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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG

Basic information

species Vitis vinifera
transcript Vv04s0044g00860.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g54170.1 (Oryza sativa), 3'ss of exon 3
agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacag-----gtttattacatatatgatc-tccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
    | ||   ||| | |   |   |    || | |   |  |     |  | | ||||  ||  ||  ||| | |      |||| | | ||| |  |  | ||||| ||||| ||| ||||  |   |  |||||||||||| |||||| | |||||||| || ||||| |||||||| || ||||||||||  || ||| |  
---tcgttgcctatcggaccaaaataa-gctgtcttgctttcaggcacacgttcatttt--aggaacagaattctgaaatcatttactccttatttactgatacagATATGTGAGTGCGCTGTTATGACTAATCGATTGGAAGTACTTAATCTGTCTGGGAATCGCCTCACAGATGCATGCGGTTCTTACCTTTTCACAATCCTAC

upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G472023_T02 (Zea mays), 3'ss of exon 12
agtgctttta-ttattgtatttactcattattgacataacta--taattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
   | | | | ||||||     | |||  |   |      |   | |  | | ||      | || ||   |   ||   ||   |   ||| |  |    |||| ||||| ||| ||||  |   || |||||||||||| |||||| | |||||||| || ||||||||||||||  | |||||||| |  || ||| || 
---gatctcacttattgacccgagtcaacacaaattctcttgctttacagcatatattcagtaaaatgctaagccactttttgcctcgttatttactgaatagATATGTGAGTGCGCTGTTTTGACTGATCGATTGGAAGTACTTAATCTATCTGGGAATCGCCTCACTGATGCATGCAGTTCTTACCTATTCACAATCCTGA

upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G32290.1 (Glycine max), 3'ss of exon 13
--agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
    | |  || ||  |  || || | |       | |  || |  ||| |       | |||| |    ||||  |  || | |     | |      ||||||||||||||  |  |||||||||||||| | ||||||||||| || ||||| |||||||| |||||||||||||||||||| |||||||| |||||  
ttcatacaattcttgattaatataataaaagaatgcttttctctttttgcatgactaatctcaaatttgcaaatgta--ttaactttgcttgttcctgtcagATTTGTGAATGTTCACTGCTATTTGCTCGACTAGAAGTGCTTAACATTTCTGGAAACCGTCTTACTGATGCATGTGGATCTTATCTTTCAACAATCTTAA

upper sequence: Vv04s0044g00860.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G15560.1 (Glycine max), 3'ss of exon 13
agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctc--------cagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
      | ||||  |  | ||  | |||| |   ||||  |  | ||   ||   ||||     ||  ||   ||  |||  || |||||| | ||         ||||||||||||||  |  ||||||||| |||| | ||||||||||| || ||||| |||||||| |||||||||||||||||||| |||||||| || ||  
-----atctatttatacaattcttgattaatagaataa--aagaatgcttatctatttttgcacgatgaatctcaaatttgcta-atatattaacttgttcctgtcagATTTGTGAATGTTCACTGCTATTTGATCGACTAGAAGTGCTTAACATTTCTGGAAACCGTCTTACTGATGCATGTGGATCTTATCTTTCAACAATATTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG
                   gactaaa  putative branch site (score: 2)
                                                tctcc  putative PPT
                                tttattacatatatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgcttttattattgtatttactcattattgacataactataattggaaatgccttttcaagtgactaaatacaggtttattacatatatgatctccagATTTGTGAATGCCCTGTGCTATTTGCTCGATTGGAAGTGCTTAATATCTCTGGGAACCGTCTCACTGATGCATGTGGATCTTACCTTTCAACTATCTTGG

- - - - - - - - - - - - - - - - acataac
- - - - - - - - - - - - - - - - - - - - - -attggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataca