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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttatgtgaactattaggtgaagtctatgttctccaaattctgttatcaatatactttccatttaattttctaatatgataataacttcttgtttcagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG

Basic information

species Vitis vinifera
transcript Vv16s0013g01140.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA10G33820.1 (Glycine max), 3'ss of exon 8
tatttatgtgaactatta--ggtgaagtctatgttctccaaattctgt-tatcaatatactttccatttaattttc-taatatga--taataacttcttgtttcagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG
      |||  ||| | |  ||     | ||| ||    |||    || ||||  |  ||     |   | ||||  |  ||| |  |  |    | | | | |||||||||||||| |||||||| |||||||||||||| || ||||| |||||||| || || |||||||||||||| ||||||||||| |||||||||||||
------tgtctactttcaatggcattctttatatttattaaaacaagtatatccttggacaaatgaagcattttttatgttattacttgtttgtgtttggctccagGTGATAGACAAATCTTTTGGATTTGATACTGCTGTGGAAGAAGCCCAGAGAGCCATTAACGCTGCACATGTGGAGGTTGAAAGTGTTGAAAATGGAGTTG

upper sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G61580.1 (Arabidopsis thaliana), 3'ss of exon 7
tatttatgtgaactattaggtgaagtctatgttctccaaattctgttatcaatatactttccatttaattttcta-atatgataataacttcttgtttcagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG
               | |       |  ||  | | ||| ||  | | |   | |   |    |  | |||  || | ||  |  | |    |||||  ||||||| ||||| || ||||| |||||||| || ||||||||||| ||  |||| || |||||||||||||| || || || || || |||||||||||||
--------------gtaaatacccattgataattttcaacttaaggtctacttttctctcatgtggagtttcttatacatcttcttcatccattgttctagGTGATTGACAAATCATTTGGCTTTGATACGGCGGTTGAGGAAGCACAACGAGCTATTAATGCTGCACATGTAGAGGTCGAGAGCGTGGAAAATGGAGTTG

upper sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S282_45V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------tatttatgtgaactattaggtgaagtct-atgttctccaaattctgttatcaa--tatactttccatttaattttctaatatgataataact--tcttgttt--------cagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG
                |  ||  ||    |||| |   || |||         | |||| | | |||||    || ||   |    | ||| | |    | |  || |  | |    |        ||||| |||||||| || ||||| |||||||| |||||||| ||||| ||| | |||||||||||||| |||||||||| ||| ||| |  | |||||  |||
gtaggtttctgacaaatccttgagtctgatattcgtgcaactctcgaaagaatcgaattgtatgatcaagtcttaattgggaccagactttgtgaggaaagacgaattgatttgacctggaattggcagGTTATAGACAAATCGTTTGGGTTTGATACAGCTGTTGAAGAAGCACAGCGCGCAATCAATGCTGCCCATGTGGAAGCTGAGAGTATTCACAATGGCATTG

upper sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S131_40V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------------------------------------------tatttatgtga-actattaggtgaagtctatgttctccaaattctgttatcaatatactttccatttaattttctaatatgataataacttcttgtttcagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG
                                                                                                        |  ||| |  ||||  |      | | ||||  || | |   | |         |      || || || ||| || ||     ||   ||  ||||| ||||| ||||| || || |||||||| || || || ||||||||| | ||||||||||| || |||||||||| ||| |||||  | |||||  |||
gtacgtcactgtcttttgatatacacttggtaggattacgtgcggtagaagtaactaagtttcaggaagctaatatttggatacgtgtgtgcgcaaagactaccagatgacatgattaattatgtattgttttcttgaagtccaagtgtgccaccgtctaatgcatatttgtcgaatgtggta----tttgaggtaacagGTCATAGATAAGTCATTCGGATTTGATACAGCAGTGGAAGAAGCTCAGCGTGCAATCAATGCAGCTCATGTGGAAGCTGAGAGTGTTCAGAATGGTCTTG

upper sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 9
--------tatttatgtgaact-----attaggtgaagt-ctatgttctccaa--------attctgt-----tatcaatatacttt---ccatttaattttctaatatgataataacttcttgttt--cagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG
        ||   | |  || |     |   | || | | || |||| | |||        ||| |||     | | | | ||  ||   | |   ||      |||   | |     | |  ||||  ||||| |||||||| || |||||||||||||| || ||||| ||||| ||| | ||||| |||||||| || ||||||| ||| |||||  | |||||  |||
gtacgttttagacacggaaattcaacaacacgatggaattctctgtttttcaatggattgaattgtgtgggtttctgattgtaggttaagcaacacaagagctgaatggaaaatatggtgcacgtttggcagGTCATAGACAAATCATTTGGTTTTGATACCGCAGTTGAAGAAGCACAGCGTGCAATTAATGCTGCGCACGTGGAAGCTGAGAGTGTTCATAATGGCATTG

upper sequence: Vv16s0013g01140.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S327_30V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------tatttatgtgaactattaggtgaagtctatgttctccaaatt--ctg---ttatcaatatactttccatttaattttctaatatgataataacttcttgtttcagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG
                         | | | | |   | | |  ||    ||   |||  ||  ||  |||   | ||   | | | |||    |  || |||  |  |||  |   |||      ||| | || || ||||| ||||| ||||| |||||||| || ||||| ||  ||||||||||||| || ||||||||||  ||||||    | ||||| ||||
gtactatacatcatccctactacacagtgacgcgctttttcacatgtgtgcttatttccacatgttgcctgaattcattcgtgtgcgttctgacttgttctcttttgggat--ttgtttcaatgaacagATAATTGATAAGTCCTTTGGATTTGACACTGCTGTGGAAGAAGCACAACGAGCAATCAATGCAGCTCATGTGGAAGCAGAAAGTACTCATAATGGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcaatatactttccatttaattttctaatatgataataacttcttgtttcagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG
                                    taataac  putative branch site (score: 1)
                                          cttcttgtttc  CT-rich tract
     aatatactttccattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttatgtgaactattaggtgaagtctatgttctccaaattctgttatcaatatactttccatttaattttctaatatgataataacttcttgtttcagGTGATAGACAAGTCTTTTGGTTTTGATACTGCTGTTGAGGAAGCTCAGAGAGCAATCAATGCTGCACATGTGGAAGTTGAAAGTGTAGAAAATGGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - tgaagtc
- - - - - - - - - - - - - - - - -ctccaaa