGAGTATTATTGTgtaagttactgagggaactat--ataaaattgtgacctaattttttcttatctccagtatctttagctatgtctgtactgcaacag
 |||||||||  ||| ||||| ||||| ||||| ||||||||||||||||||||  | ||||| ||||| |||||||||||||||||||| ||||| ||||||||||  ||  | |  ||   ||   || |      | ||||| | |   | |  |  || |       | |   ||| || ||
TAAGGCTGACGTAACTCAAGCCTTGAAACAAGTAAAATGCCAGAGAAGAATTGCACTTACTGGATCACCTCTTCAAAACAATCTCATGGAATATTACTGTgtaagtttgtgtagaagttacaaattggatggctcttaagtttttgcgtgcattctttgactctc-tagcattttatctgaaatag

upper sequence: AT1G08600.2 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: Vv14s0036g01460.t01 (Vitis vinifera), 5'ss of exon 16
CAAGGCTGACACAACGCAAGCATTGAAGCAAGTTAAATGCCAGAGAAGAATTGCCTTAACTGGCTCACCCCTTCAAAACAATCTCATGGAGTATTATTGTgtaagttactgagggaa-ctatataaaattgtgacctaattttttcttatctccagtatctt--tagctatgtctgtactgc----aacag
|| |||||| ||||| ||||| ||||| ||||| || ||||||||  | ||||| || ||||| ||||| |||||||||||||||||||| ||||||||||||||||  |  || || | ||||    | |  |   | ||| || || | | |||| |  |  || || ||||  |  |      |||||
CAGGGCTGATACAACTCAAGCCTTGAAACAAGTGAAGTGCCAGAGGCGGATTGCATTGACTGGATCACCTCTTCAAAACAATCTCATGGAATATTATTGTgtaagtttgtatggaaagccatatctcttggcaaatcattttatttttttattcagtgttgtgatatctttgtcaattttatgtggaacag

upper sequence: AT1G08600.2 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: EFJ20520 (Selaginella moellendorffii), 5'ss of exon 18
CAAGGCTGACACAACGCAAGCATTGAAGCAAGTTAAATGCCAGAGAAGAATTGCCTTAACTGGCTCACCCCTTCAAAACAATCTCATGGAGTATTATTGTgtaagttactgagggaactatataaaattgtgacctaattttttcttatctccagtatctttagctatgtctgtactgcaacag
|||||| ||||  ||   |||| |  ||| ||| ||||      |  |||| ||| | || || || || || ||||||||||| |||||||| ||||||||||||  | || |      | | |   ||||   |||||  | ||||                                    
CAAGGCGGACATTACCATAGCACTCCAGCGAGTGAAATCTGGCCGCCGAATAGCCATGACAGGATCTCCTCTACAAAACAATCTGATGGAGTACTATTGTgtaagtatccgatgctg--gtgtcattatgtggattaattgat-cttacag---------------------------------

upper sequence: AT1G08600.2 (Arabidopsis thaliana), 5'ss of exon 19
lower sequence: EFJ28345 (Selaginella moellendorffii), 5'ss of exon 17
CAAGGCTGACACAACGCAAGCATTGAAGCAAGTTAAATGCCAGAGAAGAATTGCCTTAACTGGCTCACCCCTTCAAAACAATCTCATGGAGTATTATTGTgtaagttactgagggaactatataaaattgtgacctaattttttcttatctccagtatctttagctatgtctgtactgcaacag
|||||| ||||  ||   |||| |  ||| ||| ||||      |  |||| ||| | || || || || || ||||||||||| |||||||| ||||||||||||    || |      | | |   ||||   |||||  | ||||                                    
CAAGGCGGACATTACCATAGCACTCCAGCGAGTGAAATCTGGCCGCCGAATAGCCATGACAGGATCTCCTCTACAAAACAATCTGATGGAGTACTATTGTgtaagtattcgatgctg--gtgtcattatgtggattaattgat-cttacag---------------------------------

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGCTGACACAACGCAAGCATTGAAGCAAGTTAAATGCCAGAGAAGAATTGCCTTAACTGGCTCACCCCTTCAAAACAATCTCATGGAGTATTATTGTgtaagttactgagggaactatataaaattgtgacctaattttttcttatctccagtatctttagctatgtctgtactgcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA