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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag

Basic information

species Glycine max
transcript GLYMA06G44340.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 5'ss of exon 13
GCTTGATGGCCGGGC-TAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag
  || || |  |||| | ||||  |  | ||| ||||||| || ||||| ||  | |||||||| ||||| |||||||| ||||||||||| |||||||||||       ||  |  | |  | |||||||   |||  | |  ||  | |  ||  ||   |   |   |   |||||||                             
-TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGgt-------tagctctacaaacaatatgttacttttagt-tctttccgaggaaagaatgaatctcaagaccatatcttctgtgcag-----------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G155384_T02 (Zea mays), 5'ss of exon 13
GCTTGATGGCCGGGC-TAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgtt-atttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag
  ||||| |  || | | ||||  |  | ||| ||||||| || ||||||||  | |||||||| ||||| ||||||||||| |||||||| ||||| |||||    | || |   ||   ||        ||| ||||    || |||  |||  |    |  | | | |                                        
-TTTGATTGATGGTCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAGAATTTAGCTGCAACATTTGTAAATGCATTTGTGAATGCTGGGTTTGGCCAGgttagcttttgagacaacccttactagcaatgtttttgaaaagagtttaagtttttttattgctttgtgcag--------------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
lower sequence: GRMZM2G314233_T01 (Zea mays), 5'ss of exon 5
---GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag
   | ||||||||||   | ||||  |  | ||| ||||||| || ||||||||  | |||||||| ||||| ||||||||||| |||||||| |||||  ||||  |   ||    | || | ||| ||||| | |       || ||    ||||   |   || |||| ||   |                                  
TTTGATTGATGGCCG---TGGTGCCAGCTCCAGTCTTGATTCCGCAAGACAGAATTTAGCTGCAACATTTGTAAATGCATTTGTGAATGCTGGGTTTGGCAAGgt-tagcttttgagacagttacta-atgtt-tgtgaagaaagacttcattttaac--ttctttttattactttgtgcag------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 5'ss of exon 11
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag
 || || ||| |||||||  | |||||||| || ||||| |||||||||||  | ||||| || ||||| |||||||| ||||||||||| ||||||||||||   |   |  | |  ||   |||  |  || | |  |   | |    |||||    |    |||  |                                       
ACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTTTTGGTCAGgtatggttgcagattataataaaatagatc-tagtggaagacgtgtcctcttaatatatttgcttatcgcag-------------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 5'ss of exon 11
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttc-tattcctcaatcttctacttctcacttcccattatcattgcgcag
|||||||||  |||||||  ||||| ||||||| || |||||||| || || ||  |||| |||||||| |||||||||||||||||||| || || ||||||  ||      || ||  |||  ||||   |  |     ||  || ||    ||  || ||| |||   ||  | ||  |                            
GCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGATTCGGCCAGgtatgat------tacaggatcttaatgtgcaacataagaagaactttggaagctgcccttttcatatatttccttattgcag---------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 13
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctctt-ctattcctcaatcttctacttctcacttcccattatcattgcgcag
|||||||||||||||||||||||||||||||||||| || || ||||||||||| || || |||||||| |||||||||||||||||||| ||||| |||||| |||||         |    |    |   ||  | |   ||        ||  |   ||| | | |||    |  | |     ||| ||    ||  | |   ||||
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTTTTGGACAGgtaaaatgtgtgaatttcacataaagaataaaataagataaaataaaacaaaaaaaaggacttacaagtccatgttggtgtgaaattca-ttggtttttccttgttgcag

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
lower sequence: PP1S414_22V6.1 (Physcomitrella patens), 5'ss of exon 13
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctat---atgttgtatttgttgtgattttgggtta---atgatctcttctattc--------ctcaatcttctacttctcacttcc-cattatcattgcgcag-------------------------------------
  | ||||| || || ||||| || || || || || || ||| | || ||||| ||||| |||||||| |||| |||||| ||||||||||||||   ||||   ||||   ||     | | |    || |   |||  ||  |   ||| |||   |  |   ||| ||||         |  | | ||  |||||   | |   |||     |   | |                                      
AGTGGATGGTCGTGCCAGTGCAGGAGCTAGCGTAGACTCTGCTCGTCAAAACCTGGCTGCCACTTTTGTCAATGGATTTGTGAATGCTGGCTTTGGCGTGgtatgctgttgaatattttctttgtcttgtgctacttttcgtgcaagcatggtttatgcagtactgcttttatttaaagactaccaagtgttacacttcatgcatggacatcgctgtcatgtacgttttttgtgaattaatcttcttatgtcgtgatgtag

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
lower sequence: EFJ14427 (Selaginella moellendorffii), 5'ss of exon 12
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgt----acaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag
  |||||||  | || ||||| || || ||||||||||| |||||||| |||||||| || ||||| || ||||| || || || ||||| ||||| |||||    |  |  | ||||  ||  |||  |   |  | || || |  ||   |                                                            
AATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtggacatgacctgattttcaggatctgca--ctaaaattatt-tctttccag------------------------------------------------------------

upper sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 13
lower sequence: EFJ26022 (Selaginella moellendorffii), 5'ss of exon 12
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag
  |||||||  | || ||||| || || ||||||||||| |||||||| |||||||| || ||||| || ||||| || || || ||||| ||||| |||||  ||  | |  | |   |||   |||| | | |     | ||||      |                                                        
AATTGATGGAAGAGCGAGTGCCGGAGCTAGTGTTGATTCGGCTAGACAAAACCTTGCAGCCACTTTCGTCAATGCTTTCGTCAACGCTGGTTTTGGACAGgtg-aacatgaactgatt-ttcaggatgt-gcact-aaaattatttctttccag-------------------------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCTTTGGTCAGgtacaatgttatttaaagattctatatgttgtatttgttgtgattttgggttaatgatctcttctattcctcaatcttctacttctcacttcccattatcattgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG