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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgttatgtcataagcagaagcggatttatttctatactaaaacttatttaaatctattttgacctttacatgataacttcttagttctttcaatgcagTACTCGCTTGCCAACTCAAGGGAAGAGAGAAGAAATCTATATCTGGTGCTTTTTGACTATGTTTTGCATCAAATTAATGAAACATGCATAGCTACCAGTG

Basic information

species Vitis vinifera
transcript Vv13s0019g00680.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 2
-gttgttatgtcataagcagaagcggatttatttctat-actaaaacttatttaaatctattttgacctttacatgataacttcttagttctttcaat-gcagTACTCGCTTGCCAACTCAAGGGAAGAGAGAAGAAATCTATATCTGGTGCTTTTTGACTATGTTTTGCATCAAATTAATGAAACATGCATAGCTACCAGTG
     ||||||  |  |  |      ||| | ||  || |||| |  ||||  | |   |||   ||    | ||| | |    |      ||||| | |||||| || |  |||||||||||||| ||||   |  || | |   | || || ||||||||||| ||||||||||| |||||||||| | | |||  | |  
gaggtttatgtt-tgtggtgtttttcattcagttgcatcactacattttatgcagagtcatt--aacaaagagatgtttatgcatataccttttcatttgcagTATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTATTTGACTATGTATTGCATCAAATAAATGAAACATTCTTGGCTGGCGGCC

upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA18G52540.1 (Glycine max), 3'ss of exon 8
gttgttatgtcataagcagaagcggatttatttctatactaaaa--cttatttaaatctattttgacctttacatgataacttcttagttctttcaatg-------cagTACTCGCTTGCCAACTCAAGGGAAGAGAGAAGAAATCTATATCTGGTGCTTTTTGACTATGTTTTGCATCAAATTAATGAAACATGCATAGCTACCAGTG
        ||  ||   | | |  |||  |   ||| || || |  || |||  | | |   ||     ||| |||||  |  | |  || || | |||       ||||| || ||||| |||||||| |||||||| | |||||| ||| ||||||||||||| ||  || |||||||||| |||||||||||||| ||||   |||
--------gtagtata-aaatgttgataaagccctaaaccaagatcctaattacagtgttagtttcaaattatatgatttccccctgctttttgctatgttgattgcagTATTCCCTTGCAAACTCAAGAGAAGAGAGGAAAAATCTGTATTTGGTGCTTTTTGATTACATTCTGCATCAAATAAATGAAACATGCATTGCTAGTGGTG

upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G10370.1 (Glycine max), 3'ss of exon 11
gttgttatgtcataagcagaagcggatttatttctatactaaaa-cttatttaaa---tctattttgaccttta------catgataacttcttagttctttcaatgcagTACTCGCTTGCCAACTCAAGGGAAGAGAGAAGAAATCTATATCTGGTGCTTTTTGACTATGTTTTGCATCAAATTAATGAAACATGCATAGCTACCAGTG
           |  |  | | |  |||  ||  ||| || || | | || ||| |   |   |||| |  | ||      ||   |   || ||  |   || | | ||||| || ||||| |||||||| |||||||| | |||||| |||  |||||||||||| ||  || |||||||||| ||||||||||||||||||||  |||
----------tagtataaaatgttgataaatccctaaaccaagatcctaattacagtgttagttttaaattatatgatttcaccctgcttttttgctatgttgattacagTATTCCCTTGCAAACTCAAGAGAAGAGAGGAAAAATCTGTATTCGGTGCTTTTTGATTACATTCTGCATCAAATAAATGAAACATGCATAGCTACTGGTG

upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G23240.1 (Glycine max), 3'ss of exon 14
gttgttatgtcataagcagaagcggatttatttctatactaaaacttatttaaatctat----tttgacctttacatgataacttcttagttctttcaatgcagTACTCGCTTGCCAACTCAAGGGAAGAGAGAAGAAATCTATATCTGGTGCTTTTTGACTATGTTTTGCATCAAATTAATGAAACATGCATAGCTACCAGTG
  |||    | |  |   ||  |    |  ||  ||||  |  | ||   ||||| |       ||||    |        | || ||  ||  ||  ||||||||  | ||||  |||||||| |  ||||| | ||||||  ||   |||||||||||||||||| ||||||||||||||||||  |||||||||||  |  
--tgtagaatgaagacatgatccaaggtccttgttatatcagtattt--ctaaatttgcaatacttgaaggatttcctcccatttatttctttgttggatgcagTATGCCCTTGTAAACTCAAGAGGGGAGAGGAAAAATCTGCATTCAGTGCTTTTTGACTATGTTCTGCATCAAATTAATGAAAATTGCATAGCTACTGGAA

upper sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G43560.2 (Glycine max), 3'ss of exon 11
gttgttatgtcataagcagaagcggatttatttctatactaaaacttatttaaatctat----tttgacctttacatgataacttcttagttctttcaatgcagTACTCGCTTGCCAACTCAAGGGAAGAGAGAAGAAATCTATATCTGGTGCTTTTTGACTATGTTTTGCATCAAATTAATGAAACATGCATAGCTACCAGTG
  |||    | |  |   ||     | |  ||  ||||| |  | ||  |||||| |      |||||    |        | || ||  ||  ||  ||||||||  | ||||  ||||| || || ||||| | |||||| |||  ||||||||||||||||||| |||||||| |||||||||  |||||||||||  |  
--tgtagaatgaagacatgatctaaagtccttgttataccagtattt--ttaaatttgcaatatttgaaggatttcctcccatttttttctttgttggatgcagTATGCCCTTGTAAACTCGAGAGAGGAGAGGAAAAATCTGTATTCGGTGCTTTTTGACTATGTTCTGCATCAAGTTAATGAAAATTGCATAGCTACTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttaaatctattttgacctttacatgataacttcttagttctttcaatgcagTACTCGCTTGCCAACTCAAGGGAAGAGAGAAGAAATCTATATCTGGTGCTTTTTGACTATGTTTTGCATCAAATTAATGAAACATGCATAGCTACCAGTG
                           tgataac  putative branch site (score: 2)
                                 cttcttagttctttc  CT-rich tract
     taaatctattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttatgtcataagcagaagcggatttatttctatactaaaacttatttaaatctattttgacctttacatgataacttcttagttctttcaatgcagTACTCGCTTGCCAACTCAAGGGAAGAGAGAAGAAATCTATATCTGGTGCTTTTTGACTATGTTTTGCATCAAATTAATGAAACATGCATAGCTACCAGTG

- - - - - - -aagcaga
- - - - - - - - - - - - - - - - - - - ctaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttacatg