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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgagtaattgttgcctcaactgcatttcaaatatagcttctgcataaagtctcataccttggtttggacttcag

Basic information

species Vitis vinifera
transcript Vv11s0016g04420.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 5'ss of exon 5
TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgagtaattgttgcctcaactgcatttcaaatatagcttctgcataaagtctcataccttggtttggacttcag
| | |||||||||||||| ||  | |||||  ||||||| |||||||| || || || |||||||||||| | |||||||||||||| ||||| |||||||| ||||    | || |   ||  ||    ||||   |   ||| |      || |  ||   |    ||| |||
TATCATTGTTCGACCTCTCTCAACAGTAAGTGCCCTTGTGCGATTTGCAGAAGAACCGCAGATGTTTGCATTCGAATTCAATGATGGTTGCCCGATTCATgtaagtatgcat-gcatagtctctatgcacaataccacgaatgcctcctaattcttggctgtttcctcact-cag

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G367023_T01 (Zea mays), 5'ss of exon 5
TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgagtaattgttgcctcaactgcatttcaaatatagcttctg-cataaagtctcataccttggtttggacttcag
||  ||||| ||||| || || || |||||  |  ||||||||||||| || ||||| |||||||||||| |||||||||||||||| ||||| |||||||| ||||                |  | ||| || ||    || |||  | |    | |  || |||     ||||
TGCCATTGTACGACCACTCTCAGCAGTAAGTGCTTTTGTTCGATTTGCTGAAGAGCCACAGATGTTTGCATTTGAATTCAATGATGGCTGCCCAATTCATgtaagtagacagcatacaggtctctatccaattacaggaaatgtcatctaatt--gttctatgttttt--tctcag

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G049288_T01 (Zea mays), 5'ss of exon 5
TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgagtaattgttgcctcaactgcatttcaaatatagcttctgcataaagtctcataccttggtttggacttcag
||| || || ||||| || || || |||||  | |||||||||||||  || || || ||||| |||||| |||||||||||||||| ||||| |||||||| ||||  | |           |  | | | || ||    ||| ||     | || |  || |||     ||||
TGTCATAGTACGACCACTCTCAGCAGTAAGTGCTCTTGTTCGATTTGTAGAAGAACCACAGATATTTGCATTTGAATTCAATGATGGCTGCCCAATTCATgtaagtacatatcatacaggtctctatcccattacaggaaatgc-tatgtaattattctgtgtttt---tctcag

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA17G12950.1 (Glycine max), 5'ss of exon 5
TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgagtaattgttgc----ctcaactgc-atttcaaatatagcttctgcataaagtctcatacct---tggtttggacttcag
||||| |||||| ||| ||||| | |||||  | |||||||| ||||| || |||||||||||||||||||||||||| | |||||||||||| || ||||| ||   ||||||      | |  |   ||||   ||  |  |     ||||| | ||  |||    |||  || | |  ||
TGTTACTGTTCGTCCTTTATCTTCAGTAAGTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCCATgtaagcttttgttgtgctatttagttatgatttgttatgcacttatgctataaattttctcaccaatgtggcatgaattgtag

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G08040.1 (Glycine max), 5'ss of exon 5
TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgagtaattgttgcctcaactgcatttcaaatatagcttctgcataaagtctcatacct-tggtttggacttcag
||||| |||||| ||  ||||| | ||||   | |||||||| ||||| || |||||||||||||||||||||||||| | |||||||||||| || ||||| ||   ||||||    |  |   | | |  |||    | |  | |   |||||  | | |||  || | |  ||
TGTTACTGTTCGTCCGTTATCTTCAGTAACTGCTCTTGTTCGGTTTGCTGAAGAGCCCCAGATGTTTGCAATTGAATTTAGTGATGGATGCCCCATCCATgtaagattttgttgtgctatttagttataatttattatgttt-taaattttctcacgcatgtggcatgaattgtag

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S60_221V6.1 (Physcomitrella patens), 5'ss of exon 5
TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgag-------taattgtt-gcctcaactgcatt--tcaaatatagctt--ctgcataaagt----ctcataccttggtttggacttcag----------------------------------------------------------------------------------------
 || ||||| ||| || ||||||||||       |||||||| ||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||| |||||||| |       ||| |  | ||| |  ||   ||  ||| ||||   ||   || | | |||    || |||     ||     |||  |                                                                                        
GGTCATTGTCCGATCTTTATCTGCGGTGGCTGGTCTTGTTCGGTTTGCTGAGGAACCCCAAATGTTTGCGATTGACTTCAATGATGGTTGCCCTCTTCATgtgtggttcttttaactactcgccacgtctttcttgttcatatatgttttatttgtacacagttgctctaataagacagtgccatcttttgttcctgggtttttaccgagtgttttatttaagtaattaagctgaaggactcgttgtgtgctaacgaatggtgtctctcatctgtgtag

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ24089 (Selaginella moellendorffii), 5'ss of exon 6
TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgagtaatt-gttgcctcaactgcatttcaaatatagcttctgcataaagtctcataccttggtttggacttcag
 || | || ||| ||||||||  | |||    | || ||||||||||| |||||||||||||||||||| ||||| ||   ||||||||||||  | ||||| |||  || | |     || |||| |    ||  ||||  | ||| ||  | | | |                 
AGTGAGTGGTCGGCCTCTATCGTCAGTAGCAGCTCTCGTTCGATTTGCTGAGGAGCCCCAGATGTTTGCTATTGAGTTTGGTGATGGATGCCCAGTCCATgtaagtgttttgcttttgtaagtgcact----atgaagctcttacatcaaaaccctttcag---------------

upper sequence: Vv11s0016g04420.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ35138 (Selaginella moellendorffii), 5'ss of exon 6
TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgagtaatt-gttgcctcaactgcatttcaaatatagcttctgcataaagtctcataccttggtttggacttcag
 || | || ||| ||||||||  | | |    | || ||||||||||| |||||||||||||||||||| ||||| ||   ||||||||||||  | ||||| |||  || | |     || |||| |    ||  ||||  | ||| ||  | | | |                 
AGTGAGTGGTCGGCCTCTATCGTCAGCAGCAGCTCTCGTTCGATTTGCTGAGGAGCCCCAGATGTTTGCTATTGAGTTTGGTGATGGATGCCCAGTCCATgtaagtgttttgctttggtaagtgcact----atgaagctcttacatcaaaaccctttcag---------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTATTGTTCGACCTCTATCTGCGGTAAGCTCCCTTGTTCGATTTGCCGAGGAGCCCCAGATGTTTGCAATTGAATTCAATGATGGATGCCCTATTCATgtgagtaattgttgcctcaactgcatttcaaatatagcttctgcataaagtctcataccttggtttggacttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA