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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTTGCATTGTTGGTGTTGCACGTACGCCAATGGGTGGCTTTTTGGGTACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaacctcctttttttgtttgtttgtttatccccattggtttattctcttttgcttcaaaatttatgggttttgatattttcataggcatttgcccccatccaatttgggactcaaattaattataaaagcaggagttcttaaatgttgttttgtgtcaacttgtag

Basic information

species Vitis vinifera
transcript Vv12s0057g01200.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G47860.2 (Glycine max), 5'ss of exon 3
ATGTTTGCATTGTTGGTGTTGCACGTACGCCAATGGGTGGCTTTTTGGGTACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaacctcctttttttgtttgtttgtttatccccattggtttattctcttttgcttcaaaatttatgggttttgatattttcataggcatttgcccccatccaatttgggactcaaattaattataaaagcaggagttcttaaatgttgttttgtgtcaacttgtag
|||||||||||||||||||||||||||| ||||||||||| ||| | ||||| || |||||| |||| || |||||||| || |||||||| ||||||||| |            | | | ||||      |||  |  |  | |||||   ||    ||  || | | || ||||  |||||||      ||| |||                                                                         
ATGTTTGCATTGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTACCCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaa-----------ctatgtctttggaaacctatgtcagt--gcttattacattgcattt-gaattatttgtgtttacatattttt-cgttcatctgcag-----------------------------------------------------------------------

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G00760.1 (Glycine max), 5'ss of exon 3
ATGTTTGCATTGTTGGTGTTGCACGTACGCCAATGGGTGGCTTTTTGGGTACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaacctcctttttttgtttgtttgtttatccccattggtttattctcttttgcttcaaaatttatgggttttgatattttcataggcatttgcccccatccaatttgggactcaaattaattataaaagcaggagttcttaaatgttgttttgtgtcaacttgtag
|||||||||| ||||||||||||||||| ||||||||||| ||| | ||||| || |||||| |||| || |||||||| || |||||||| ||||||||| | |       | | | |   |  |   |  || ||  |||    | |   || || ||  | |||| | | |      || | ||                                                                                    
ATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatggaagcctatgtcagtgctaattacattccatttgaa--acttatttgtgtttacatatttttcgttc-----atctgcag-----------------------------------------------------------------------------------

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G00760.2 (Glycine max), 5'ss of exon 1
-ATGTTTGCATTGTTGGTGTTGCACGTACGCCAATGGGTGGCTTTTTGGGTACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaacctcctttttttgtttgtttgtttatccccattggtttattctcttttgcttcaaaatttatgggttttgatattttcataggcatttgcccccatccaatttgggactcaaattaattataaaagcaggagttcttaaatgttgttttgtgtcaacttgtag
 |||||||||| ||||||||||||||||| ||||||||||| ||| | ||||| || |||||| |||| || |||||||| || |||||||| ||||||||| | |       | | | |   |  |   |  || ||  |||    | |   || || ||  | |||| | | |      || | ||                                                                                    
GATGTTTGCATCGTTGGTGTTGCACGTACACCAATGGGTGGATTTCTTGGTACTCTGTCATCTCTATCTGCCACCAAGCTAGGCTCTATAGCTATTGAAGgtaactatggaagcctatgtcagtgctaattacattccatttgaa--acttatttgtgtttacatatttttcgttc-----atctgcag-----------------------------------------------------------------------------------

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|110398909|gb|EC965389.1|EC965389
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110699364|gb|EE076300.1|EE076300
EST:     ATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACCAGAAGTTTTCT
genomic: ATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110403296|gb|EC964774.1|EC964774
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|71859096|gb|DT008151.1|DT008151
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110701385|gb|EE078893.1|EE078893
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|161716985|gb|FC066530.1|FC066530
EST:     TACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|161717757|gb|FC064725.1|FC064725
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|71866622|gb|DT015677.1|DT015677
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|161712803|gb|FC062326.1|FC062326
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110398035|gb|EC964108.1|EC964108
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|32269649|gb|CD718808.1|CD718808
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|71875811|gb|DT024866.1|DT024866
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110723077|gb|EE099979.1|EE099979
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110686757|gb|EE064757.1|EE064757
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|161720962|gb|FC070684.1|FC070684
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110698167|gb|EE075418.1|EE075418
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110685325|gb|EE063616.1|EE063616
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110723249|gb|EE100343.1|EE100343
EST:     CATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: CATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|71855093|gb|DT004148.1|DT004148
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|34543095|gb|CF511327.1|CF511327
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|77587675|gb|DV223012.1|DV223012
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|30299187|gb|CB975981.1|CB975981
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110702702|gb|EE078902.1|EE078902
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|110364569|gb|EC927918.1|EC927918
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
EST: gi|77586011|gb|DV222101.1|DV222101
EST:     TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAG                         CCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT
genomic: TACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaac ... caacttgtagCCGCTCTTAAAAGGGCAAATGTTGATGCATCACTTGTACAAGAAGTTTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTTGCATTGTTGGTGTTGCACGTACGCCAATGGGTGGCTTTTTGGGTACACTTTCATCTTTATCAGCTACCAAGCTTGGATCTATAGCCATTGAAGgtcagtcaacctcctttttttgtttgtttgtttatccccattggtttattctcttttgcttcaaaatttatgggttttgatattttcataggcatttgcccccatccaatttgggactcaaattaattataaaagcaggagttcttaaatgttgttttgtgtcaacttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG