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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggatggtcgtgtacgtgcatgtgcatgtgtgtattactccacatgcatgtatttttttttaggatcatatttaacagctgcttcttgtgttttgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG

Basic information

species Vitis vinifera
transcript Vv10s0003g04530.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 12
tggatggtcgtgtacgtgcatgtgcatgtgtgtattactccacatgcatgtatttttttttaggatcatatttaacagctgcttcttgtgtt-------ttgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG
    | ||       || | |  |||    | | ||| | ||     ||   ||| | ||||  ||  |  ||  ||  | |||     |||       || | ||||||||||||| |||||||| ||||| |||||||| || ||||| ||||||||||| ||||| ||||| |||||  || | ||||| |||||||| |||||
----ttgtttaacttgtactttcgcacaaatattttaatgcaaccttat---tttgtctttataatactgctttccacttacttggatcgttctctcaatttttcagTGATCATGTTTTTGATATCCTGGTCTTTTACTGTTGTCTCCCTTGCCCTTGCAAGCCTCATCTATTACTATGTGAGCTTAAAAGGTAAGGCTGGAGACTG

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 10
tggatggtcgtgtacgtgcatgtgcatgtgtgtattactccacatgcatgtatttttttttaggatcatatttaacagctgcttcttgtgttt--tgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG
|   | |||      || | | |  ||   | |  |  |  | |  || | ||  ||  |  | |  |||||  | || || || |     ||  | | |||| ||||||||  |||| |||||| | ||||||||||| ||||| ||||||||||| |||||||| || |||||  || | ||||| ||||| ||||||||
tctctagtccacctagttcttttttattaatatgattttatagaatca-gcatccttagtgtgcagtatatt-gatagatgattttccctcttaatttccagTTATCATGTTTATGATCTCTTGGACTTTTACTGTGGTCTCCCTTGCCCTTGCAAGCCTCATATACTACTATGTCAGCTTAAAAGGAAAGGCAGGGGACTG

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G113276_T01 (Zea mays), 3'ss of exon 6
--tggatggtcgtgtacgtgcatgtgcatgtgtgtattactccacatgcatgtatttttttttaggatcatatttaacagctgcttcttgtgttttgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG
  |   |  || |||   | ||   |||  | | ||       |||  |||| |    ||| ||     |  | |         |  |||| |    | ||||||| |||||  |||| || ||||| || ||||| || ||||| ||||||||||| ||||| ||||| |||||  |||| |||||||||||||| |||||
tattatttatcatgttt-tacaatagcaaatatctaac-tgaaacagccatgaaagcatttataattataagtgttgacatgaatctttgtatcaatttcagTGATTATGTTTCTGATCTCCTGGTCTTTCACTGTTGTCTCCCTTGCCCTTGCAAGCCTCATCTATTACTATGTGAGCATAAAAGGGAAGGCTGGAGACTG

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G401874_T01 (Zea mays), 3'ss of exon 6
tggatggtcgtgtacgtgcatgtgcatgtgtgtattactccacatgcatgtatttttttttaggatcatatttaacagctgcttcttgtgttttgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG
                ||| | | | |   |  |||  |  || ||   |  | |  |  |||    |||  ||     |    | | |   |  |||||| ||||||||  |||| || ||| ||||||| ||||||||||| ||||| ||||| || || || || || ||  || | ||||| ||||||||||||||
-------------gtatgcttcttcgtccctacattgttgaac-tgttggagtctaatggtagatagataggtagataatttcccctctaaat-atgcagTTATCATGTTTATGATCTCATGGACATTTACCGTGGTGTCCCTCGCCCTCGCAAGCCTAATCTACTACTACGTGAGCTTAAAAGGAAAGGCTGGGGACTG

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 10
--tggatggtcgtgtacgtgcatgtgcatgtg--tgtattactccacatgcatgtatttttttttaggatcatatttaacagctgcttcttgtgttttgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG
  | | | |   |        | |||| |     |||  |||| |   ||  ||  | ||   ||   |    |||     | || | |||      | |||||||||||||||| | || ||||||||||| || ||||||||  |   ||||||||| ||||||||| | || ||  |||| ||||| ||||||||||||||
catagtttgctattattcattaggtgcttaccactgtggtactgctgctgtgtgagtgttacattgaaacttgattctgtgg-tgatccttac---ctatgcagTGATCATGTTCCTAATCTCTTGGTCATTCACCGTGGTGTCTTTGCTCCTTGCAAGCCTCATATATAAGTACGTGAGCATTAAAGGAAAGGCTGGGGACTG

upper sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G30450.3 (Arabidopsis thaliana), 3'ss of exon 11
------------------------------------------------------------------tggatggtcgtgtacgtgcatgtgcatgtgtgtattactccacatgcat------gtatttttttttaggatcatattta--------acagctgcttcttgtgttttgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG
                                                                  | ||   ||   |  |  |     | || |  | |||   ||| || ||       | | || ||  |    | | || |        |    |  || || | || | ||||||||||||||||||||||||||||||||| ||||||||  || | || ||||||||||| |||||  | || ||  || | ||||| ||||||||||||||
gtatgaaattttcaaatactcacggagaaagtgtctttcccagtctacctatgtagtccattcctatagaaattctgatttgaactaccacgtg-gcttcttatctcacctgaatcctgagatgtcttattacaaagccttgttgagtttttaaattattattttttctattct-tgcagTGATCATGTTCTTGATATCTTGGTCATTCACTGTGGTTGCCATTGCACTTGCAAGTCTTATATACAAATACGTTGGCCTAAAAGGAAAGGCTGGGGACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgtatttttttttaggatcatatttaacagctgcttcttgtgttttgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG
                        atttaac  putative branch site (score: 3)
     tatttttttttaggat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggatggtcgtgtacgtgcatgtgcatgtgtgtattactccacatgcatgtatttttttttaggatcatatttaacagctgcttcttgtgttttgtgcagTGATCATGTTCTTGATATCTTGGTCATTTACTGTGGTGTCCCTAGCCCTTGCAAGTCTCATATATTATTATGTATGCATCAAAGGGAAGGCTGGGGACTG

tggatgg
- - - - - - - - - catgtgc
- - - - - - - - - - - - - tgtgtgt
- - - - - - - - - - - - - - - - - - -ctccaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcttc