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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaacttttatcttttagctttctttttgctaaaacctgtggatacctcctgtcaactctaattaaaatctctttcaaaattgtactcaag

Basic information

species Vitis vinifera
transcript Vv12s0028g01120.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os04g53190.1 (Oryza sativa), 5'ss of exon 4
GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaa-cttttatcttttagctttcttt---ttgctaaaacctgtggata----cctcctgtcaactctaattaaaatctctttcaaaattgtactcaag----
||||||||  | ||||| ||||| || || |||||  |  |||| ||||||||||| ||||| ||||||||||| ||||||||||| |||| |   |  | |||   |   || | |   ||  |  ||   ||||  |        |||  | |  || ||  ||||   ||| |  ||||           
GTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTGgtgaggttcctctctgacaatattttctgaattatttgaaatggtggcaaaagtttatctggaaccattatttttaatccacttccattttgtgtgagcatcag

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os04g53195.1 (Oryza sativa), 5'ss of exon 3
GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaacttttatcttttagctttctttttgctaaaacctgtggatacctcctgtcaactctaattaaaatctctttcaaaattgtactcaag
||||||||  | ||||| ||||| || || |||||  |  |||| ||||||||||| ||||| ||||||||||| ||||||||||| |||| |  ||      | |  |  | ||||  || ||   | || |    |      |                                    
GTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTGgtgaggttcc--tctctgacaatatttt--ctgaattatttgaaatggtggcaaaag-----------------------------------

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G396856_T02 (Zea mays), 5'ss of exon 4
GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaacttttatctttt-agctttctttttgctaaaacctgtggatacctcctgtca-actctaattaaaatctctttcaaaattgtactcaag---
||| ||||  ||||||| |||||||||||||||||  | ||||| ||||| ||||| ||||| ||||| || ||  |||||||||| |||| |  |    |||||| | |||||    ||      ||      | | || ||    | |  | | |   | | |||||  |||    |  ||   
GTTATTCTTCTGGAATCTCGTGATAGAATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCAGTCGATTTGGGAGCATCTTGgtgagttccattcttttgaactttcaccatgt----gcccaaaagttcatcttgaaggaatgcattgagtgtttttttcatcatttctattgagaag

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G14620.1 (Glycine max), 5'ss of exon 3
-GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaacttttatcttttagctttctttttgctaaaacctgtggatacctcctgtcaactctaattaaaatctctttcaaaattgtactcaag
 |||||||| || || ||  | |||||||||||||| ||  |||| |||||||||||||||||||||||||||||||||||||||||||||||||  ||  ||| ||   || ||| |||| |||     |  ||   || | |  | | |  |  |  |||    |  | |     |  | 
GGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATggtaaatcttattctctttatttgcttattgcaaaatttcttccatttgtcttttttattttgttgtagttctaaaacttactaacttttca-

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA08G41570.3 (Glycine max), 5'ss of exon 3
GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaacttttatcttttagctttctttttgctaaaacctgtggatacctcc-tgtcaactctaattaaaatctctttcaaaattgtac----tcaag
|||||||| || || ||  | || ||||||||||| ||  |||| |||||||||||||||||||||||||| ||| ||||||||||||||||||  |   ||| ||    | ||| ||   | ||  |     | | ||| | |      |  ||    |     | ||| ||  ||    |  ||
GTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATGgtaaagctacttctctttatctgcttattatgagaatgtaaaatttcttccatttttttatttgtttttttagtactaaaagttacacatttttcag

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G45140.1 (Glycine max), 5'ss of exon 3
GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaacttttatcttttagctttctttttgctaaaacctgtggatacctcctgtcaactctaattaaaatctctttcaaaattgtactcaag--------------
||| ||||  | ||||| || || |||  |||||| ||  |||| ||||||||||||||||| |||||||||||||| || ||||| |||||||| ||   || || | | || ||||  ||     | |  ||     |    |  |   |||      | ||| |  |||  |                    
GTTATTCTTCTAGAATCACGGGAAAGACCTGGTGGCCGAATTCACACTGATTACTCATTTGGCTTTCCTGTTGACCTTGGTGCATCGTGgtaaaccttacactctttgttctccttttttta---ttttttcatgttgacaagaatgtggcatttctccattttttagtattaaaaatggatgactgtgattcag

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G03610.2 (Glycine max), 5'ss of exon 3
GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaacttttatcttttag-----ctttctttttgctaaaacc--tgtggatacctcctgtcaactctaattaaaatctct--ttcaaaattgtactcaag
||| ||||  | ||||| || || ||| ||||||| ||  |||| ||||| ||||||||||| ||||||||||||||||| ||||| |||||||  ||   || || |     |||| |||||  | |         | ||    | | ||  |  |  |||  ||      |  |  | |||  |  ||
GTTATTCTTCTAGAATCACGAGAAAGACTTGGTGGCCGAATTCACACTGACTACTCATTTGGCTTTCCTGTTGACCTGGGTGCATCGTGgtaaagcttaccctctttgttctcctttttttttcttcatgttgacaagaatgttgcatttctccattttttagtattaaaaatggatgactgtgattcag

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G43020.1 (Arabidopsis thaliana), 5'ss of exon 3
GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaactttta--tcttttagctttctttttgctaaaacct--gtggatacctcctgtcaactctaattaaaatctctttcaaaattgtactcaag
||| |  |  |||| || ||||| |||||||||||||| ||||| ||||||||||||||||||||||||||||| || || |||||||||||| ||      ||||| | | |    || | | |    |  ||       |   || |||| ||    ||  |     ||   || |     ||
GTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATGgtaatctcacggctctttcatcctgtcattagatgatgttttggttttggtttttggttaactttaggctaacacagcaacatcgttatgtcacag

upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G59050.1 (Arabidopsis thaliana), 5'ss of exon 2
-----------GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaactttta--tcttttagctt--tctttttgctaaaacctgtggatacctcctgtca---actctaattaa--aatctc-tttcaaaattgtactcaag
           |||||| | ||||| || ||||| |||||||||||||| ||||| ||||||||||||||||||||||| ||||| || || ||||| ||||||  |  |   || || | | |    ||||  || |   ||||    | ||  |||||   |  | || |||  ||| || |||    |  |        
CTTCCTTTCAGGTTGTTGTATTGGAGTCTCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCAGTTGATCTCGGTGCATCTTGgtaatatcatggctccttcaacctatctttttcactgattgctgtttggatcttttgtcatcgatgccaactaagcaatatcgttttgtgacag--------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110697943|gb|EE075393.1|EE075393
EST:     GTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG                         GCTTCATGGGGTCTGCAAAGAGAATCCCTTGGCACCTTTGATCAGCAGACT
genomic: GTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaactttt ... tgtactcaagGCTTCATGGGGTCTGCAAAGAGAATCCCTTGGCACCTTTGATCAGCAGACT
EST: gi|110698188|gb|EE075460.1|EE075460
EST:     GTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG                         GCTTCATGGGGTCTGCAAAGAGAATCCCTTGGCACCTTTGATCAGCAGACT
genomic: GTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaactttt ... tgtactcaagGCTTCATGGGGTCTGCAAAGAGAATCCCTTGGCACCTTTGATCAGCAGACT
EST: gi|30303658|gb|CB980452.1|CB980452
EST:     GTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG                         GCTTCATGGGGTCTGCAAAGAGAATCCCTTGGCACCTTTGATCAGCAGACT
genomic: GTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaactttt ... tgtactcaagGCTTCATGGGGTCTGCAAAGAGAATCCCTTGGCACCTTTGATCAGCAGACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATGgtaaacttttatcttttagctttctttttgctaaaacctgtggatacctcctgtcaactctaattaaaatctctttcaaaattgtactcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA