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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccatcaaagtggaattttaacagtgctgttgttgttgcccaacggtccatatgttgctaagcttttctaattcattttaatatatccaacataa...

Basic information

species Vitis vinifera
transcript Vv10s0003g01640.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GRMZM2G019358_T03 (Zea mays), 5'ss of exon 12
ACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccatcaaagtggaattttaacagtgctgttgttgttgcccaacggtccatatgttgct----aagcttttctaattcattttaatatatccaacataa
 |||||||| ||  | || ||  | ||||| ||||| ||||||||||||||||| || |||||||| |||||||| ||||| || || ||||| || || ||||     |  | |  | | || | |  || | ||    || | ||| |  |  | | || |     ||    || |||     || || | |||  |     
TCGGGAAAGCGGTATTCCGTACACTATTGTAAGGCCATGTGCATTAACTGAGGAACCAGCTGGAGCCGATCTCATGTTTGACCAGGGGGACAACATCACAgtat----gtataggaagcacttcatcc-tgatattccaatt-cacaatgtgctctttcttcccccaaaaatgattttaacattcttcaa-acatcttag----

upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA08G12480.1 (Glycine max), 5'ss of exon 14
ACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccatca----aagtggaa--ttttaacagtgctgttgttgttgcccaacgg----tccatatgttgctaagcttttctaattcattttaatatatccaacataa----------------------------------------------------------
  | ||||||||  | || |||||||| ||||||||||||||||||||||||||||||||||| ||  |||| ||||||||||||||||| ||||| |||||||||  |  |    |  ||||   ||||  | ||||   || | || |  |||      |||  || |   |  |||| | | |||  ||||   | || ||   |||                                                          
TAGAGAAAGTGGCATTCCCTATGCAATCGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGTGCCAATCTTATTTTTGATCAAGGAGATAATATTACGgtattgtgaaaacaaaagatggatacttttctctgtgcaagtgctcttactaaactacctctcctgatatatttccgcttct-tgatttcttttggca-attcatggtaactatatagtagcattttgctcatttttccaaatgccaatctaatacaaaacttaacag

upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: GLYMA05G29330.2 (Glycine max), 5'ss of exon 14
ACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccat----caaagtgga--attttaacagtgctgttgttgttgcccaacggtccatatgttgctaagctt-----ttctaattcattttaatatatccaacataa--------------------------------------------------------------
  | ||||||||  | || |||| ||| ||||||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||| ||||| |||||| ||  |      ||  ||||   ||||  | || |   || | || |  |||   | || |  || ||   ||     |  | |||  ||||     || ||   |||                                                              
TAGAGAAAGTGGCATTCCCTATGTAATCGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGTGCCGATCTTATTTTTGATCAAGGAGATAATATTACGgtactgtgaaaacaaaagatggatgcttttctcggttcaagtgctcttactaaactaccaatctcatgatatatttccgcttcttgatttctttttggcaattcatggtaactatatagtagcatgcattttgctcatttttccaaatgccaatctaatacaaagcttaacag

upper sequence: Vv10s0003g01640.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT4G18810.1 (Arabidopsis thaliana), 5'ss of exon 14
ACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccatcaaagtggaattttaacagtgctgttgttgttgcccaacgg-tccatatgttg-ctaagcttttctaattcattttaatatatccaacataa
||| || || ||  | || | |||||||||  |||| ||||| ||||| || |||||||| ||||||||||||||||| || ||||||||||| || ||||||||  ||          ||||         | |  |||    |||||   ||  || |||  |||| ||   | | || |  || |||||          
ACGCGACAGCGGGATTCCATTTGCAATTGTACGGCCATGTGCTTTAACAGAAGAGCCTGCCGGAGCTGATCTCATTTTCGAACAAGGAGACAACATTACGgtattttca----------atttcgct-----tctccttgaaatccaacaactctttaagttaactaacctaaccaactttacctttatatag---------

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|30329616|gb|CD012878.1|CD012878
EST:     AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACG                         GGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
genomic: AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccat ... tgatctacagGGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
EST: gi|351013609|gb|FQ429750.1|FQ429750
EST:     AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACG                         GGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
genomic: AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccat ... tgatctacagGGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
EST: gi|110724595|gb|EE100559.1|EE100559
EST:     AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACG                         GGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
genomic: AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccat ... tgatctacagGGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
EST: gi|161721461|gb|FC070452.1|FC070452
EST:     AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACG                         GGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
genomic: AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccat ... tgatctacagGGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
EST: gi|351019257|gb|FQ429417.1|FQ429417
EST:     AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACG                         GGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
genomic: AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccat ... tgatctacagGGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
EST: gi|110361661|gb|EC925153.1|EC925153
EST:     AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACG                         GGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA
genomic: AGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccat ... tgatctacagGGCAAGGTATCTAGGGAAGAGATTGCTCGCATTTGCATTGCTGCTCTAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGGAAAGTGGAGTGCCTTATGCAATTGTGAGGCCTTGTGCATTAACTGAGGAGCCTGCTGGAGCTGATCTCATTTTTGATCAAGGAGACAATATAACGgtattgccatcaaagtggaattttaacagtgctgttgttgttgcccaacggtccatatgttgctaagcttttctaattcattttaatatatccaacataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA