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

TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatgataacattgttcaagtcttatcaatggtttgtgtagccctattaactgatgctgatgtttgctgcttctag

Basic information

species Vitis vinifera
transcript Vv14s0060g01680.t01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 21
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatg-ataacattgttcaagtcttatcaatggtttgtgtagccctattaactgatgctgatgtttgctgc--ttctag
 || ||||||||  |||| || || |||||||||||||| |||||||| || |||||||| ||||| |||||||| || ||||||||  ||||||||||||||  | |||  |||| ||| | ||  |  | | | |  ||     |   ||||| | | ||  |||  |||  |    ||| ||
AGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgta-ctgcatacataaaatt-tgcacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccag

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 21
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatgataacattgttcaagtcttatcaatggtttgtgtagccctattaactgatgctgatgtttgctgcttctag
 || ||||| ||  |||| || || ||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||  |||||||||||||||| |     |||  |          ||||  ||  | ||  |      ||| |    | ||||  |||   | ||  ||
AGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCATCCACATATACAATGTCAGGGTAGATGAGgtaatcagtgtctaatctctgatgcagtttat-gattctgtggatcatttcattcagcctt-ctgaccttt-tggttttcag

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GRMZM2G416836_T01 (Zea mays), 5'ss of exon 19
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatgataacattgttcaagtcttatcaatggtttgtgtagccctattaactga---tgctgatgtttgctgcttctag
 || ||||| ||  |||| || || |||||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| ||| ||||  |||||||| |||| || | |||   |   | |     |    |  ||||||  |||    |  || | | |   | ||||  ||||  | |||   
AGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCATTCACATATACGATGTCAGGGTAGATAAGgtgataa-atgcctaatctat---gatgcagtttatggttc-tgtgaatcatttcattcagccttctgacctttggggtttcag-

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 22
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattac-atgataacattgttcaagtcttatcaatggtttgtg-tagccctattaactgatgctgatgtttgctgcttctag----------
 || || ||||| ||||| ||||| |||||||| ||||||||||||||||| || ||||||||||| || || ||||| ||||||||| | || |||||||| ||||| ||  | ||    ||    | || |  ||  |   || ||    | |||| |  ||   || ||| ||  |    |          
CGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAATTCACATATACAATGTTAGAGTGGATGAGgtgattactatctttactgcttttttttttttttcattttaaatgctattatttttaatttgtgtc-atattttctcttgggggtatcttctag

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA19G41840.3 (Glycine max), 5'ss of exon 21
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatgataacattgttcaagtcttatcaatggtttgtgtagccctattaactgatgctgatgtttgctgcttctag----------
||| || ||||| || || ||||| |||||||| || |||||||||||||| || ||||||||||| || || ||||| || |||||| | || |||||||| |||||    |   | ||||    || | | || | ||| |||     | || | |    || || ||| ||  |    |          
TGCCTCTACCTTTCTGGCTTTCCACCCTCAAGATAACAACATCATAGCCATTGGGATGGAGGATTCAACAATTCACATATATAATGTTAGAGTGGATGAGgtgattactatctttaactgtttttttcattttaa-gatttatgttattatttttaatttgtctcatattttctcttgggtgtatattctag

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA20G38230.1 (Glycine max), 5'ss of exon 22
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatgataacattgttcaagtcttatcaatggtttgtgtagccctattaactgatgc-tgatgtttgctgcttctag-------------
|||||| ||||||||||| |||||||| || || || ||||| || ||||| || ||||||||||| ||||| ||||| || |||||  | || |||||||| ||| |    |   | |  |    || | |  ||  ||  | ||    |  |||      |   || ||| |  ||| | |             
TGCTTCTACCTTCCTAGCTTTCCATCCCCAGGATAACAACATTATTGCCATTGGGATGGAGGATTCAACCATTCACATCTATAATGTCAGAGTCGATGAGgtgattgctatctctaactagttttatcgttttgatatttactctattatttctaataatctcaccattttttccccttttgggggtatgttccag

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: GLYMA10G29090.1 (Glycine max), 5'ss of exon 22
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgta-attac-atgataacattgttcaagtcttatcaatggtttgtg--tagccctattaactgatgctgatgtttgctgcttctag-------------
|||||| ||||||||||| |||||||| || || || ||||| || ||||| || ||||| ||||| ||||| ||||| || |||||  | || ||||||||  ||| | ||    |  |||||    || | |  ||  |||     ||   ||| |  || |  |  || ||| |  ||| | |             
TGCTTCTACCTTCCTAGCTTTCCATCCCCAGGATAACAACATTATTGCCATTGGGATGGACGATTCAACCATTCACATCTATAATGTCAGAGTGGATGAGgtggattgctatctctaacttgttttt-tcgttttgatattttactattatttctaatgtctcacacc-attttttccccttttgggcgtatgttccag

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 5'ss of exon 21
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatgataacattgttcaa-gtcttatcaatggtttgtgtagcc-----ctattaactgatgctgatgtttgctgcttctag------------
 || ||||| ||  | || ||||||||||| ||||||||| |||| ||||| |||||||| || ||||| || ||||| || ||||| || || |||||||||| ||  |  ||  | |   ||  | |   |   | || | | |   |     | |  ||    |  |||   || |   || |              
AGCATCAACGTTTTTGGCGTTCCATCCTCAGGACAATAACGTCATCGCCATTGGAATGGAAGACTCTACGATTCACATCTATAATGTCCGAGTGGATGAGgtaagtagtttctagtactaaccattgccacttatgtagtctttttgatctatgacaaggaaaaacttgtgaaccttacgttttttgaagaaatggttct

upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 21
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 21
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatgataacattgttcaagtcttatcaatggtttgtgtagccctattaactgatgctgatgtttgctgcttctag-------------------------------------
 ||  | || || || || |||||||| |||||||| |||||||| |||||||||||||||||||| || || || ||||| |||||||| |||||||||||| ||  |  |   | || ||    | | |||    ||   | |     | |  | |  |     ||| | ||   ||  |                                     
AGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAATACAGATTTATAATGTTCGTGTAGATGAGgta-ttttaccaggccgttctttctttgtgatctcccgtacctatgttgatttgtattcgtcagtttgtattctagatcccgaataatgtgcctaattagagctttctgctgttggcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCATCCACATTTACAATGTTCGGGTAGATGAGgtaattacatgataacattgttcaagtcttatcaatggtttgtgtagccctattaactgatgctgatgtttgctgcttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT