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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcttttagggattctattttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagagtacttgattgtgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG

Basic information

species Vitis vinifera
transcript Vv04s0008g06500.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
------------tgtct-tttagggattctattttacaatggtagtccaggttaaagtcctatgtgaaggaattcaga----gagagtacttgattgtgattttctatttttt----gcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
            | | |   |    |||  | || | |  | |  |     || ||  | ||   | || | ||         |  ||   | ||| |  | |||| |||  |    |||||| || |||||||| ||||||||| | || |||||||||||||| || || ||||||||||| ||||||||||||||||||||||||||||  ||  | |
gtaatttcctaatatttacctgttcattaaaattcatagggatcatttgatttcaa-ccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG

upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------tgtcttttagggatt-ctattttacaat---ggtagtccaggttaaagtcctatgtgaaggaattca----gagagagtacttgattgtgattttctattttt----tgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
                                                                              ||| | | |   | | ||  | ||   |   |  || | |  ||  | || ||   | |  | ||      |  |  |||  | ||| |  | ||    |       |||||||||| || ||||| || |||||| | || |||||||| ||||| ||||| || |||||||||||||| ||||||||||||||||||||||   |  | |
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcagaaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G882708_T03 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------tgtcttttagggatt-ctattttacaat---ggtagtccaggttaaagtcctatgtgaaggaattcagag----agagtacttgattgtgattttctattttttg----cagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
                                                             ||| | | |   | | ||    ||   |   |  || | || ||  | || ||   | |  | ||         |  |||  | ||| |  | || |  |   ||    |||||||| || ||||| || |||||| | || |||||||| ||||| || || || |||||||||||||||||||||||||||||||||||||   |  | |
gtaaactttgcatgttaatttgtaattcctggggactagaaatgttcatctgaataacatttgtttctcaaaaactactgacatatgttcctgaaagcctagatttcaatcataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G882708_T01 (Zea mays), 3'ss of exon 1
tgtcttttagggattctattttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagagtacttgattgtgattttct-attttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
      | |   ||  |  |  |       | | ||     ||   | ||     |  | | | ||  |   | |  || |  | | || | |   |||||||||| || ||||| || |||||| | || |||||||| ||||| || || || |||||||||||||||||||||||||||||||||||||   |  | |
-actactgacatatgttcctgaaagcctagatttcaatcataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG

upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 2
------tgtcttttagggattctattttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagagtacttgattg-tgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
      ||  |  | |  |||  || ||   ||| |  || | |  |||    ||      | ||  |||     || ||| |||  |  | |||| ||  || |||||| | |||||||| || |||||||| ||||||||||| |||||||| ||  |||| |||||||||||||| ||||||||||||||||||||| || |||
cattgatgcatgct-gaaatttgatgtttttatgctgttctatgagaaaacttta------gaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG

upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G06930.1 (Glycine max), 3'ss of exon 3
tgtcttttagggattctattttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagagtacttgattg-tgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
||     |    ||| | | ||  | | ||  | ||  | |   |  | ||     |  ||||||    || ||| |||  |  | |||  ||  || |||||| | ||||| ||||| |||||||| ||||||||||| |||||||| ||  |||| |||||||||||||| ||||||||||||||||||||| || |||
tgcaaaattaatattttttcttcaagttgttatacacatcatt-tattttgattttgctttcagaagtggttctttattaattttcttccgttgctttcagTATCTATCAAACGCTGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTGTTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG

upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G32170.1 (Glycine max), 3'ss of exon 2
----------------tgtcttttagggattcta-ttttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagag----tacttgattg---tgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
                ||   | |     || || ||   ||     |   || |   | ||   ||||  ||    | | | ||      || || ||||      |||||| || ||| |||||| | ||||||||||| ||||| || ||||||||||| |||||||| ||  |||| || |||||||||||||||||||| ||||||||||  ||| |||
gtgaggaagttaagattgatatctcaattttgtagttaggcagaaccaaagcatgcataggtttgatgtttagtctgttatatagtattgttattttattgattcatttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCGCGAACAAGTGTTGCAAGTACAACAGTATTATCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGCTTATGG

upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G14010.2 (Glycine max), 3'ss of exon 1
-------------------tgtctt--ttagggattctattttacaatggta-gtccaggttaaa-gtcctatgtgaaggaattcagagagagtacttgattgtgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
                   | ||||  || |   ||      ||| |  | | |   ||||| |  ||    | ||  | |    || |  | |  || | |    |||||| || ||| |||||| | ||||||||||| |||||||| ||||| ||||| |||||||| ||  | || || |||||||||||||||||||| ||||||||||   ||||||
gtaagtaactcaagattgatatcttgatttgtagttaagcagtaccaaagcatgcataggttcagtgtttagtctgttgtatagtagtgttatttttttaattcctttttctgttgttttcagTATCTATCAAATGCTGCCCTTGCACGAACAAGCGTTGCAAGTACAACAGTATTGTCATCTACTTCAGGACTCTTCACTCTCTTCATTGGTGTGTTTTTGG

upper sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G32140.1 (Arabidopsis thaliana), 3'ss of exon 2
------tgtcttttagggattc----tatt-ttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagagtacttgattgtgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
      | ||||| |     ||    |||| ||   ||||| || |  |  |  ||||| | | ||  |  |  |      || ||| |||   ||||  ||  |   |||||| | || |||||||| ||||| ||||||||||| || ||||| || ||  | |||||||| || ||||| || ||||| |||||||||| | ||||||
gtgaattttctttgatatgctcgttgtattgttttgatggtggtgcctgaaagtgtcctcttttaa--accttggtattgatatttgtttgctgtttttgatgat--acagTATCTGTCCAATGCTGCTCTTGCTCGTACAAGTGTGGCAAGTACTACTGTATTGTCTTCAACCTCGGGACTGTTTACTCTGTTCATTGGTGTATTTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctatgtgaaggaattcagagagagtacttgattgtgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG
                          acttgat  putative branch site (score: 5)
                                      ttttctattttttgc  putative PPT
                                   tgattttctatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcttttagggattctattttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagagtacttgattgtgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG

- - - - - - - - - - - - - - - - - - - - - - -cctatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - gaaggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agagaga