Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT

Basic information

species Vitis vinifera
transcript Vv18s0041g02070.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
|||| |||  | ||   |    |     |  |||   ||||| | |   |||      |  |||    |||    || ||   |||  ||||||||||||||||||||||||||||||||||||||| || ||  |||| || ||| |||||||  |||| ||||| ||||||||| | ||||||||||||||
gtaatttc-ccttcccttttgctc--ctacaaatgttctttcaaattgttttacaaactagactagc-atacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT

upper sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G44600.1 (Glycine max), 3'ss of exon 3
gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
|||| |||  || |   |         ||   | |||  ||  |   |   |     || |    || |||    ||  |   |||  | ||||||||||||| |||||||||||||||||||||||||| || ||||| || || ||||||||  | || ||||| ||||||||| | ||||||||||||||
gtaatttcccccaccttttgctcctgccaaatactaatgtttcaaataccctgccaaatactaacatcatatccatggctgtgcaaattgtagGTTTTGATGGGGTTGAGATCCATGGGGCTCATGGCTACCTGCTTGAGCAATTTATGAAAGATAAAGTGAATGACCGAACAGACGAATATGGTGGATCCCT

upper sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
------------gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttac---ccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
            | |||   |   ||  | |||  || | |    || |  || ||   ||| |     ||| | || | |  || |    |||    | || | ||||||||||||| ||||||||||| || |||||||||||  ||||||| || ||||| |||||| | || ||||||||||  ||    ||||||||||||||
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatga--aatgtaatg-taagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT

upper sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G35410.1 (Glycine max), 3'ss of exon 4
------------gtaaattcatcctctaatacaat-taatcatga-attaactttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
            ||  | |    || |||||  || || ||||||  ||||  |    || | | ||   |||   |   |  |||      || |  ||| | |||| ||||||||||||||||| |||||||| ||||| | |||| |||| |||||  ||||||| || || || ||  |||||||||| ||||||||||||  
tcatatacctgagtggagtttcactttaatatgatatagtcatgatgttaaact----gtgattctcaaagatattcaattcctaaccgcaattgc--aat-tgtagGGTTTGATGGAGTTGAGATACATGGGGCACATGGTTTTCTAATTGATCAGTTTTTGAAAGATCAAGTTAACGACAGAACAGACAAATATGGTGGATCCAC

upper sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
----gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgat-gcactgatga--taatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
    ||  | |    || ||||  |  | ||   |   | |  ||  | |    || |   ||     | || |  |  ||      |    |  | |||| |||||||||||||||||||||||||| ||||| | |||| |||| || ||  |||||||||| || || ||  |||||||||| || ||||||||  |
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT

upper sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ20558 (Selaginella moellendorffii), 3'ss of exon 4
gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
                          |  | || ||   ||||       |  ||  |||  || | || ||  | |           | |||| |||||||| |||||||||||||||||||| ||||||||  | ||||| ||| ||||| |    ||||| ||| |||| ||  |||||||||| ||  |
-------------------------gtgttaaactatgcttctttctttctagtttcatgggctaacgaaaaactgg----------gtgtagGCTTTGATGGTGTTGAGATCCATGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAAATGGTGTCAACGATAGAACGGATGAGTATGGTGGTTCTTT

upper sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ28624 (Selaginella moellendorffii), 3'ss of exon 4
gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
                          |  | || ||   ||||       |  ||  |    || | || ||  | |           | |||| |||||||| ||||||||||| |||||||| ||||||||  | ||||| ||| |||||||    ||||| ||| |||| ||  |||| ||||| || ||
-------------------------gtgttaaactatgcttctttctttctagtttcacaggctaacgaaaaactgg----------gtgtagGCTTTGATGGTGTTGAGATCCACGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAGATGGTGTCAACGATAGAACGGATGAGTACGGTGGTTCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
                      cactgat  putative branch site (score: 3)
                                       tttaccc  putative PPT
                           atgataatattgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgatgcactgatgataatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA