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

gtcaatgaaataaagttttgttgttattataataaaagaaatgcatgatcattgagcgatatttgttgctaaacttcctggaacaacttgtgatcttttctatttgcagTTCCTTTATGAACCATTTCCAGTTGAGAGTAGTCTGAGGGAGCACTTTCATGATCACATCAATGCAGAGATAGTTTCTGGAACAATTTGTCATAAAGAGG

Basic information

species Vitis vinifera
transcript Vv17s0000g07230.t01
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g07230.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: LOC_Os03g11470.1 (Oryza sativa), 3'ss of exon 18
gtcaatgaaataaagttttgttgttattataataaaagaaatgcatgatcattgagcgatatttgttgctaaacttcctggaacaacttgtgatcttttctatttgcagTTCCTTTATGAACCATTTCCAGTTGAGAGTAGTCTGAGGGAGCACTTTCATGATCACATCAATGCAGAGATAGTTTCTGGAACAATTTGTCATAAAGAGG
               |  | ||  | ||  | |           |  | ||||       || | |  || || ||     |||||    |    | |  ||||  |||||||| ||||||||||| || ||||| |||| ||| ||||||||||| ||||||||||| ||||| ||||| ||||| || || ||  || |||||||||
------------gtttcatattactttttcactttgtctgcctaacaaacattctaatgcatatttatctgaagttt----aacaatgaata--ttgtaatattctcagTTCCTGTATGAACCATTCCCTGTTGAAAGTAATCTAAGGGAGCACTTGCATGATCACATAAATGCGGAGATTGTTTCCGGCACTATCAGTAATAAAGAGG

upper sequence: Vv17s0000g07230.t01 (Vitis vinifera), 3'ss of exon 25
lower sequence: GLYMA06G21970.1 (Glycine max), 3'ss of exon 20
gtcaatgaaataaagttttgttgttattataataaaagaaatgcatgatcattgagcgatatttgttgctaaacttcctg----gaacaacttgtgatcttttctat-ttgcagTTCCTTTATGAACCATTTCCAGTTGAGAGTAGTCTGAGGGAGCACTTTCATGATCACATCAATGCAGAGATAGTTTCTGGAACAATTTGTCATAAAGAGG
                             | | ||  || ||  ||||| ||  |   || |||| || | | | |  ||    ||  |   |||  ||| || ||| ||||||||| | |||||||| || || |||||||||||| |||| ||||| || ||||||||||| ||||| || ||  |||||||||| ||||| |||||| | |
----------------------------gtcaaaattgagattgatgattat--acttatctttgctgattagcctaatgtgctgagaatactgttttctcttttatgttgcagTTCTTGTATGAACCCTTCCCGGTTGAGAGTAGTTTGAGAGAGCAGTTGCATGATCACATTAATGCCGAAATTATTTCTGGAACCATTTGCCATAAACAAG


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgatatttgttgctaaacttcctggaacaacttgtgatcttttctatttgcagTTCCTTTATGAACCATTTCCAGTTGAGAGTAGTCTGAGGGAGCACTTTCATGATCACATCAATGCAGAGATAGTTTCTGGAACAATTTGTCATAAAGAGG
            tgctaaa  putative branch site (score: 2)
                                       tcttttctatttgc  putative PPT
                                         ttttctattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaatgaaataaagttttgttgttattataataaaagaaatgcatgatcattgagcgatatttgttgctaaacttcctggaacaacttgtgatcttttctatttgcagTTCCTTTATGAACCATTTCCAGTTGAGAGTAGTCTGAGGGAGCACTTTCATGATCACATCAATGCAGAGATAGTTTCTGGAACAATTTGTCATAAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG