Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacag

Basic information

species Arabidopsis thaliana
transcript AT1G36160.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 5'ss of exon 21
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaa-------aagcctacagttctgtttaaattgattaacccatccattattt-ttttcacag
 || ||||| ||||||||||| ||||||||||||||||| ||  | ||||| ||||| || || || ||| ||  ||||||||| || ||||| |||||||| || | |     |  |   |         ||  |||      ||| || | | || ||  |   || ||| || |   ||
ACCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCCCTCTTATCACCCGCTTCTGGTGTCATACATGTTGTAATGTCTGAGGGCCAAGCAATGCAGgtacattcctacattccattcattgtgctgtgctgacatgaacatttcaagtaaata-cctgtaacttgtttattattctag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: AC197672.3_FGT002 (Zea mays), 5'ss of exon 19
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacag----------------
||| ||||| ||||||||||| ||||||||||||||||| ||  | ||||||||||| || || || |||| ||  |||||||| || || ||  ||||||||   |||||   |   ||     | | || |  || ||  ||    ||     ||   ||   ||| |  |                 
GCCATATGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCGTTGCAGgttatattcatacatgtccattc--cttgcattgttgctttcatcacatagtatttcatgtaaaatttaccaacttatattttgttttag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GRMZM5G858094_T01 (Zea mays), 5'ss of exon 19
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttt---tcacag----------
 || || || ||||||||||| ||||||||||||||||| ||  | ||||||||||| || || || |||| ||  |||||||| || || ||  ||||||||   |||     |   ||        |  || || |    |   | ||   |||  |  |||| |    | | |           
ACCATACGCGGAAGTTGAGGTTATGAAGATGTGCATGCCTCTCTTGTCACCTGCTTCTGGTGTCATTCATTGTATGATGTCTGAGGGCCAGGCATTGCAGgttatattcgcacatgtccattccttgcattgtgctttcatcacataatatttcatgtaacatttatcaacttatattttgttttag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA04G11550.1 (Glycine max), 5'ss of exon 18
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcat--tgctaaacaaaaagcctacagttctgtttaaattgat-----taacccatccattatttttttcacag
 || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||||| ||  |||| ||||| |||||||||||||| ||||| ||||||||  |   |||  |  |  ||| |     |||| ||  ||| |||||||      |||   |    |      |||  |||
ACCGTATGCTGAAGTTGAGGTCATGAAAATGTGCATGCCTCTTCTTTCGCCTGCTTCTGGGATTATTCATTTCAAAATGTCTGAAGGTCAAGCAATGCAGgtatatagcattctattccacataggaagtacaatt--gttgaaattgaaaaagataataaaattgtatcaccttttgcag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA06G11120.1 (Glycine max), 5'ss of exon 18
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgtt-----cacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacag
 || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||||| ||  |||| ||||| |||||||||||||| ||||| ||||||||      || |  ||| |  |    ||   |    ||||   || ||     |||   |    |     | ||  |||
ACCATATGCTGAAGTTGAGGTCATGAAAATGTGCATGCCTCTTCTTTCGCCTGCTTCTGGGATTATTCATTTCAAAATGTCTGAAGGTCAAGCAATGCAGgtatatagcattctattccacattggaagtacaggtgttcatattgaaagagataataaaatagtatcactgtttgcag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 5'ss of exon 19
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacag
 || ||||| || |||||||| ||||||||||| |||||||||||||| |||||||| ||| |||| || ||||| ||||||||||| ||||| ||||||||  | |   || |  |    ||    ||   | || |      | |   |   |   || |  ||||    ||
ACCGTATGCAGAGGTTGAGGTTATGAAGATGTGTATGCCACTTCTTTCGCCTGCTTCTGGAATTATTCAATTTAAGATGTCTGAAGGTCAAGCAATGCAGgtaaaatatgttccatattggaagttttagtatcctatccttggt-agagattaagaaatcacattttgtgtag

upper sequence: AT1G36160.1 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: EFJ11422 (Selaginella moellendorffii), 5'ss of exon 17
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacag
 || |||||||| || || || ||||| ||||||||||| ||||||||||| ||||| ||    ||||| || ||    |  |||| |||||| |||  ||| |     |  |       |         |  |   |||   | | |    || | ||               
ACCCTATGCCGAGGTGGAAGTTATGAAAATGTGCATGCCTCTTCTTTCACCGGCTTCCGGCACAATCCACTTCAAGCATTTGGAAGCACAAGCAATGGTGgtacgtgctaccgtcggtttagtgtttgttatcttgctttgtgtggttctgtccgtgcag--------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTATGCCGAAGTTGAGGTCATGAAGATGTGCATGCCACTTCTTTCACCTGCTTCAGGAGTTATCCATTTTAAAATGTCTGAAGGACAAGCCATGCAGgttcacttcattgctaaacaaaaagcctacagttctgtttaaattgattaacccatccattatttttttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG