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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggtcatctttcaatattcttttggtattatttcattttattgtgtcttaaggtaggaatgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA

Basic information

species Vitis vinifera
transcript Vv05s0077g00460.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g00460.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os12g37720.1 (Oryza sativa), 3'ss of exon 10
gtaagttggtcatctttcaatattcttttggtattatttcattttattgtgtcttaaggt-aggaatgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA
                         |     || ||| | |||||  | |  || || || |   ||  |  ||  || |  | |  |   | || | | | |  |  | ||||     ||||||| |||||| | |||||||||||||| ||||| || |||||||||||||| |||||| | || || || ||||| ||||| ||||| || || || |
------------------------gtgagtttaatatattattttgctattcctaaatgttaaagattgagtgctcatatagatta-ggcctgttgaacctgc--tcctgttgttg--cagGTTTGCCACAGCAAAGCATGGGATTCAAAAATTGTTACCAGTGCTTGGTGGGTGTATCCTTATCAAGTTAGCAAAACAGCTCCCACTGGCGAGTACCTAA

upper sequence: Vv05s0077g00460.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G063544_T01 (Zea mays), 3'ss of exon 1
gtaagttggtcatctttcaatattcttttggtattatttcattttattgtgtcttaaggtaggaatgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA
                                      | | || |   | | |  |   |   | | | |  |  | |  |   | | |  |        ||     || ||     ||||||| |||||| | |||||||||||||| ||||| ||||||||||||||||| ||||| || || || || || || ||||||||||| || || ||||
-------------------------------------gtgagttaaagatttttctaaacattta-ggataatacctttaaaaagtcagtgctcatatgatcatggccttcgtgcttcagGTTTGCCACAGCAAAGCATGGGATTCAAAAATTGTTACAAGTGCTTGGTGGGTGTATCCACATCAAGTTAGCAAGACAGCTCCTACTGGCGAGTACCTTA

upper sequence: Vv05s0077g00460.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G03670.1 (Glycine max), 3'ss of exon 9
gtaagttggtcatctttcaatattcttttggtattatttcattttattgtgtcttaaggtaggaatgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA
        ||     || || |   |     || ||| | |  | | | |   ||  |||    |   | | || || |  |||    ||||        ||| |  ||||| ||  ||||| || || |||||||| |||||||| || ||||| || ||||| ||||||||||||||||| ||||| ||||||||||||||||| || |||||||| |
--------gtatgtgtttaacaccttccc--tactatgttaactaaatttactttttggtcatcaactaaaccaaatgttaact----attaccacttccaca-tcattttggaatgtagGTCTGCCATAGCCAGGCCTGGGATTCGAAAATTGTTACTAGTGCCTGGTGGGTTTATCCTCATCAGGTTAGTAAAACTGCTCCTACAGGCGAATATCTGA

upper sequence: Vv05s0077g00460.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G14560.2 (Glycine max), 3'ss of exon 9
gtaagttggtcatctttcaatattcttttggtattatttcattttattgtgtcttaaggtaggaatgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA
        ||     || || |         || ||  | || | | | |   ||  |||    |   | | || || |  ||     ||||        ||| |  ||||| ||  ||||| || || ||||||||||||||||| || ||||| || ||||| ||||||||||||||||| || || ||||||||||||||||| || |||||| | |
--------gtatgtgtttaacacctgccc--tactaggttatctaaatttactttttggtcatcaactaaaccaaatgttaacc----attaccacttccaca-tcattttggaatgtagGTCTGCCATAGCCAGGCATGGGATTCGAAAATTGTTACTAGTGCCTGGTGGGTTTATCCTCATCAAGTTAGTAAAACTGCTCCTACAGGCGAATATTTGA

upper sequence: Vv05s0077g00460.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G49930.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagttggtcatctttcaatattcttttggtattatttcattttattgtgtcttaaggtaggaatgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA
                               | | || |  | || | ||   || |  || |  |||| |   |  |       |||  |      |||     | |  | | |   |||||||||| || ||||| |||||||| |||||||| || ||||| ||||||||||||||||| ||||||| |||||| ||||||||||| ||||| ||||
-----------------------gtaagcaatttcatctactattttggttgtttgaattatg--tgaatatggtg-caatgtcttga--tggcagacttttggatataatatgatgcagGTTTGTCATAGTCAGGCCTGGGATTCCAAGATTGTTACTAGTGCATGGTGGGTTTATCCTCATCAGGTCACTAAAACAGCTCCTACTGGGGAATACCTTA

upper sequence: Vv05s0077g00460.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ34355 (Selaginella moellendorffii), 3'ss of exon 10
gtaagttggtcatctttcaatattcttttggtattatttcattttattgtgtcttaaggtaggaatgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA
                              |||        |||  || | | |       | ||||  |||    |  ||  | |   || |||   ||     |||||  |   | ||||||||| ||| || ||||||||||| |||||  | ||||||||||||||||| |||  ||| || || || || || || || || || |||||||| |
------------------------------gtaacgagctgtttgtttatctttc------gcaatg--cagttccttcgctttttttgttttttttttt-----tttttgttttgacagGTTTGTCGCAGTCAAGCATGGGATTCCAAGATCATTACAAGTGCTTGGTGGGTATATGATCATCAAGTGAGCAAGACGGCCCCGACGGGTGAATATCTCA

upper sequence: Vv05s0077g00460.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ31247 (Selaginella moellendorffii), 3'ss of exon 10
gtaagttggtcatctttcaatattcttttggtattatttcattttattgtgtcttaaggtaggaatgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA
                              |||        |||  || | | |       | ||||  |||    |  ||  | |   || |||   ||    ||||||| |   | ||||||||| ||| || ||||||||||| |||||  | ||||||||||||||||| |||  ||| || || || || || || || || || |||||||| |
------------------------------gtaacgagctgtttgtttatctttc------gcaatg--cagttccttcgctttttttgttttttttgttttt-tttttttttttgacagGTTTGTCGCAGTCAAGCATGGGATTCCAAGATCATTACAAGTGCTTGGTGGGTATATGATCATCAAGTGAGCAAGACGGCCCCGACGGGTGAATATCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA
                              agcttac  putative branch site (score: 3)
                                       tttttttgt  putative PPT
                    tgaattatttagctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttggtcatctttcaatattcttttggtattatttcattttattgtgtcttaaggtaggaatgaacagcatatctgcactctgaattatttagcttacaatttttttgtaaaatagGTTTGTCACAGCCAGGCATGGGATTCAAAGATTGTCACAAGTGCTTGGTGGGTTTATCCTCACCAGGTCAGTAAAACTGCTCCTACTGGAGAATATCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA