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

TTTGCGAAGCCAACTCAATTCAATACAAGAAGCTTCTGGTGGCAAGCGGATATCCATCAATGATCTTGTAATTAAGgtactaaattttcctagcaaaataactcttcatggttgagacatgcaaattgttttctattctcgtccatgttaaaaccccaaggggatagtgaagatgc...

Basic information

species Vitis vinifera
transcript Vv09s0002g01800.t01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: LOC_Os06g01630.5 (Oryza sativa), 5'ss of exon 14
TTTGCGAAGCCAACTCAATTCAATACAAGAAGCTTCTGGTGGCAAGCGGATATCCATCAATGATCTTGTAATTAAGgta----------ctaaattttcctagcaaaataactcttcatggttgagacatgcaaattgttttctattctcgtccatgttaaaaccccaaggggatagtgaagatgc----------------------------------------------------
 ||||||||  |  | ||| |  | || ||  | ||||||||||||  ||||||||| ||||||||||| || ||||||            | | | | ||  |   |   ||       ||| |||| ||   | ||  | |     || | | |||| | ||   ||     |     || | |                                                    
GTTGCGAAGTGAGTTGAATCCTCTGCAGGATACCTCTGGTGGCAAGAAGATATCCATAAATGATCTTGTTATCAAGgtaaattttgatgtgatactcttctttcctcaaggcttagttaagtttagacttgatcaatgcatgcgcaaatcattcctgttcagac---aaacaattttcagagttactattttgcatgagtggtaggatgttttacctaaattattgtccaatatgcag

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 14
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 5'ss of exon 13
TTTGCGAAGCCAACTCAATTCAATACAAGAAGCTTCTGGTGGCAAGCGGATATCCATCAATGATCTTGTAATTAAGgtactaaattttcctagcaaaataactcttcatggttgagacatgcaaattgttttctat-tctcgtccatgttaaaaccccaaggggatagtgaagatgc
| || | || || || |||||| |  |||| ||||||||||| || ||||||||  |||||||||||||  |||||||||   || || || |   |   ||| | ||||    || ||  || ||  | |   || ||      || | |          |               
TCTGAGGAGTCAGCTTAATTCATTCAAAGAGGCTTCTGGTGGGAAACGGATATCTGTCAATGATCTTGTTGTTAAGgtac---atctttcttgtgtat--actttacatg--caagcca-acagatcttctaaaatatcctactgatatcatgcgtttttag---------------
















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|110407843|gb|EC973460.1|EC973460
EST:     GCAAGCGGATATCCATCAATGATCTTGTAATTAAG                         GCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC
genomic: GCAAGCGGATATCCATCAATGATCTTGTAATTAAGgtactaaatt ... cttattgcagGCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC
EST: gi|33405959|gb|CF211586.1|CF211586
EST:     AAGAAGCTTCTGGTGGCAAGCGGATATCCATCAATGATCTTGTAATTAAG                         GCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC
genomic: AAGAAGCTTCTGGTGGCAAGCGGATATCCATCAATGATCTTGTAATTAAGgtactaaatt ... cttattgcagGCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC
EST: gi|161714484|gb|FC064459.1|FC064459
EST:     AAGAAGCTTCTGGTGGCAAGCGGATATCCATCAATGATCTTGTAATTAAG                         GCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC
genomic: AAGAAGCTTCTGGTGGCAAGCGGATATCCATCAATGATCTTGTAATTAAGgtactaaatt ... cttattgcagGCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC
EST: gi|22009599|gb|BQ794633.1|BQ794633
EST:     AAGAAG-TTCTGGCAGCAAGCGGATATCCATCAATGATCTTGTAATTAAG                         GCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC
genomic: AAGAAGCTTCTGGTGGCAAGCGGATATCCATCAATGATCTTGTAATTAAGgtactaaatt ... cttattgcagGCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC
EST: gi|30132039|gb|CB917378.1|CB917378
EST:     CGGATATCCATCAATGATCTTGTAATTAAG                         GCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC
genomic: CGGATATCCATCAATGATCTTGTAATTAAGgtactaaatt ... cttattgcagGCTGCTGCTTTGGCTCTTCGAAAAGTTCCTCAATGCAATAGTTCATGGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCGAAGCCAACTCAATTCAATACAAGAAGCTTCTGGTGGCAAGCGGATATCCATCAATGATCTTGTAATTAAGgtactaaattttcctagcaaaataactcttcatggttgagacatgcaaattgttttctattctcgtccatgttaaaaccccaaggggatagtgaagatgc

- - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggata