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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttattcttgttctatatatcatgctatcttttagattataatgtggaggattgaggaatatttcatcattctgtgtaacactttttttgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCTGCACTCACGGAAGCTTTGGATCAGAGTGGGAAGCCGTGGGAG

Basic information

species Vitis vinifera
transcript Vv01s0026g00340.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 13
tctttattcttgttctatatatcatgctatcttttagattata-atgtggaggattgaggaatatttcatcattc--tgtgtaacactttttttgtaat---gtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCTGCACTCACGGAAGCTTTGGATCAGAGTGGGAAGCCGTGGGAG
      ||      | |||  |  |  | | || |   ||| | ||        || |  ||  |||  | |||   | | |  ||  | ||   || |   ||||||||||||||||||||| |||||| | | ||| ||||| ||||||||   ||| || |  |||||||| ||| |   ||| ||||| ||| ||
------ttgcaaaccaatacttgttttttttttctcatttaaagataacatctgtttaataacgttttgttatttgtttttttgcatgtgttgaatacttgagtagAGGCCAGAGAAATACCTAGGAGATATTGCAACTTGGGACAAAGCTGAAAGTGCTCTTAAAGAAGCTTTAGATGATTTTGGCAAGCCTTGGCAG

upper sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 14
---tctttattcttgttctatatatcatgctatcttttagattataatgtggaggattgaggaatatttcatcattctgtgtaacactttttttgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCTGCACTCACGGAAGCTTTGGATCAGAGTGGGAAGCCGTGGGAG
    | |  ||  || | | |  | ||    ||||   ||||  ||  ||   |   |||    | | |   |    | | |     ||  |||  | |  ||||||||||||| |||||||||||||| ||||||||||| |||||||| || |  ||||  |||||| | ||      ||| ||||| |  | |
gtaccatatttgatgatttcttcaccagtgcatctaccagatcttatagtcttgacatgacatgtttctttgcccattatttgcatgttaatttaaatttcagAGGCCAGAGAAGTACCTTGGAGATTTGGAAACATGGGATAAAGCTGAAGCGGATCTCAAAGAAGCTATAGAAGCTTTTGGAAAGCCATTAGTG
















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|30325956|gb|CD009218.1|CD009218
EST:     ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACA                         AGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
genomic: ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACAgtatgcatct ... tgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
EST: gi|30325105|gb|CD008367.1|CD008367
EST:     ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACA                         AGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
genomic: ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACAgtatgcatct ... tgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
EST: gi|32268540|gb|CD717699.1|CD717699
EST:     ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACA                         AGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
genomic: ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACAgtatgcatct ... tgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
EST: gi|30323442|gb|CD006704.1|CD006704
EST:     ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACA                         AGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
genomic: ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACAgtatgcatct ... tgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
EST: gi|32249386|gb|CD715205.1|CD715205
EST:     ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACA                         AGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
genomic: ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACAgtatgcatct ... tgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
EST: gi|110360907|gb|EC924350.1|EC924350
EST:     ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACA                         AGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
genomic: ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACAgtatgcatct ... tgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
EST: gi|156735898|gb|EV240019.1|EV240019
EST:     ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACA                         AGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAAGCT
genomic: ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACAgtatgcatct ... tgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
EST: gi|30327091|gb|CD010353.1|CD010353
EST:     ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACA                         AGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT
genomic: ATTATGCCTATAACATATTTGGGTTCACTTATGAGCTGAAGCTATCAACAgtatgcatct ... tgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtggaggattgaggaatatttcatcattctgtgtaacactttttttgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCTGCACTCACGGAAGCTTTGGATCAGAGTGGGAAGCCGTGGGAG
                              gtgtaac  putative branch site (score: 3)
                                    cacttttttt  CT-rich tract
                                       tttttttgtaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttattcttgttctatatatcatgctatcttttagattataatgtggaggattgaggaatatttcatcattctgtgtaacactttttttgtaatgtagAGGCCAGAGAAATACCTTGGAGATTTAGAAACATGGGAAAAAGCTGAGGCTGCACTCACGGAAGCTTTGGATCAGAGTGGGAAGCCGTGGGAG

- - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattctg