Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacgggagaaataaaacaaatttcttaagctttcttttctgtatctttaccactgtcatgtaaaacagtgaaagaagtttatctcattggcttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTTCCAGACACAAATATTGTCATCGACAGATGTGCTCTGATCGGTAACCTGA

Basic information

species Vitis vinifera
transcript Vv09s0002g06980.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g06980.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G22740.1 (Glycine max), 3'ss of exon 6
----aacgggagaa-ataaaacaaatttcttaagctttcttttctgtatctttaccactgtcatgtaaaacagtgaaagaagtttatctcattggcttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTTCCAGACACAAATATTGTCATCGACAGATGTGCTCTGATCGGTAACCTGA
    |    || |  || ||| ||| |   |   |     |      ||    | || |       |  ||  ||||    || ||      |    |  || ||||  | || |||||  |||||||||| || ||||||||  ||||||||||||||||||||||||  || ||   || ||||||| |||| |||||  || 
atgaattttgacactattaaagaaactaaatgtacaacaatggaatcattcagagcattagttaacatgaccctgaattgggtgtac-----tattctgtggtagGGCTTGGCGGAGGAACTGAGTAAAGAAGGAGCATGCGAGCAAGCAATATTTCCAGACACAAATAAAGTTATAACCAAATGTGCTATGATTGGTAATTTGT

upper sequence: Vv09s0002g06980.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G03360.2 (Glycine max), 3'ss of exon 5
-----aacgggagaaataaaacaaatttcttaagctttcttttctgtatctttaccactgtcatgtaaaacagtgaaagaagtttatctcattggcttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTTCCAGACACAAATATTGTCATCGACAGATGTGCTCTGATCGGTAACCTGA
      || |  ||  ||  | | |   |  |||        |  | ||||||   | | | |  ||| |         |  ||      | |   ||  || ||||  | || |||||  |||||||||| || ||||| ||  ||||||||||||||||||||||||   | ||   || ||||||| |||| |||||  || 
tttgacactgatgagttattaaagaaaccaaaagtacaacaatg-gaatcttttagagtattagttaacatgaccctgaa--ttgggtgtacta--ttgtggtagGGCTTGGCTGAGGAACTGAGTAAAGAAGGAGCATGTGAGCAAGCAATATTTCCAGACACAAATAAAATTATAACCAAATGTGCTATGATTGGTAATTTGT
















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|110362989|gb|EC926554.1|EC926554
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
EST: gi|110377543|gb|EC942616.1|EC942616
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
EST: gi|26256962|gb|CA808025.1|CA808025
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTTGAGTAAAGAG
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAG
EST: gi|32249446|gb|CD715265.1|CD715265
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
EST: gi|32249285|gb|CD715104.1|CD715104
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
EST: gi|110363813|gb|EC927432.1|EC927432
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
EST: gi|28961921|gb|CB340979.1|CB340979
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTAGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
EST: gi|27579355|gb|CB002050.1|CB002050
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTT-A--A-                         ----T--CAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
EST: gi|110385730|gb|EC950281.1|EC950281
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
EST: gi|32269789|gb|CD718948.1|CD718948
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
EST: gi|110371008|gb|EC934697.1|EC934697
EST:     TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAG                         GGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT
genomic: TTCAAGTTCCCAAGGCTTGGCGAAACAAACCAATTGAATTCTTTAATCAGgtaataaaat ... cttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaccactgtcatgtaaaacagtgaaagaagtttatctcattggcttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTTCCAGACACAAATATTGTCATCGACAGATGTGCTCTGATCGGTAACCTGA
            atgtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacgggagaaataaaacaaatttcttaagctttcttttctgtatctttaccactgtcatgtaaaacagtgaaagaagtttatctcattggcttaaggcagGGTCTAGCAGAGGAGTTGAGTAAAGAGGGTGCATGCGACAAAGCAATATTTCCAGACACAAATATTGTCATCGACAGATGTGCTCTGATCGGTAACCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - aaataaa
- - - - - - - -acaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - ctgtcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagaa