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'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTTAAGgttggctccttgtttctttgcttccacatatgccttttgtgtttgtatctatatatgtcttcttatctctagatgtgaacttatcttgtagccacattaacttaatgtgtatcgcattctaatcttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G71220.2
intron # 31
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 31
lower sequence: GLYMA08G13400.1 (Glycine max), 5'ss of exon 34
CGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTTAAGgttggctccttgtttctttgcttccacatatgccttttgtgtttgtatctatatatgtcttcttatctctagatgtgaacttatcttgtagccacattaacttaatgtgtatcgcattctaatcttgcag
 || || ||  | |||||||||||||| ||||| || ||||| ||  |||||||||| ||||||||||| || ||||| || ||||||||||  |||||||||   |        |     ||  |    | | ||||   |   ||| ||| |    | |   ||   || | ||  | | ||    | |||  |    || ||    | | |    || | | | |||
TGAACGCTTTATGAAGATTATGATTCTAAGTGTTCTAAAGAATACTCATCGTCCTGTTAAATTCTGGTTCATAAAGAACTACCTCTCTCCTCCTTTTAAGgttatatatcca---cccaagttatatgcttacattttaattcattatatat-tggaacgttaaatggttaaa-gtagaatgatgagtttgcctgacatcctgaactgttttggttgacttaacatacag

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 31
lower sequence: GLYMA05G30230.1 (Glycine max), 5'ss of exon 32
CGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTTAAGgttggctccttgtttctttgcttccacatatgccttttgtgtttgtatctatatatgtcttcttatctctagatgtgaacttatcttgtag-ccacattaacttaatgtgtatcgcattctaatcttgcag
 || || ||  | |||||||||||||| ||||| || ||||| ||  ||||||| || ||||||||||| || ||||| || ||||||||||  |||||||||   |        |     ||  |    | | ||||   ||  | | ||||| ||   | | |  |  |    |||  ||  ||   |  |   |  |  ||  |     |  ||| |           
TGAACGCTTTATGAAGATTATGATTCTAAGTGTTCTAAAGAATACTCATCGTCCAGTTAAATTCTGGTTCATAAAGAACTACCTCTCTCCTCCTTTTAAGgttatatatcca---cccaagttatatgcttacatttta-attcatttgtatat-tggaatgtaaagtagaatgatgagtttgcctgacattctgaaccattttggttgacttaacatacag---------

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 31
lower sequence: GLYMA08G20020.1 (Glycine max), 5'ss of exon 31
CGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTTAAGgttggctccttgtttctttgcttccacatatgccttttgtgtttgtatctatatatgtcttcttatctctagatgtgaacttatcttgtagccacattaacttaatgtgtatcgcattctaatcttgcag----
 || || || || |||||||||||||| ||||| || ||||| ||  | ||||| || ||||||||||| || ||||| || || |||||||  |||||||||          | | |     |   ||||||||    |||||  ||  || | | | ||   |  |  |  ||  |  | ||    | ||   | |  ||  |  | | | || |  |    |  ||     
TGAACGCTTTCTAAAGATTATGATTCTAAGTGTTCTAAAGAATACACACCGTCCAGTTAAATTCTGGTTCATAAAGAACTACCTGTCTCCTCCTTTTAAGgtta---------tacatccacacagtatatgcctca-atgttt--attcatttgtatattggaactttaaagtggaatataatgagtttgctcaacttcctcgaactattttgcttgttgtcttaacaaacag

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 31
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 5'ss of exon 32
CGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTTAAGgttggctccttgtttctttgcttccacatatgccttttgtgtttgtatctatatatgtcttcttatct-ctagatgtgaact-tatcttgtagccacattaacttaatgtgtatcgcattctaatcttgcag
 || ||||| || || || |||||||| |||||||||||||||| |||||| || ||||||||||||||||| ||||| ||||| |||||||||||||||||||   || | ||  ||  ||          | ||| |||||| |  || |   ||| ||||| |    || ||||   |  | |||| | |  | | |  |||  ||| | |    ||  |||   |   
TGAACGTTTTCTGAAAATCATGATTCTAAGTGTCCTGAAGAACAGCAATCGCCCCGTAAAATTCTGGTTTATAAAGAACTATCTTTCTCCTCAATTTAAGgttgcaaccattttctttcactctt-------cttttagtgttt-tgactgtcgttgttttcttctaaattaaatgtagtcaatttcttatggggaaactctcttt-tgt-tgttaactttcaatgcag---

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 31
lower sequence: PP1S25_65V6.1 (Physcomitrella patens), 5'ss of exon 13
CGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTTAAGgttggctccttgtttctttgcttccacatatgccttttgtgtttgtatctatatatgtcttcttatctctagatgtgaacttatcttgtagccacattaacttaatgtgtatcgcattctaatcttgcag
|||||| ||  | |||||||||||  | |||||  |||||||||| || || ||||| ||||| ||||| || ||||||||  | || ||||||||||||||| | | |||   | | ||   | |   |  |  | ||  || ||     ||  |  ||| || | |    ||         |||||| |  | | | ||    ||   || |                
CGAGCGGTTTTTGAAGATTATGATGTTGAGTGTGATGAAGAACACAAACCGACCTGTTAAATTTTGGTTCATAAAGAATTACTTATCCCCTCAATTTAAGgtttgattctttcctttatgaaactaacaaaac--tatgctttggtgaac-tacttagcttattgtttaataat---------tcttgttg--aaaattacgggttgaaaattg----------------

upper sequence: AT1G71220.2 (Arabidopsis thaliana), 5'ss of exon 31
lower sequence: EFJ07070 (Selaginella moellendorffii), 5'ss of exon 28
CGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTTAAGgttggctccttgtttctttgcttccacatat--gccttttgtgtttgtatctatatatgtcttcttatctctagatgtgaacttatcttgtagccacattaacttaatgtgtatcgcattctaatcttgcag
||||||||| || ||||||||||| ||||| ||  ||||||| || |  || || || ||||| |||||||| ||||||||||| ||||| |||||||||||||||    |  |   | || || |  |    |  ||| |||                                                                                         
CGAGCGTTTTCTAAAGATTATGATGCTCAGCGTTTTGAAGAATACTAGACGGCCAGTGAAATTTTGGTTTATCAAGAATTATCTTTCTCCACAATTTAAGgttggcggacttgtaaatcgcgtctagctgacaggatttcgtgcag--------------------------------------------------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGCGTTTCCTTAAGATTATGATTCTCAGTGTCCTGAAGAACACCAATCGTCCTGTAAAATTCTGGTTTATTAAGAATTATCTCTCTCCTCAATTTAAGgttggctccttgtttctttgcttccacatatgccttttgtgtttgtatctatatatgtcttcttatctctagatgtgaacttatcttgtagccacattaacttaatgtgtatcgcattctaatcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC