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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgagttatagatgaattgttttttaatgtattgaggctctttaatgaaaatgtaaagcttacccattggcgttctttgttctcctctctgtcatgcagGAGAATCTAATTCGTGATGATAACAAACTTATTTTGCTGGCTTCTCTTAGTGATTCATTGGAGTATGTTGCAGACTCAATTGAAAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04770.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA10G35190.2 (Glycine max), 3'ss of exon 16
----------------------------------gctgagttatagatg-aattgttttttaatgtatt-gaggctctttaatgaaaatgtaaag-------cttacccattggcgttctttg------ttctcctctctgtcatgcagGAGAATCTAATTCGTGATGATAACAAACTTATTTTGCTGGCTTCTCTTAGTGATTCATTGGAGTATGTTGCAGACTCAATTGAAAG
                                   ||   || | |||  |||| | ||   || | || | ||   |||| |||| |  |   |       | ||   |||    |||| ||      || |  | | | |  | ||||| || ||||| | |||||| |||||||||||| || |||| || |||||||| ||||| ||||||||||||||||| ||||||||
gtttggttttctgtgtaatctaacaaattactattcttgcttgttgatataattttcttcctattttttagtggaattttactgaacaccttggggttccttcctatttattatgcttctctggtgactttgttgtatttttgcttcagGAAAACCTAATCCATGATGACAACAAACTTATTCTGTTGGCATCCCTTAGTGACTCATTAGAGTATGTTGCAGACTCTATTGAAAG

upper sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA20G32370.1 (Glycine max), 3'ss of exon 19
--------------------------------------gctgagttatagatgaattgttttttaatgtattgaggctctttaatgaaaatg---------taaag-------cttacccattggcgttctttg------ttctcctctctgtcatgcagGAGAATCTAATTCGTGATGATAACAAACTTATTTTGCTGGCTTCTCTTAGTGATTCATTGGAGTATGTTGCAGACTCAATTGAAAG
                                      ||| | | |||  | | ||  ||  || | |   | ||   |||| |||| ||          |   |       | ||   |||    || | ||      || |  | | | |  | ||||| || ||||| | |||||| |||||||||||| || |||| || |||||||| ||||| ||||||||||||||||| ||||||||
gtttgtttttctgtgtatactaacaaattactattcttgcttaatgata--taattttcttcctatttttgagtggaattttactgaacatcccctctccttgggggtcccttcctatttattatgcttgtctggtgactttgttgtatttttgcttcagGAAAACCTAATCCATGATGACAACAAACTTATTCTGTTGGCATCCCTTAGTGACTCATTAGAGTATGTTGCAGACTCTATTGAAAG

upper sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT3G10380.1 (Arabidopsis thaliana), 3'ss of exon 19
gctgagttatagatgaat-tgttttttaatgtattgaggctctttaatgaaaatgtaaagcttacccattggcgttctttgttctcctctctgtcatgcagGAGAATCTAATTCGTGATGATAACAAACTTATTTTGCTGGCTTCTCTTAGTGATTCATTGGAGTATGTTGCAGACTCAATTGAAAG
         || |   || |||| | | ||   |        | || | | ||| |     | |  |  ||  | |  ||    |  | |||    | ||||| ||||||||||||||||| |||||||| |||||| | |||||||| ||||| ||  | || || || |||||||| ||||| ||
--------gtaaaaatatgtgttctctgatactta------ttctagtaagaattt----ttcattcggtgaagataattaagttgttttct----tacagGATAATCTAATTCGTGATGACAACAAACTGATTTTGTTAGCTTCTCTCAGTGACTCGCTTGAATACGTGGCAGACTCTATTGAGAG

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|110363229|gb|EC926805.1|EC926805
EST:     TGAGTTTGCGGCCGATAAAGCAG                         GAGAATCTAATTCGTGATGATAACAAACTTATTTTGCTGGCTTCTCTTAGT
genomic: TGAGTTTGCGGCCGATAAAGCAGgtattatgtt ... tgtcatgcagGAGAATCTAATTCGTGATGATAACAAACTTATTTTGCTGGCTTCTCTTAGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaaatgtaaagcttacccattggcgttctttgttctcctctctgtcatgcagGAGAATCTAATTCGTGATGATAACAAACTTATTTTGCTGGCTTCTCTTAGTGATTCATTGGAGTATGTTGCAGACTCAATTGAAAG
            agcttac  putative branch site (score: 3)
                          cgttctttgttctcct  putative PPT
     aatgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgagttatagatgaattgttttttaatgtattgaggctctttaatgaaaatgtaaagcttacccattggcgttctttgttctcctctctgtcatgcagGAGAATCTAATTCGTGATGATAACAAACTTATTTTGCTGGCTTCTCTTAGTGATTCATTGGAGTATGTTGCAGACTCAATTGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - -atgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttaccc