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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAGgtattttcaatgacataagtttcgccaatgtgtgcacatcaaaatggcataaacttagctgtgtttgatgactgttatccttttag

Basic information

species Oryza sativa
transcript LOC_Os04g35420.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g35420.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G319573_T02 (Zea mays), 5'ss of exon 12
GTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAGgtattttcaatgacataagtttcgccaatgtgtgcacatcaaaatggcataaacttagctgtgtttgatgactg--ttatccttttag
|||| |||||||||||||| || |||||||| |||||||| |||||||| ||||||||||||||||||||||||| |   || ||  |||||||    |  || |||||    ||  | | |  |  |||||| |  | ||  ||   ||| ||  |||
GTATCAATAAACCTGATGTTCGCTTTGTTATTCATCATTCACTGCCCAAGTCAATTGAAGGATATCATCAGgtatatctcataactgaagtttcat-gacatgagcacaatggaactgtaaagtcgaagctgtat--ggtggttgatctattctcatag

upper sequence: LOC_Os04g35420.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G319573_T01 (Zea mays), 5'ss of exon 14
-----------------------------GTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAGgtattttcaatgacataagtttcgccaatgtgtgcacatcaaaatggcataaacttagctgtgtttgatgactg--ttatccttttag
                             |||| |||||||||||||| || |||||||| |||||||| |||||||| ||||||||||||||||||||||||| |   || ||  |||||||    |  || |||||    ||  | | |  |  |||||| |  | ||  ||   ||| ||  |||
GTGTTCCAATCTAATAGGACAAACTGTAGGTATCAATAAACCTGATGTTCGCTTTGTTATTCATCATTCACTGCCCAAGTCAATTGAAGGATATCATCAGgtatatctcataactgaagtttcat-gacatgagcacaatggaactgtaaagtcgaagctgtat--ggtggttgatctattctcatag

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

upper sequence: LOC_Os04g35420.1 (Oryza sativa), 5'ss of exon 15
lower sequence: AT1G10930.1 (Arabidopsis thaliana), 5'ss of exon 16
GTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAGgtattttcaatgacataagtttcgccaatgtgtgcacatcaaaatggcataaacttagctgtgtttgatgactgttatcct-tttag---------------------------------
| || || || ||||||||||| |||||||| ||||| || || || || || || ||||| |||||||||||||||| ||| | | ||       ||||   || | |||  | |    | |    |  |  |  |    |||||||||   | |||                                 
GAATCAACAAGCCTGATGTCCGCTTTGTTATTCATCACTCGCTCCCAAAGTCTATAGAAGGCTATCATCAGgtatttttaattatacaa------tcaat-catgtaaatcttattaaactgattccacataaggctagatactgttatctcgtctagaaactcacataagctatattatttgtaatcaag

upper sequence: LOC_Os04g35420.1 (Oryza sativa), 5'ss of exon 15
lower sequence: AT1G60930.1 (Arabidopsis thaliana), 5'ss of exon 16
GTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAGgtattttcaatga-ca-taagtttcgccaatgtgtgcacatcaaaatggcataaacttagctgtgtttgatgactgttatccttttag------
| || ||||| |||||||| |||||||| || |||||||| || || || || || ||||| ||||||||||| ||||   ||| || | | ||      ||    | | |   |  |   |  | | ||| |    |  |    |||  |  || |        
GAATCAATAAGCCTGATGTTCGTTTTGTAATTCATCATTCTCTACCAAAGTCCATAGAAGGCTATCATCAGgtgttttatttgaacactgaattataaatatcctagtaaactgatttataaatatcctag-taaactgaaaagatgtattttttctcatacaag

upper sequence: LOC_Os04g35420.1 (Oryza sativa), 5'ss of exon 15
lower sequence: Vv12s0035g00400.t01 (Vitis vinifera), 5'ss of exon 12
GTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAGgtattttc----aatgacataa--gtttcgccaatgtgtgcacatcaaaatggcataaacttagctgtgtttgatgactgttatccttttag----------------------------------------------
|||| || ||||| |||||||| ||||| || |||||||| || || |||||||||||||| |||||||||||| |||     |||||  | |   | |   |||  ||| |  || |||    | ||   ||         || |||  |   | |||                                                  
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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTAATAAACCTGATGTCCGTTTTGTTATCCATCATTCCCTGCCCAAATCAATTGAAGGATATCATCAGgtattttcaatgacataagtttcgccaatgtgtgcacatcaaaatggcataaacttagctgtgtttgatgactgttatccttttag

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