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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcag

Basic information

species Vitis vinifera
transcript Vv03s0038g02140.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 4
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtactat---acatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttat-ttatttatttatttgttaatgggcag----------------------------
 || || |||||||||||| | |||||||| ||| | ||| |  |||||||||| ||||| |||||||||||| | || || |||||| |||||||||||||| ||    ||| |     |||        ||     |  | |    |  |    | | ||         ||   |  |  |||||   ||   |  |  ||   |                             
CCCGTCGTTCCACAACTACCGGATCTGGTCATTCCTCGGCCTCGTCATGACCACCTACACGGCCTGGTACCTCGCCGTCGCCTCCCTCATCCATGGCCAGgtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcag

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 5'ss of exon 2
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaa-atgattttatttatttatttatttatttatttgttaatgggcag-
 || ||||||||||||||| | || ||||||||| | ||| |  |||||||||| ||||| ||||||||| || | || || |||||| |||| || |||||||   | |||||||| |   ||  |   ||   |    |||  |  |  |    |||  ||||| |     |   ||||| |     ||||| ||      || 
CCCGTCATTCCACAACTACCGCATTTGGTCCTTCCTCGGCCTCCTCATGACCACCTACACCGCCTGGTACATCGCCGTCGCCTCCCTCATCCACGGACAGgtac---atatatatcttacataat-attcatagcagttttatagttcttgaggaggtatcatgatgta--ccaaaaatttaatataaaatttggtacctcatagt

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G149481_T02 (Zea mays), 5'ss of exon 4
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtactatacatatatctcattcaacca-aatatcca------aaacatatgatattaaaatt---agtaaatgattttatttatttatttatttatttatttgttaatgg-gcag
 || || |||||||||||| | |||||||| ||| ||||| |  |||||||||| ||||| || ||||||||| | || || |||||| |||||||||||||||    ||    |  | || || || ||||| ||         | | ||   |      |    || |  |         || | | |  || |     | |   ||  ||||
CCCGTCGTTCCACAACTACCGGATCTGGTCGTTCCTGGGCCTCGTCATGACCACCTACACGGCGTGGTACCTCGCCGTCGCGTCCCTCATCCATGGCCAGgtac---gcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtgtgtgcttctgctgctctacttgttgcag

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G045057_T02 (Zea mays), 5'ss of exon 4
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtac-tatacat---atatctcattcaaccaaatatccaaaacatatgatattaaaatta-gtaaatgattttatttatttatttat-ttatttatttgttaatgggcag-----------
 || || |||||||||||| | |||||||||||| | ||| |  |||||||||| ||||| || |||||||||||  ||||  || ||   || || ||||||  ||| |        | | ||   |   | ||  | |   ||    |  |     || ||  |  |  |  | ||| |     |   |   |||  || |||| |             
CCCCTCCTTCCACAACTACCGGATCTGGTCCTTCCTCGGCCTCCTCATGACCACCTACACCGCATGGTACCTCACCATTGCCGCCATCGCACACGGTCAGgtatatatgcgctgagcgtgtgatatgatgcactagtcgattgatcgcctgcttgcgctatgtccagcagatcgtgtatatggccgtaccaaacattaattgatggacgacaatattatag

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G00690.1 (Glycine max), 5'ss of exon 4
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtactatacatata---tctcattcaaccaaatatccaaa-acatatg-atattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcag-------------------------
 ||||| ||||||||||||||||||||||||||  | ||| |  ||||||||||||||||||| ||||||||||||||||| || ||||| || ||||||||| ||   || ||   |  ||   ||  ||||    | | | | ||  ||||  | ||   || |||| ||  | |||||||| | |   |  | |  ||||  ||                           
CCCTTCCTTCCACAACTACAGAATCTGGTCCTTTCTTGGCCTCCTCATGACCACTTACACTGCTTGGTACCTCACTGTTGCCTCTCTCCTTCACGGCCAGgtaataacaatttagatttgcaaataaataaatgcatatatatacatatatatatatatatatatatgaattattatatttatt-agtggctactataataatatgcgatcttgatgttactatgattgtgtag

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G00640.1 (Glycine max), 5'ss of exon 4
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcag-----------------------------
 ||||| ||||||||||||||||||||||||||  | ||| |  ||||||||||||||||||| ||||||||||| ||||| || ||||| || ||||||||| ||   || ||  |  | |||  |||||  || |  |||| ||    |   |  |  |||| |   | | |||  ||| |   |  | |  ||||  ||                               
CCCTTCCTTCCACAACTACAGAATCTGGTCCTTTCTTGGCCTCCTCATGACCACTTACACTGCTTGGTACCTCACAGTTGCCTCTCTCCTTCACGGCCAGgtaataataatttagatt-tgcaaataaataatcata-tatattattcctactgtgatctatgaatcattatgttt-cttagtggctactataataatatgcgatcttgatgttactatatatgattgtgtag

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA12G03490.1 (Glycine max), 5'ss of exon 4
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatg-ggcag-----------------------------------
|||||| || ||||||||||||||||||||||| |||||| |  ||||||||||||||||||||||||| ||||| ||||| || ||||| || || |||||   |   ||||   ||||  ||  || | | ||||  || |  |||||  |||| |  ||   || | ||||| ||    | |     |  |||||   | ||                                   
TCCTTCCTTTCACAACTACAGAATCTGGTCCTTTTTGGGCCTCCTCATGACCACTTACACTGCCTGGTATCTCACAGTTGCCTCTCTCCTTCACGGTCAGgtgacaacaatat---tcata-aattaagt-tacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcattaatatagtagtaatgctatgtttttccaattgttattatgcttag

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G11310.1 (Glycine max), 5'ss of exon 4
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatt-tatttatttatttgttaatgggcag-----------------------------------
|||||| || ||||||||||||||||||||||| |||||| |  | ||||||||||||||||| ||||| ||||| ||||| || ||||| || || ||||||  |   ||| || |    ||| || |||   |  || ||   |||||  |||| ||      || | ||||| ||| |||  | || |   | | |  | ||                                   
TCCTTCCTTTCACAACTACAGAATCTGGTCCTTTTTGGGCCTCCTTATGACCACTTACACTGCTTGGTATCTCACAGTTGCCTCTCTCCTTCACGGTCAGgtaacaataataaattta---caaacagatacgtactac-tacattattattattattactgatattcaattattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgttattatgcttag

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 5'ss of exon 4
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgta-ctatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcag
|||||| |||||||||||||| |||||||| ||  | ||  |  | ||||||||||||||||| |||||||||||  |||| ||  |||||||||| |||||| |||    | | | | ||  ||  |  |   |||    |   | |||| ||| ||    |||| || |   || |      |    |    | ||       
TCCTTCCTTCCACAACTACAGGATCTGGTCTTTTCTTGGACTCTTGATGACCACTTACACTGCTTGGTACCTCACCATTGCCTCTATCCTCCATGGACAGgtaactagttctttctttaatctaattagtt--tcaacgagttaaagattagaat-agctggtgatgttgtggcttaaggggact-caaaaacatcaacaaagt-

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTTCATTCCACAACTACAGAATCTGGTCCTTCTTGGGCTTGATCATGACCACTTACACTGCCTGGTACCTCACTGTTGCATCCCTCCTCCATGGCCAGgtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC