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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAGgtactgacagaacataaaaatgtgtttggcatataggttttgcttctgttggcttacatgtatgatatatattttcctttcag

Basic information

species Glycine max
transcript GLYMA08G20070.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20070.1 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os04g35420.1 (Oryza sativa), 5'ss of exon 15
GTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAGgtactgacag-aacataaaaatgtgtttggcatataggttttgcttctgttggctta--catgtatgatatatattttcctttcag
||||||| |||||||||||||| ||||| |||||||||||||| || ||||| |||||||| |||||||||||| |  ||   ||||||   |       |  |  |  |     |    |   ||||    ||| ||||   | || |||||| ||
GTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAGgtattttcaatgacataagtttcgccaatgtgtgcacatcaaaatggcataaacttagctgtgtttgatgactgttatccttttag

upper sequence: GLYMA08G20070.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G319573_T01 (Zea mays), 5'ss of exon 14
-----------------------------GTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAGgtactgacagaacataaaaatgtgtttggcatataggttttgcttctgttggcttaca--tgtatgatatatattttcctttcag--
                             |||| || ||||||||||| |||||||| || |||||||| || || || || |||||||| |||||||||||| |  |  |  |   || | |   || |||        ||   ||||    |   |  |||||| |   |  | |  | |||   
GTGTTCCAATCTAATAGGACAAACTGTAGGTATCAATAAACCTGATGTTCGCTTTGTTATTCATCATTCACTGCCCAAGTCAATTGAAGGATATCATCAGgta-tatctcataactgaagttt-catgacatgagcacaatggaactgtaaagtcgaagctgtatggtggttgatctattctcatag

upper sequence: GLYMA08G20070.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G319573_T02 (Zea mays), 5'ss of exon 12
GTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAGgtactgacagaacataaaaatgtgtttggcatataggttttgcttctgttggcttaca--tgtatgatatatattttcctttcag--
|||| || ||||||||||| |||||||| || |||||||| || || || || |||||||| |||||||||||| |  |  |  |   || | |   || |||        ||   ||||    |   |  |||||| |   |  | |  | |||   
GTATCAATAAACCTGATGTTCGCTTTGTTATTCATCATTCACTGCCCAAGTCAATTGAAGGATATCATCAGgta-tatctcataactgaagttt-catgacatgagcacaatggaactgtaaagtcgaagctgtatggtggttgatctattctcatag

upper sequence: GLYMA08G20070.1 (Glycine max), 5'ss of exon 18
lower sequence: AT1G10930.1 (Arabidopsis thaliana), 5'ss of exon 16
GTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAGgtact-----------gacagaacataaaaatgtgtttgg--------catataggttttgcttctgttggctta----------catgtatgatatatattttcctttcag-
| || ||||| ||||||||||||||||| || ||||| || |||||||| ||||| |||||||||||||||||| |            |   | |||  |||| |  ||          || ||| |  | | | |||||  ||            ||  || | |||||  |||    |||  
GAATCAACAAGCCTGATGTCCGCTTTGTTATTCATCACTCGCTCCCAAAGTCTATAGAAGGCTATCATCAGgtatttttaattatacaatcaatcatgtaaatcttattaaactgattccacataaggctagatactgttatctcgtctagaaactcacataagctatattatttgtaatcaag

upper sequence: GLYMA08G20070.1 (Glycine max), 5'ss of exon 18
lower sequence: AT1G60930.1 (Arabidopsis thaliana), 5'ss of exon 16
GTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAGgtact--gacagaacataaaaatgtg-----tttggcatataggttt-tgcttctgttggcttacatgtatgatatatattttccttt-cag-
| || || || |||||||| || |||||||| |||||||| || ||||| || || |||||||||||||||||  |      |||||   || | |        | | | |  | ||| |   | |  | |   ||    | ||| ||| |||||   | ||  
GAATCAATAAGCCTGATGTTCGTTTTGTAATTCATCATTCTCTACCAAAGTCCATAGAAGGCTATCATCAGgtgttttatttgaacactgaattataaatatcctagtaaactgatttataaatatcctagtaaactgaaaagatgtattttttctcatacaag

upper sequence: GLYMA08G20070.1 (Glycine max), 5'ss of exon 18
lower sequence: Vv12s0035g00400.t01 (Vitis vinifera), 5'ss of exon 12
GTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAGgtactgacagaacataaaaatgtg--tttggcatataggttttg----------cttctgttggcttacatgtatgatata--tattttcctttcag-----------------------------------------
|||| |||||||| |||||||||||||| || |||||||| || |||||||| |||||||| |||||||||||| |    ||| || |   |      ||  || || | | ||           ||  |||||   ||      ||||     || ||   |||||                                          
GTATCAACAAACCAGATGTCCGCTTTGTCATTCATCATTCTCTTCCAAAATCAATTGAAGGGTATCATCAGgtaatttgtgaaaatgattttaccatctttacaaattgttcttataaaatattcctattgttgatctaagatggtgatgggagtacttagttttcactcaatggttttatagtttcaccatattctctcatgacccag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTAACAAACCTGATGTCCGCTTTGTAATCCATCATTCCCTCCCAAAATCTATTGAAGGCTATCATCAGgtactgacagaacataaaaatgtgtttggcatataggttttgcttctgttggcttacatgtatgatatatattttcctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG