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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctattttagaactgctttgtcctgcagggtaacttatatatctatatgttgcagTATTGGTTTGACAGATAGGGAAGAGGGGGACTTGGGACCCATATATGGGTTCCAGTGGAGACACTTTGGTGCCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g12940.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 6
------------------------------------gttctattttagaact--gctttgtcctgcag--ggtaact---tatatatctatatgttgcagTATTGGTTTGACAGATAGGGAAGAGGGGGACTTGGGACCCATATATGGGTTCCAGTGGAGACACTTTGGTGCCAG
                                    || | | ||    | |   |||| |  |||||   |||| |   | || || | | | ||||||| ||||||||||||| ||||| ||||| |||||||||||  | |||||||| || ||||| ||||||||||||||
tgatgggcaagcatgactatatattttaacttttaagtacaaattgtacatttttctttatgttgcagtttgtaattggctttacatttttttattgcagTGTTGGTTTGACAGAGAGGGAGGAGGGCGACTTGGGACCTGTTTATGGGTTTCAATGGAGGCACTTTGGTGCCAG

upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 6
-------------------------------gttctattttagaact--gctttgtcctgcag--ggtaact---tatatatctatatgttgcagTATTGGTTTGACAGATAGGGAAGAGGGGGACTTGGGACCCATATATGGGTTCCAGTGGAGACACTTTGGTGCCAG
                               || | ||||    | |   |||| |  |||||   |||| |   | || || | | | ||||||| |||||||||||||  |||| ||||| |||||||||||  | |||||||| || ||||| ||||||||||||||
gcaagcatgactatatatttcaactttttaagtacaatttgtacatttttctttatattgcagtttgtaattggctttacattttt-tattgcagTGTTGGTTTGACAGAGCGGGAGGAGGGTGACTTGGGACCTGTTTATGGGTTTCAATGGAGGCACTTTGGTGCCAG

upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 5
------------------------------------gt-tctattttagaactgctttgtcctgcagggtaactta-tatatcta-tatgt---tgcagTATTGGTTTGACAGATAGGGAAGAGGGGGACTTGGGACCCATATATGGGTTCCAGTGGAGACACTTTGGTGCCAG
                                    || |  |||  | |  |  | | | ||     || | | | |  || || ||| |   | ||| |||||||||||||| ||||| ||||| ||||| |||||  | |||||||| |||||||| |||||||| |||| 
gtaccttgataggcaagcatgaccatctactaatttgtattaattgcaaattttttcttttctatgcagttattaactggatttagtatttatatacagCATTGGTTTGACAGACAGGGAGGAGGGTGACTTAGGACCTGTTTATGGGTTTCAGTGGAGGCACTTTGGAGCCAA

upper sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 6
-----------------------------------gttctattttagaactgctttgtcctgcagggtaacttat----atatctatatgt-tgcagTATTGGTTTGACAGATAGGGAAGAGGGGGACTTGGGACCCATATATGGGTTCCAGTGGAGACACTTTGGTGCCAG
                                    ||  |||    |  |  | | | ||     || | | |      |  |||| | | | ||| |||||||||||||| |||||  |||| ||||| |||||  | |||||||| |||||||| |||||||| |||| 
gtaccttgataggcaagcataaccatctactaatttttgaattgctaattttttcttttctatgcagttattaaccggagttgctatttatatacagCATTGGTTTGACAGAAAGGGAGAAGGGTGACTTAGGACCTGTTTATGGGTTTCAGTGGAGGCACTTTGGAGCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctattttagaactgctttgtcctgcagggtaacttatatatctatatgttgcagTATTGGTTTGACAGATAGGGAAGAGGGGGACTTGGGACCCATATATGGGTTCCAGTGGAGACACTTTGGTGCCAG
                           gggtaac  putative branch site (score: 3)
                              taacttatatatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctattttagaactgctttgtcctgcagggtaacttatatatctatatgttgcagTATTGGTTTGACAGATAGGGAAGAGGGGGACTTGGGACCCATATATGGGTTCCAGTGGAGACACTTTGGTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA