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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA

Basic information

species Vitis vinifera
transcript Vv06s0004g03650.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g17570.4 (Oryza sativa), 3'ss of exon 5
gtaagtatcattttagtgttttca---ttttcatagaaat-ttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA
||||||| |||| | |      ||   ||||||   | ||  |  | |  ||||    || ||  ||   |  |  ||   ||  | |   |  |||| |   |||| ||||||||||||| ||  |||| || ||||||| ||||||||||||| |||| || || |||||||| ||| | ||||| ||||| || |||||||||||||| ||
gtaagtagcattcttgctcaaccacatttttcacttatatactgtgacacatttctacataaccttt-tagtctgaatatgtttgactg--atgctgatgtcattttcatgcagTGATGTCTTCGAATGACTCAATGGGTACAGTCTTTAAGTGTTTGTCAAAAGGAGCAGTTGACTTTCTAGTGAAGCCTATACGTAAGAATGAACTTAAGAA

upper sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g49460.3 (Oryza sativa), 3'ss of exon 5
gtaagtatcattt-tagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA
||||||| | ||  |    | | || |   ||     |  ||    | |   | | ||| |  |     ||  |||| || |  | | || |||  |   ||| | |||||||||||| ||  ||||| ||||||||| ||| ||||||||| |||| ||||| || ||||| || || || || || || || |||||||||||||| ||
gtaagtagctttcctcaactctacagtacaattcttgtacaaaatgt-tgcccttgtcatttatttactttctatgcttttagctgctacactgttgtggtttatgtgcagTGATGTCTTCAAATGATGCTATGGGTACAGTTTTTAAGTGTTTGTCAAAGGGCGCTGTTGACTTCTTAGTCAAGCCCATACGTAAGAATGAACTTAAGAA

upper sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G033962_T01 (Zea mays), 3'ss of exon 2
gtaagtatcattttagtgt----tttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA
||||||| | ||    |||    | |  ||   ||    ||  ||   ||  |||| |   | |  |   | |   |||| || |  | | || | || |   ||||| |||||||||||| ||   ||||  |||| ||| ||||||||| |||||||| || ||||| ||||| |||||||| || ||||| || |||||||||||||| ||
gtaagtaactttcctctgtacagtgtagttcatatcatgatcaaaatgttgctttcttg--atttatttagttccaatgcttttagctgctacaccgatgtggtttttgtgcagTGATGTCTTCGAGTGATGATATGAGTACAGTCTTTAAATGTCTGTCAAAAGGTGCTGTTGACTTTTTGGTCAAGCCTATACGTAAGAATGAACTTAAGAA

upper sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G095727_T04 (Zea mays), 3'ss of exon 6
gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA
|||||||         | |  |||  | |    |       |   | || || | | | |  |   | ||  || | || |  | | || |||| |   |||  |||||||||||||  |  ||||||||||| |||| || ||||||||| |||| ||||| ||||||||||| ||||| |||||  | || |||||||| ||||| ||
gtaagta-------gatttcctcaactaccctaatgcacgtgaaattttatcttgttaattgttgggtttaaatacttttagctgctacactgatgtgttttgcatgcagTGATGTCTACGAATGATTCTATGAGTATGGTGTTTAAGTGTTTGTCGAAGGGAGCAGTTGATTTCTTGGTAAAACCACTACGTAAGAATGAGCTTAAGAA

upper sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G005732_T02 (Zea mays), 3'ss of exon 2
----gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA
    |||| | |||| |      | |  ||   ||    ||| ||   ||  ||||  |||| |  |   |     |||| || |  | | || |||| | | ||| | |||||||||||| ||   |||| ||||| ||| ||||||||| ||| |||| || ||||| ||||| ||||| || || ||||| || |||||||||||||| ||
gtaagtaactttcatctctacagtgtagttcatatcatgattaaaatgttgctttc--atcatttatttagtcccaatgcttttagctgctacactgatgttgtttgtgtgcagTGATGTCTTCGAGTGATGCTATGAGTACAGTCTTTAAATGTTTGTCAAAAGGTGCTGTTGACTTTTTAGTCAAGCCTATACGTAAGAATGAACTTAAGAA

upper sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G07860.1 (Glycine max), 3'ss of exon 2
gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA
|||||   |||   |  ||| | | | |  |  |||||||||  |   ||| | || ||| ||||| || || ||  |||  | |    | ||   |  |    |||||||||||||||| |||||||||||||||||||||||||||||| |||| || ||||||||||||||||| |||||||||||||| | |||||||||||||||
gtaagcggcataccaaagttat-actctgttccaaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgttcaaatac--atgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGTGCAGTTGATTTTTTAGTGAAACCTATTCGGAGGAATGAACTTAAAAA

upper sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G15580.1 (Glycine max), 3'ss of exon 3
gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA
||||||  | |   |  ||| |  |||| |   |||||||||  |   ||| | || ||| ||||| || || ||  |||  | |    | ||   |  |    |||||||||||||||| |||||||||||||||||||||||||||||| |||| || || |||||||||||||| |||||||| ||||| | |||||||||||||||
gtaagtggcgtaccaaagttatactttttact-aaatttaagtatatattttcaatgactattgctcatgtggtgttttgtttattgcacatgttcaaatgc--atgcagTGATGTCATCTCATGATTCTATGGGTATAGTCTTTAAGTGTTTGTCAAAAGGCGCAGTTGATTTTTTAGTGAAACCAATTCGGAGGAATGAACTTAAAAA

upper sequence: Vv06s0004g03650.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G60100.3 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA
    ||||    | |     || |||       ||||||  |  ||||    || ||| | |  |    |   |   |  || |       ||| | |  |||| || |||||||||||| ||||||||||||| | | |||||||||||| |||| || ||||| ||||||||| | |||||||| ||| ||||||| ||||| || ||
----gtatttactcaaatccttgatt-------aaatttttg-tttatccagct-tcaatatgccatgctcagtttgtgtaactcaagatgtgatgtttctttt-tgtagTGATGTCATCACATGATTCTATGGTTCTGGTCTTTAAGTGTTTGTCGAATGGTGCTGTTGATTTTCTCGTGAAACCCATTAGAAAGAACGAACTAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA
                                 ccctgac  putative branch site (score: 3)
                                          tctttttat  putative PPT
                                         atctttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatcattttagtgttttcattttcatagaaatttaaggcttattttcctatcactcttgctgatttgatgcattgaatttccaccctgacgatctttttatgcagTGATGTCATCCCATGATTCTATGGGTATAGTCTTTAAGTGTCTGTCCAAGGGTGCAGTTGATTTTTTGGTGAAACCTATTCGAAAGAATGAACTTAAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA