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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgttcaatacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaactttcag

Basic information

species Arabidopsis thaliana
transcript AT4G29900.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 26
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 5'ss of exon 8
ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgttca-atacatttacattcctcgtatgtgtaagctttaaaaatacac-------tgttatt----------gaggatcac--actttctgtgttgccccccaactttcag---------------------------
 || | |||||||||||| || ||  || | ||||| | ||  ||  | || || ||||| ||||| |||||||| ||||||||||||||| |||| ||||| || | | | ||       | || |     |  |  ||  ||| ||       | |||||          || ||  |   |   |   |||||   | ||  | | |                            
TCCAAGTGACAAACTTCTCCTAGTAAAAGCACTGAAAAAGAAAGGCAATGTTGTTGCTGTTACTGGAGATGGAACGAATGATGCTCCTGCATTGCATGAGgtacatacataattgggaattttgttttgaacaaataaaaggataaacataatggttttatttcaatcagatgaagacaatcgatcatgcatgttgatgcacatttctaattttgatctcttattcctcctaatttag

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 26
lower sequence: GRMZM5G893864_T01 (Zea mays), 5'ss of exon 4
ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgttcaatacattt--------acattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctg----tgttgc-cccccaactttcag---------------------------------------------
 || |||||||||||||| || ||  || | || ||||  |  || || || || ||||| |||||||||||||| ||||||||||||||| |||| ||||| || |  ||||        | |||     |   |  |||  || || || || ||| |||        |||| | ||    |   || |  | ||| |   |                                             
TCCTAATGACAAACTTCTCCTAGTAAAAGCTCTTAAGAAAATAGGCCATGTTGTAGCTGTTACTGGTGATGGAACGAATGATGCTCCTGCATTGCATGAGgtacattcaatttgggagttcatattttaaatgaatacaagaattcaacatgca-tgtgattatatgaagcactatttggtaatacagcacttctaacatgttgaggtttcttccccttctcaatcttatcattattcccacttatcag

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 26
lower sequence: GLYMA13G00420.1 (Glycine max), 5'ss of exon 25
ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgtt--caatacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaactttcag-------
 || |||||||| ||| | ||||||||| |  ||| ||||| ||| || || |||||||| ||||| |||||||| |||||||||||||||||||| ||||||  |||  |||||    |  |  |  |  |  ||||| |   | || | |   |     | |   |        |       |    | |        
TCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGGAGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAATGATGCTCCTGCACTGCATGAGgtttgcaaggcatttcttatgtttttgggcatgtgcttttatttttcattttagatacatgttaagatgatgacagtaattataattaatgatacaattg

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 26
lower sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 24
ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgttca-atacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaa-ctttcag--------
 ||||||||||||||  | || || ||| |  ||| ||||| ||| || || |||||||| ||||| |||||||| ||||||||||||||||| || ||||||   ||| || ||   |  | | | |  |  ||||| |   |       |||  |  |  |   |  |  || ||       | | || ||        
TCCCAATGACAAACTATTGCTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatatatatatgatatttg-aggcttgtgcttttattgtttgtaagtatccattacaatgatgacattgatggtaatggagcatttagtttgatta

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 26
lower sequence: GLYMA09G06890.1 (Glycine max), 5'ss of exon 24
ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgttc----aatacattt-acattc----ctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgcccc-ccaactttcag-
 ||||||||||||||  |  | || ||| |  ||| ||||| ||| || || |||||||| ||||| |||||||| ||||||||||||||||| || ||||||     | ||  ||| | |||     || ||   |||  | |||   | ||  |  |||  || ||| ||| |    ||  ||   |    | ||| |  
TCCCAATGACAAACTATTGTTAGTACAAGCATTGAGGAGGAAGGGTCATGTTGTGGCTGTAACTGGGGATGGAACAAATGATGCTCCTGCACTTCATGAGgtttgcatagtattttttatatttgaggcttgtgcttgtgtggtttgttagtattc-attac-gatgatgacattgatggtaatggagcatttagtttgatt

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 26
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 27
ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgttcaatacatttacattcctcgtatgtgtaagctttaaaaatacact---gttattgaggatcacactttctgtg-ttgccccccaactttcag-----
 || |||||||| ||||||||||||||| |  |||| | ||  || || || || ||||| ||||| |||||||| ||||||||||||||||| |||||||||        |     |      ||          || ||||    |    |  |||   |   ||| | ||    || |    | ||| | |      
TCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATGCTCCTGCACTACACGAGgtttggcgagctctagatagaatgatagaccgatggtagaaatctgtttgaatctttggataagtcacatacttcaattacttggccactgttaacctat

upper sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 26
lower sequence: PP1S8_288V6.1 (Physcomitrella patens), 5'ss of exon 26
ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgttcaatac-atttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgt-gttgccccccaactttcag-------------------
 || | ||| || ||    || ||| |  |  |||||   ||     | |||||||||||||||||||||||||| || || || || ||  |||| |||||  ||  | |  ||         | | |  | | |||     |    |||   | |   |   | ||||||| |  | | |    ||    |                   
TCCTACTGATAAGCTCAAGCTGGTGAAGGCATTGAAGCAAAGATCGAATGTCGTGGCTGTGACTGGTGATGGAACTAACGACGCACCCGCGTTGCATGAGgtaaaaggctacctattgatactttctttcaacggttttggcgtgatgtgtatgtcacagtttaattttctgtcgaggtcacgaggctgatggtacattattggcactgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCCAATGACAAACTTCTTCTTGTGCAATCGCTGAAGAGGAGGGGACACGTCGTGGCTGTGACTGGTGATGGAACCAATGATGCTCCTGCACTGCACGAGgttcaatacatttacattcctcgtatgtgtaagctttaaaaatacactgttattgaggatcacactttctgtgttgccccccaactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA