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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG

Basic information

species Vitis vinifera
transcript Vv17s0000g02570.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|||| ||| | | | || ||| || || | ||| |||| |||| | | || | | | | |||| |||||||| ||||| |||||||||||||| ||||||| ||||||||||| ||||||||||||| || || ||||| ||||||||||| ||||| || ||||
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggc-ttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 3
-----cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
| | |||| ||| | | | ||| | | | |||| || || | | ||| | | || | | || | | |||| |||||||||||||| ||||||||||||||| | || || |||||||| |||||||||| ||||| || || ||||| || || ||||| || || || ||||
atgccatgctcttgaactatcgatacatatgcttagcataccaatttgga--taatttcaaatgcact-tgcaccatactaaactcaaatgtgtt--ttttgcagTACACTCCTGCAATTGATATTTGGAGCGTCGGTTGTATATTTGCTGAAATGCTTATGGGAAAGCCACTTTTTCCTGGAAAGAATGTGGTACATCAATTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatat-----caaatttcttaaaaccttctccattttt-cagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
| | || | | | || | | || | || ||||||| ||| | |||| ||| |||| || | | |||| |||||||||||||| ||||||||||||||| |||| || |||||||| ||| |||| ||||| || || || ||||| ||||| ||||| ||||| |||||||
----tacttgaacagtgtgtacatagtgtg-gagtttgatgtatcagcttgttttac-aaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G375975_T01 (Zea mays), 3'ss of exon 3
---------cttttgatgaaatatgacctct-ttggtttataaaatttaagtggagttatgttttattaaactatat-atcaaatttc-------ttaaaacctt---ctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
||| | | || ||| | | | | | || ||| || | | | | | | || | | |||| ||| ||| | || ||||| ||||| ||||||||||||||||| |||||| |||| || |||||||| |||||||||| ||| || || || ||||| || || ||||| || || || |||
gtcggatagttttcacccggacacaacttctactagctcttcattgctatatggttttttactgtttaagagtacaccacttcattttgctgaatttacaacttaacacttaattttgcagTATACTCCTGCGATTGATATCTGGAGCCTAGGTTGTATATTTGCTGAAATGCTTATAGGGAAGCCTCTCTTTCCTGGCAAGAATGTGGTACATCAACTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 4
----------cttttgatgaaatatgacctctttggttta-taaaatttaag----tggagtta--tgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
||| | || || |||| |||| | || |||||||| || | || || | |||| || ||| || ||||| |||| | ||| |||| ||||||||||| || ||||||||||||||||| ||||||||||||||||||||||| || || || || ||||||| ||||||||||| |||||||| ||||
gtaagtttcttcttttttttaacatcttttcttgggttgaatataatttaagcaattgaacatacttggtgtattgaaatatgcatgtaattt--taaatttatttcctttttgcagTACACTCCAGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
--------cttttgatgaaatatgacctctttggtt-tataaaatttaagtgg--agttatgttt----tattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
||||| | || || |||| |||| |||| ||| |||| ||| || |||| || ||| || ||||| |||| | ||| |||| |||||||| ||||| ||||||||||||||||| || |||||||||||||||||||| || || || || ||||||| ||||||||||| |||||||| ||||
gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattgaacatgcttgatatattgaattatgcatgcaattt--taaatttatttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
--cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttt---tattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|| || ||| | || ||| | | | | ||| ||| |||| |||| | | |||||| ||| |||| || |||| ||||| || ||||| ||||||||||||||||| ||||||||||||||||||||||| | || || || ||||||| || ||||||||||||||||| ||||
cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatatatttaagtattgcacta-gtgtgtaatttc--aaatccttgtc--ttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
-cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttt---tattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|| || ||| | || ||| | | | | ||| ||| |||| | || | | ||||| ||| |||| || |||| ||||| || || || ||||| ||||||||||| ||||||||||||||||||||||| | || || || ||||||| || ||||||||||||||||| ||||
ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttc--aaatccttgtc--ttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
cttttgatgaaata-tgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccattttt-----cagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
| ||| ||| | | | | ||| |||| || || | | | | |||| | || | | | || | | | | || || ||||| |||||||| |||||||| |||||||||||||||||||||||||||||||| || || || || ||||||| ||||| ||||| |||||||| ||||
-gtaaaatgcaattctctattttcttttttgcaaaagttgtctg-attcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
cttttgatgaaatatgacct-ctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
| | || | | | ||| || | ||| | | ||||| | | || | || | ||| || ||| | | | ||||| || ||||||||||||||||||||| | || ||||||||||| |||||||| ||| || ||||| ||||| || |||||||| || ||||| ||||
ccacttttgtatgaaggcctgctctagttagctatctacaagtgt-gcaggataaggtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------cttttgatgaaatatgacc---tctttggtttataaaatttaa--gtggagttatgttttattaaactatatatcaaatttcttaaa--------accttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|| |||| | | | | ||| || ||| | ||| ||| | | | || | | || ||| || || | || |||||||| || |||||||||||||| ||||| | || ||||| ||||| ||||||||| || || || ||||||| |||||||| || |||||||| ||||
gtaagattctttttcaccaaacccaactactcttgctatttctccctaccaggaaaatgcttctagttttctattttgtagaatattgttgtgtggttctatagtgttgttgagaagaccagccatctcaagctaagtctactcttgttatatttcagTATACCCCTGCGATTGATATCTGGAGTGTCGGTTGCATTTTTGCGGAAATGCTTTTGGGTAAGCCTTTGTTTCCCGGGAAAAACGTTGTGCACCAATTGG

upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 4
----------------------cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|| | |||| | | || || ||| | | | | | ||||| || | | | || | | | || | | ||||| ||||||||||| ||||| ||||| ||||| || |||||||| ||| || | || ||||| ||||| ||||| || || ||||| || || || |||
gtgagcagcactagtacccttcgttctattgaactttatgtactgtga--cgcaaattgttattaagaacacgtttt-ttgtgtggtgtgactaaataag-attatgttacttgtgctgcagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACTGGAAAGCCGCTTTTTCCTGGAAAGAATGTCGTTCATCAACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
                                      ccttctccatttttc  CT-rich tract
 ttttattaaactatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - -tgaaata
- - - - - - - tgacctc
- - - - - - - - - - - - - - -ataaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttaaaa