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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g04980.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 7
---gaagtcacgggttatgttgagatgattagtttggactgtca-tgattttcctaatttctcaactgaaatgaagttaaccttattcatttt-tgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
          |  ||  |  | |   |||| ||||||| ||  | || ||        |  | ||||    |     |||| | | | | |       |||  ||||||||||||||||||| || | | | || || |||||||||||||| ||||| ||||| ||||| ||||| |  |||| | | ||| | |||
gtttgttcttcttgtagttatcaagagatt-gtttggattgcaagtgtttagtgcccatagttaactctggtctttctaacatgagtaactcaactttcttgcagGTTCATAATGATGATGAGGTTAGGACATTATTTAAGCAAGTTCAAGGCGAAGTACCTGGTTCCCCAATATTTATCATGAGGCTAGCTGCTCAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 5
--gaagtcac-gggttatgttgagatgatt-agtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
  ||| || | | |   |||  | || ||  |||||||  |||   ||     |||| ||  |   |   ||    ||||  | | |     | |      |||||||||||||||||||| || |  ||  |||| |||||||| ||||||||||| ||||||||||| ||||| |  |||| | |||| ||||||
gtgaactctctgtgaactgtgcacattatggagtttgg--tgtggggag----ctaactttccctttttgatatgattaaaatcaattcccctgg------tagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTATCATGAGGCTTGCATCCCAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G377341_T02 (Zea mays), 3'ss of exon 3
-------------------------------gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaacc-ttattcatttt------tgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
                                 ||    ||    | || | |   | |  ||  | | ||| |        |||   |||||||  |  || ||  |  | |||    |       || |  | ||||||||||| |||||||| || | |||  ||||||||||||||||||| ||||| |||||||| || ||||| |  ||||| || || || |||
gtttgttttctttttcaactgaactgtggaaagagagggggccgctattaaaaaagtgaagttaaagtttcagg---caaaaaatagatcaactgtcactaatttttctgtcatttgcatcattgcatggatctgtagGTTCATAACGATGATGAGGTGAGGGCGCTGTTCAAGCAAGTTCAAGGAGAAGTCCCTGGCTCACCTATATTTATTATGAAAGTGGCATCTCAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
----------------gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
                ||    ||    | ||  ||  ||   |  ||||| | |  ||         |   | |   ||| ||||        | | |||||||    ||   ||||||||||||||||||| || |  ||  |||| |||||||| ||||||||||| ||||||||||| |||||    |||| | |||| ||||||
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagctaccccccttttgacatga-------ttaaatcattttcc--ctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 3
gaagtcacgggttatgttgagatgattagtttggactgtcatgattttccta--atttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
    | |     |||    | | ||  | ||||  |     | |||||  ||  |||| |      || |  ||  |     |  ||| |  || |||||||||||||||||||||||| || | ||| ||||||||||||||||||||||||||||| || || |||||||| |  ||||||||||| ||||||
tgcataaatacctataagaacaagaa-actttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaacaggcatatg-gatcttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCAGGTTCTCCCATATTTATAATGAAGGTTGCATCCCAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
gaagtcacgggttatgttgagatgattagtttggactgtcatgattttccta--atttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
    | |     |||    | | ||  | ||||  |     | |||||  ||  |||| |      || |  ||  |    ||  ||| |  ||  ||||||||||||||||||||||| || | ||| ||||||||||||||||||||||||||||| || || |||||||| |  ||||||||||| ||||||
tgcataaatacctataagaacaagaa-actttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaataggcatatg-gattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 4
gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttt---tagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
                         |  | ||     |  |||| | ||  | ||| || ||| |    ||||  || |  |  | ||||  | |||    ||||||||||||||||||| || | |||| | |||||||||||||||||||| || || ||||| || ||||| |  |||||||||||||| |||
------------------------gtctgcttctgtagatatgactgtc--actttttccactaagccaaagtgtacttattgtagtttttcattttggtaagGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAAGGTGAGGTCCCGGGCTCGCCGATATTTATAATGAAGGTTGCTTCACAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 4
gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
   ||||  | || ||| || |||  |   || || |||   || |   |  ||| ||  |        ||||  || |  |    |||| || || |||||||||||||||||||| || | |||| | |||||||||||||| ||||| || || ||||| || |||||||  ||||||||||| || |||
---gtca--gcttctgtagatatgcct---tttgattgtg--gactaagccgattactatat-------aagt--acttattctggttttaaatttatagGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAGGGTGAGGTCCCAGGCTCACCAATATTCATAATGAAGGTTGCGTCACAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ11248 (Selaginella moellendorffii), 3'ss of exon 3
gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
                          || ||| ||     | | ||  | |  ||  |   ||    |  || | ||       | | ||   | | |||||||| || || || || |||||||||||||| |||||||| ||||| ||||| || ||||| || || || |  ||||| ||||| || |||
-------------------------gtattttagagcaaaaagtttcgctttcttcgtgctcttctttatagctgact------actgttcctcctgtagGTTCACAACGACGAAGAGGTCAAGGCTTTGTTTAAGCAAGTGCAAGGCGAAGTACCGGGCTCGCCGATCTTTATCATGAAAGTTGCCTCTCAG

upper sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ11422 (Selaginella moellendorffii), 3'ss of exon 3
gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
                          || ||| ||  |  |  | ||||    | |     ||    |    |||    |    | | ||   | | |||||||| || || || || |||||||||||||| |||||||| ||||| ||||| || ||||| || || || |  ||||| ||||| || |||
-------------------------gtattttaga--gctaaaactttcgctttcttcgtgctcttct----ttatagctgaatactgttcctcctgtagGTTCACAACGACGAAGAGGTCAAGGCTTTGTTTAAGCAAGTGCAAGGCGAAGTGCCCGGCTCGCCAATCTTTATCATGAAAGTTGCCTCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG
                                                ctttt  CT-rich tract
                                 ttattcatttttgaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagtcacgggttatgttgagatgattagtttggactgtcatgattttcctaatttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG

- - - - - - - - - - - - - - - - - -ctgtcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaa