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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaaattcttacttggcattttatgctcttggggcactattatatgcatctttaacactgatcaagtgattccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGAAAGCGCATGGACGAAGTTATGGGAAACTTTTTGCGAGAAGGCCTTGAAC

Basic information

species Vitis vinifera
transcript Vv03s0038g00970.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 11
gtagaaaattcttacttggcattt-tatgctcttggggcactattatatgcatctttaacactgatcaagtgattccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGAAAGCGCATGGACGAAGTTATGGGAAACTTTTTGCGAGAAGGCCTTGAAC
|||     || | |||||  |||| |      ||    ||| |  ||    || | |   |    | || |   | | || ||||| ||||||| |||| |||| | |||| |||||||||| ||| |  |||||||||||||||| |||||||| || |||||||| ||||||||||| ||||
gtaagggtttatgacttgctatttctgcttctttacttcaccaccatgcaaatatgtgctaa-attaaaatctcttctcttcagATCAGCCATCACTGTATGGTCACTGAATTGCAGCGGTTCCCTTTCTTGAGAAAGCGCATGGATGAAGTTATTGGGAACTTTTTACGAGAAGGCCTAGAAC

upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 11
gtagaaaattcttacttggcattttatgctct-tggggcactattatatgcatctttaacactgatcaagtgattccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGAAAGCGCATGGACGAAGTTATGGGAAACTTTTTGCGAGAAGGCCTTGAAC
|||| ||  |     ||   | ||| |  ||| ||  |   |  | |||| |   |     || |  || |   | | || ||||| |||||||||||| |||||| |||| ||||||| || ||| |  || | ||||||||||| |||||||| || |||||| | ||||||||||||||||
gtaggaagatggc-tttaaaagtttgtcttctctgttgtcttgctttatgaacaatgtgt-ctaaaaaaatcccttctcttcagATCAGCCATCGCTGTATGGTGACTGAACTGCAGCGATTCCCTTTCTTGCGGAAGCGCATGGATGAAGTTATAGGGAACTTTCTACGAGAAGGCCTTGAAC

upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 11
gtagaaaattcttacttggcattttatgctcttggggcactattatatgcatctttaacactgatcaagtgattccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGAAAGCGCATGGACGAAGTTATGGGAAACTTTTTGCGAGAAGGCCTTGAAC
|||| ||  |     |     |||        ||  |   |  | |||| |   |   |    |  || |   | | || ||||| |||||||||||| |||||| |||| ||||||| || ||| |  || | ||||||||||| |||||||| || |||||| | ||||||||||||||||
gtaggaacatggctttaaaagtttgtcatctctgctgtcttgctttatgaagaatgtgcctaaacaaaatcccttctcttcagATCAGCCATCGCTGTATGGTGACTGAACTGCAGCGATTCCCTTTCTTGCGGAAGCGCATGGATGAAGTTATAGGGAACTTTCTACGAGAAGGCCTTGAAC

upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 11
gtagaaaattcttacttggcattt-tatgctcttggggcactattatatgcatctttaacactgatcaagtgattccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGAAAGCGCATGGACGAAGTTATGGGAAACTTTTTGCGAGAAGGCCTTGAAC
|||     || | |||||  |||| |      ||    ||| |   ||   || | |   |    | || |   | | || ||||| |||||||| ||| |||| | |||| |||||||||| ||| |  |||||||| ||||||| |||||| | || |||||||| ||||||||||| ||||
gtaagggtttatgacttgctatttctgcttctttacttcaccaccttacaaatatgtgctaa-attaaaatctcttctcttcagATCAGCCATCGATGTATGGTCACTGAATTGCAGCGGTTCCCTTTCTTGAGAAAGTGCATGGATGAAGTTCTTGGGAACTTTTTACGAGAAGGCCTAGAAC

upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA04G16340.1 (Glycine max), 3'ss of exon 11
gtagaaaattcttacttggcattttatgctcttggggcactattatatgcatctttaacactgatcaagtgattccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGAAAGCGCATGGACGAAGTTATGGGAAACTTTTTGCGAGAAGGCCTTGAAC
|||| ||        |    |||||   |||| |  |   |  | |||  |   |   |    |  |  |   | | || ||||| |||||||||||| |||||| |||  ||||||| || ||| |  || | ||||||||||| |||| | | || |||||||| ||||||||||| ||| 
gtaggaacagggctttaaagattttcatctct-gttgtcttgctttatcaagtatgtgcctaaacaatatcccttctctgcagATCAGCCATCGCTGTATGGTGATTGATCTGCAGCGATTCCCTTTCTTGTGGAAGCGCATGGATGAAGCTCTAGGGAACTTTTTACGAGAAGGCCTAGAAG

upper sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT2G14120.3 (Arabidopsis thaliana), 3'ss of exon 12
gtagaaaattcttacttggcattttatgct-cttggggcactattatatgcatctttaacactgatcaagtgattccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGAAAGCGCATGGACGAAGTTATGGGAAACTTTTTGCGAGAAGGCCTTGAAC
||   |  ||  |    |    |||||| | ||    |     ||| ||| | | | ||   | |       | |    | ||||| || ||||  ||| || |||  ||  | |||||||||||  | |||  |||||||||||| || ||||| || |||||| |||||||||| |||||||
gtgttatttttatttgcgtttctttatgatgctaactgttgatttacatg-accatgaattttaaattgaaaaattatgtacagATTAGTCATCAGTGTATGATGAAAGAGTTACAGCGGTTTCCAGTCCTGCAAAAGCGCATGGATGAGGTTATTGGGAACTTTCTGCGAGAAGGTCTTGAAC

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|122689415|gb|EC938921.1|EC938921
EST:     TAGATCCAAGCCTTCAGTGTGCTAGATTCATATATGATGAGTTAGTAAAG                         ATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGA
genomic: TAGATCCAAGCCTTCAGTGTGCTAGATTCATATATGATGAGTTAGTAAAGgtagaaaatt ... tccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGA
EST: gi|352764636|gb|FQ469711.1|FQ469711
EST:     TAGATCCAAGCCTTCAGTGTGCTAGATTCATATATGATGAGTTAGTAAAG                         ATAAGCCATCGCT
genomic: TAGATCCAAGCCTTCAGTGTGCTAGATTCATATATGATGAGTTAGTAAAGgtagaaaatt ... tccactccagATAAGCCATCGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttggggcactattatatgcatctttaacactgatcaagtgattccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGAAAGCGCATGGACGAAGTTATGGGAAACTTTTTGCGAGAAGGCCTTGAAC
                              cactgat  putative branch site (score: 3)
                                            ttccactcc  putative PPT
          actattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaaaattcttacttggcattttatgctcttggggcactattatatgcatctttaacactgatcaagtgattccactccagATAAGCCATCGCTGTCTGGTGAGTGAAATGCAGCGGTTTCCTATTCTGAGAAAGCGCATGGACGAAGTTATGGGAAACTTTTTGCGAGAAGGCCTTGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA