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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcctacatctttttgttttggtgtgttaaaccatttttctgttctgctattttaactgcttgtcgttatgttgtagGTTAAGTTACATAAAGATCTTGTGCACTTTGAAACTGCTTATGTTGTCAAACTGCACAATGTAGCAAGGCTTGCTCCTTGTAAACCG

Basic information

species Vitis vinifera
transcript Vv04s0008g03120.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03120.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 12
gtatgtcctacatctttttgttttggtgtgttaaaccatttttctgttctgctattttaactgcttgtcgttatgttgtagGTTAAGTTACATAAAGATCTTGTGCACTTTGAAACTGCTTATGTTGTCAAACTGCACAATGTAGCAAGGCTTGCTCCTTGTAAACCG
        ||  |   | |  | |         |||| |       || ||   ||| || ||  |    ||||     || | ||   |||||||||| |||  || ||||||||||| |||||||||||||| |||    ||||||| ||||| ||     || ||
-------gtaagtgcctctactatatcaatgataaccgtaagatatttatggagtttgaagtgaattggtttatac---agATCAAAGCACATAAAGATATTGCACATTTTGAAACTGCATATGTTGTCAAACTACACCGAATAGCAAGACTTGCACCAACACAATCG

upper sequence: Vv04s0008g03120.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT4G31120.2 (Arabidopsis thaliana), 3'ss of exon 18
gtatgtcctacatctttttgttttggtgtgttaaaccatttttctgttctgctattttaactgcttgtcgtt-atgttgtagGTTAAGTTACATAAAGATCTTGTGCACTTTGAAACTGCTTATGTTGTCAAACTGCACAATGTAGCAAGGCTTGCTCCTTGTAAACCG
||| || || |  ||||||| | ||   |   ||   | ||||| | |   ||     |  |  || || |  || | | ||||||||   ||||||||||||| ||||||||||||||||||||||||||| ||||| | |||||||| |||||||||||   |  | 
gtaggttcttctgctttttgctatgtactcgcaag--agttttcagattaact---caagttctttttcatccatttggcagGTTAAGGCTCATAAAGATCTTGCGCACTTTGAAACTGCTTATGTTGTCAAGCTGCATAGTGTAGCAAAGCTTGCTCCTTCCCAGTCT


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttaaaccatttttctgttctgctattttaactgcttgtcgttatgttgtagGTTAAGTTACATAAAGATCTTGTGCACTTTGAAACTGCTTATGTTGTCAAACTGCACAATGTAGCAAGGCTTGCTCCTTGTAAACCG
                            ttttaac  putative branch site (score: 2)
                          tattttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcctacatctttttgttttggtgtgttaaaccatttttctgttctgctattttaactgcttgtcgttatgttgtagGTTAAGTTACATAAAGATCTTGTGCACTTTGAAACTGCTTATGTTGTCAAACTGCACAATGTAGCAAGGCTTGCTCCTTGTAAACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG