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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTTAGCCAAGAAACATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaagctttactttatccagatgtttattgctatttatattgctcaattatccaaatgggttctgagttcaatttctgtcttgtggctccaaat...

Basic information

species Vitis vinifera
transcript Vv14s0036g00520.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0036g00520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G36590.2 (Glycine max), 5'ss of exon 3
ATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTTAGCCAAGAAACATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaagctttactttatccaga--tgtttattgctatttatattgctcaattatccaaatgggttctgagttcaatttctgtcttgtggctccaaat
||||||  | |  ||||||| ||||||||||||||||||||| ||||| |||||  | |||||||| |||||||| ||||||||||| ||||||||| |||| || |||   | |  ||||   |    |  |||    |||||||| |      ||||         ||     ||   |        | |  |  |||| 
ATGCCTCTCAGTTGAATATACAGACAGAGTTGGAGAGTTAGCTAAGAAGCATGGACTGAAGCTTCACATTGATGGGGCCCGTATTTTTAATGCATCAGTTgtaag-aaattttgtgttttacttatgctttcttaaaaatatttataataaagctttatagtggcacatttgattttgtgtaaaaaatatctcacagcaaa-

upper sequence: Vv14s0036g00520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G30880.3 (Glycine max), 5'ss of exon 3
ATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTTAGCCAAGAAACATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaagctttactttatccagatgtttattgctatttatattgctcaattatccaaatgggttctgagttcaatttctgtcttgtggctccaaat--
||||||  | |  ||||||| ||||||||||||||||||||| ||||| |||||  | |||||||| |||||||| ||||||||||| || |||||| |||| || |||   | |  ||||   |    ||  |    || | ||      |  | |  |  |||    || | |   |||   |  |        | ||  
ATGCCTCTCAGTTGAATATACAGACAGAGTTGGAGAGTTAGCTAAGAAGCATGGACTGAAGCTTCACATTGATGGGGCCCGTATTTTTAACGCATCAGTTgtaag-aaattttgtgttttacttatgctttcttgaaaatatttacaataaagctttatag-tggcacatgtgatttgtttacttactaaatacatacattt

upper sequence: Vv14s0036g00520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA03G41120.1 (Glycine max), 5'ss of exon 3
ATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTTAGCCAAGAAACATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaagctttactttatccagatgtttattgctatttatattgctc--aattatccaaatgggttctgagttcaatttctgtcttgtggctccaaat--
||| ||| | |  ||||||| ||||||||| |||||| | || || |||||||| || |||||||| |||||||||||||| || || ||||||||| |||| ||||||   |||  ||||   |    || |||  | || | |   ||   | | |    | ||       ||   ||||| || ||      | ||  |  
ATGTCTTTCAGTTGAATATACAGACAGAGTAGGAGAGGTTGCTAAAAAACATGGATTGAAGCTTCACATTGATGGAGCCCGAATATTTAATGCATCAGTTgtaagtaaa---ttttgtttacttatgatttgatt-ttgttcacaaaactttaagtaaaatcactgcaaatcaagaaaaatttgtgcctgaaaaatgcacctag

upper sequence: Vv14s0036g00520.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G04520.2 (Arabidopsis thaliana), 5'ss of exon 3
ATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTTAGCCAAGAAACATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaagctttactt-tatccagatg--tttattgctatttatattgctcaattatccaaatgggttct----gagttcaatttctgtcttgtggctccaaat-------
||||||||||  |||||||||||||| ||| ||||| ||||||||||||||||| || |||||||| ||||| |||||  | |||||||| || ||  | || |||| |  | | | |  | | ||  ||  |||  |   ||||   || |||   ||     |||| | ||       ||     |   |||| | | ||  |||       
ATGCCTTCCTATAGAATATATAGACAAAGTCGGAGAATTAGCCAAGAAACATGGTTTGAAGCTTCACATTGACGGAGCTAGGATTTTCAACGCTTCTGTGgttagtatacacataattcgttttcatttgcattttctctgatttcatttactcgtatacgtgtatggatgctttgaagattatgagtgcatcttttcggtcttaattttgaag

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|161719590|gb|FC069398.1|FC069398
EST:     GCGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATT                         GCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
genomic: ATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaa ... gtttccccagGCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
EST: gi|30300481|gb|CB977275.1|CB977275
EST:     GCGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATT                         GCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
genomic: ATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaa ... gtttccccagGCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
EST: gi|110379523|gb|EC944723.1|EC944723
EST:     TGGGTTAAAGTTTCATATTGAATGGAGCCCGTATTTTCAATGCATCAATT                         GCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
genomic: TGGGTTAAAGCTTCATATTG-ATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaa ... gtttccccagGCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
EST: gi|110727225|gb|EE103744.1|EE103744
EST:     GCGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATT                         GCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
genomic: ATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaa ... gtttccccagGCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
EST: gi|110362584|gb|EC926127.1|EC926127
EST:     GCGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATT                         GCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
genomic: ATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaa ... gtttccccagGCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
EST: gi|29785385|gb|CB342317.2|CB342317
EST:     GCGGGTTATAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATT                         GCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG
genomic: ATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaa ... gtttccccagGCACTTGGTGTACCAGTTCACAGGCTTTTACAAGCTGCTGACTCAGCTTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCCTTCCTGCAGAATATATAGACAGAGTTGGAGAGTTAGCCAAGAAACATGGGTTAAAGCTTCATATTGATGGAGCCCGTATTTTCAATGCATCAATTgtgagtaaaagctttactttatccagatgtttattgctatttatattgctcaattatccaaatgggttctgagttcaatttctgtcttgtggctccaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA