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

...tgatttttttttctataacatctcttatgtgttgttttatataatcaatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC

Basic information

species Vitis vinifera
transcript Vv05s0020g01780.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 5
----------------------tgatttttttttctat-aacatc----tcttatgtgttg--ttttatataatca-atttacttttgatcaatcagaatatactgacaacttggtattcctaccac-cagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
                      || |     | || || |||||     |  ||  | |||  | ||||||  | |   ||| ||    |  || ||   ||| |     | ||  || | |  |   |||||||| || |||||  | ||||| || ||  |  | || ||| |||||||||||||||||||||| |||||||||||||||||||| ||||| || ||||
gtactctattgctcttcattgttgttacacatatcaattaacattaagattatacttattgactcttatatggttatgcttaattcaacttcatgagctcatatt--tggcatgaaatccttctcgttcagGGTCTTGGAAAAACCCTTCAAACTATATCACTGCTTGGATATTTGCATGAGTTTAGAGGAATAACCGGTCCCCACATGGTTGTTGCACCAAAGTCCACTC

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 5
-tgatttttttttctataacatctcttatgtgttgttttatataatcaatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
 |   ||  || | ||   |    |  | ||    |   || |   |||| || | ||||   ||   | | | || | |  |    | || | |   |||||||| || |||||  | ||||| |||||  |  |||| ||||||||||| || || |||||||||||||| |||||||||||||| ||||| || ||||
gtatgttagttgtgtactcctaagccaaagt-caataaaatgtccccaatatattattgaatgat---actgtgcttatacttataaaatcat-cattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 5
-tgatttttttttctataacatctcttatgtgttgttttatataatcaatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
 |   ||  || | ||   |    |  | ||    |   || |   |||| || | ||||   ||   | | | || | |  |    | || | |   |||||||| || |||||  | ||||| |||||  |  |||| ||||||||||| || || |||||||||||||| |||||||||||||| ||||| || ||||
gtatgttagttgtgtacccctaagccaaagt-caataaaatgtccccaatatattattgaatgat---actgtgcttatacttataaaatcat-cattcagGGTCTTGGGAAAACTCTTCAAACTATTTCGCTGCTGGGCTATCTGCATGAATTCAGGGGAATAACTGGTCCGCACATGGTTGTTGCACCAAAGTCTACTC

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 2
---------------tgatttttttttctat-aacatctcttatgtgttgttttatataatcaatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
               | || ||  ||   || | | | |  |   | ||||| | | | | || ||||  |||||       | || |  |   || ||| ||||         ||||||| || |||||| | ||||| ||||| ||  |||| |||||||||||||| ||||| ||| ||||||| |||||||||||||| ||||| || ||||
gtatgcgataggtgttaatcttgattaagattatcttttactccattttgttgtgtttga-cactttaactttgaat-----gtatgtttttttaaattgttattt--------agGGTCTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAGCTGGTCCTCACATGGTTGTTGCGCCAAAGTCCACTC

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 5
tgatttttttttctataacatctcttatgtgttgttttatataatcaatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
 |  |  |   | | | | ||||    |  | || | | | || || ||||  ||||| |              |||   | |  | ||         |||| || || |||||| | ||||| ||||| ||  |||| |||||||||||||| ||||| ||||||||||| |||||||| ||||| || || || || |
-gtatgctacatgtgtta-atcttgattaagatgatct-tctactctattttgttttgtttggcactttggctttgaatgcatacttttttataatttagGGACTTGGGAAAACACTTCAAACTATTTCATTGCTGGGCTATCTGCATGAGTTCAGAGGTATAACTGGTCCTCACATGGTGGTTGCGCCGAAGTCCACCC

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------tgatttttttttctataacatctcttatgtg-ttgttttatataatcaatttact----tttgatcaatcaga---atatactgacaacttggtattccta---------------------ccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
                                                 | ||     || || |  ||| | | || || | | || | || ||  | ||||     |  ||    | ||    | ||  ||| || ||||| |  |||                         ||||| || ||||||||||||||||| || || ||||| ||||||||||| ||||| |||||||| |  ||||| || ||||| ||||| |||||||| ||||
gtaggtgtttggtgggcttgcagttgtgtctaattgaattaacttcatgtaatgcaagttgctttgtcatgtgtaatttgatagattgagatgatttagttaccccactcagaggggtaaggcttagatgttgataagttggtttagctaagtaatgacaaatgaatgtgattggcagGGGCTTGGTAAAACATTGCAAACTATATCCTTATTAGGTTATCTGCACGAGTTCAGAGGAATCAAAGGTCCTCATATGGTGGTTGCTCCAAAATCTACTC

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------tgatttttttttctataacatctcttatgtgttgttttatataatcaa---tttacttttgatcaatcagaatatac---tgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
                                                                          | ||||  |   ||        |    | |     |  |||     ||   ||   | ||||| | |  |  || |    | |  ||       |   |    ||||| || ||||||||||||||||| || || ||||| |||||| |||| |||||  ||||||| |  ||||| || ||||| ||||| |||||||| ||||
gtaggtgtttggtgggcttgcagttgtgtctaattgaattaactgcatgtaaatgcaagttgctttgtcatgtgtaatttgatagactgaggtgatttagttatcccacta-ataggggtaaggcttagatgttgataagttggtttagataagtaatgacaaatagatgtgatttgcagGGGCTTGGTAAAACATTGCAAACTATATCCTTATTAGGTTATTTGCACGAGTTCCGAGGAATCAAAGGTCCTCATATGGTGGTTGCTCCAAAATCTACTC

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 5
-----------------------------------------tgatttttttttctataa-catctctt-atgtgttgttttatataat-caatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
                                          | |   | |   || ||  | || || |  |||  ||| ||  |||   | ||  || | |  |  ||   |  | | | || |   |||         ||||| ||||| |||||||| ||||| || ||||| || || ||  | |||||||| ||||||||||| || || || ||||| ||||| |||||||| ||||
gtaggtagcagatgctggcctcagataaatcacattcaagtagctgcatatgaatacaagtacctgttgacatgtaatttgatggaatatgagttgattgttaaaagccatggtgaaat-ataaataaatatattgtttttcagGGGCTGGGCAAAACATTACAAACAATATCTTTGTTAGGCTACTTACATGAGTTCAGAGGAATAACAGGCCCTCATATGGTGGTTGCTCCAAAATCTACTC

upper sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 5
tgatttttttttctataacatctcttatgt-gttgttttatataatcaatttacttttgatca--atcagaatatactgacaacttggtattcctacca-ccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
             || | ||    |||| |     | | |||  ||   |   || |  |     ||| ||   || |    | |   | |    |    | |||||||||| || ||  | |||||||||||||| |||| ||| ||||||||||  || ||||| | ||| || || ||||| ||||| |||||||| || |
------------gtaaaccactaattatcttagcatataataagatttttcagctctctaatgttatctgatgctaatctttattgtttttgttcatggtctagGGTCTGGGGAAGACGCTTCAAACCATTTCTTTGTTGGCTTACCTGCATGAGTACAGGGGAATTAATGGCCCTCATATGGTAGTTGCTCCAAAATCAACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC
                          tactgac  putative branch site (score: 1)
                                          ttcctacc  putative PPT
                    agaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatttttttttctataacatctcttatgtgttgttttatataatcaatttacttttgatcaatcagaatatactgacaacttggtattcctaccaccagGGTCTGGGTAAAACATTGCAAACCATTTCTTTATTGGGTTATCTGCATGAGTTTAGAGGAATAACTGGTCCCCACATGGTTGTTGCCCCAAAATCGACTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - catctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacaa