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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcttttgctttttggtaaatttaagattggaaagaggaggttttggttttagattgatacatgatgtggagagatgattatctgtttgttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG

Basic information

species Vitis vinifera
transcript Vv09s0018g02130.t01
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 30
-ttttcttttgctttttggtaaatttaagattggaaagaggaggttttggttttagattgatacatgatgtggagagatgattatctgtttgttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG
   ||       ||||  |  | ||  |   |  | |  |    ||| ||||||  ||| | | |     |  |   || ||  | | ||||  || |||||||||||||||| ||||||||||||||||| ||| | ||| | |||
gcattggagaagttttgaggcacttgcatgctctagatggttcatttgggttttgaattaaaatacacgctttaactattatcttatatttggctt-tcagAGAACCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 27
----ttttcttttgctttttggtaaatttaagattggaaagaggaggttttggttttagattga-tacatgatgtggagagatgattatctgtttgttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG
     ||      | |||  || |  |  | |     |  ||  |  ||| ||||||  ||| | |||| | | |  |   |||||  | | ||||  || |||||||| ||||||| ||||||||||||||||| ||| | ||| | |||
tggcattgaagaagttttgaggcagttgcatgccctaatggatca--tttgggttttgaattaaatacacgcttt--aactatgatcttatatttggctt-tcagAGAATCTCTTATAACAAATATCATGTGGAGAAACTTGATCGTACAG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 29
ttttcttttgctttttggtaaatttaagattggaaagaggaggttttggttttagattgatacatgatgtggagagatgattatct---gtttgttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG
                                |   |    | ||||  ||| | ||| | |   ||  |||    |  |  ||||   |||||  || |||| ||||||||||| |||||| |||||||||||||| |   | | |||
--------------------------------gtttgtttggctttttatttcaaattaaaagcagacttgggcttactaacatcttatgtttggctt-tcagGGAACCTCTTATAACAAATGTCATGTGGAGGAACTTGGGCGTACAG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 29
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 27
------------ttttcttttgctttttggtaaatttaagattggaaagaggaggttttggttttagattgatacatgatgtggagagatgattatctgtttgttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG
            |   | |    ||||    | | ||    |  |||| || |   ||   || | | || |  | | |||    | |||| ||   |  ||| |||  ||| ||||||||||| ||||| ||||||||||||||| |  |  |||||
gtataaacatgttgcacatgatgttttcctcatacttttagt--gaaacagaatagttatattgtggtttcagtcgt-atggttcgtgatggtttgtttcttgatttg-cagGGAACCTCTTATAACAAACATCATGTGGAGGAACTTGCTTGTTCAG

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|110357398|gb|EC920911.1|EC920911
EST:     ACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAAG                         AGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG
genomic: ACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAAGgttagaactt ... gttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttttagattgatacatgatgtggagagatgattatctgtttgttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG
         gattgat  putative branch site (score: 4)
                                      tctgtttgttttctc  putative PPT
     tttagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcttttgctttttggtaaatttaagattggaaagaggaggttttggttttagattgatacatgatgtggagagatgattatctgtttgttttctcagAGAACCTCTTATTACAAATATCATGTGGAGGAACCTAATCATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - cttttgc
- - - - - - - - - - - - - - - -ggaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgatg