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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATATCTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtttgatttccatggttgccacaattttcttttcctgtttgtttttctaaactattcagtttaaataattactgattcttaatattcttccattttaattatatcattaactacagctacttttccttggatcag

Basic information

species Vitis vinifera
transcript Vv06s0009g01800.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 5'ss of exon 11
AGAATATCTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtt----tgatttccatggttgccacaattttcttttcctgtttgtttttctaaactattcagtttaaataattactgattcttaatattcttccattttaattatatcattaactacagctacttttccttggatcag
|| ||||| || || ||||||||||| || ||||||||||||||||| || || || |||||||| |||||||     ||||    |   ||| |||     |  |  |  | ||  || |   |||| | ||  | | | |                                                                    
AGGATATCGGCAAAAGATGCACTTGACGCGGAGTATTTCTGGACTGATCCCTTACCGTGTGATCCAAAGAGgtacatatgatggttaaatttgtcacg---ctgctaactagcttaattctaataactttgcatctgatacag-------------------------------------------------------------------

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA20G10960.1 (Glycine max), 5'ss of exon 10
AGAATATCTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtttgatttcc-------atggttgccacaattttcttt-tcctgtttgtttttcta--aactattcagttt------aaataattactgattcttaatattcttcc-----attttaattatatca-ttaacta-cagctacttttccttggatcag--------------------------------------
|||||  ||||||||||||||||||||||||||||||||||||| || || || || |||||||| ||||||| |||  |||       ||| |    |  |||| ||   |  || || |  ||| |  || |||    | |       | ||||| || ||      | ||||| |     || ||  || | ||| | ||||| ||  |||| ||  ||   |  |                                      
AGAATTACTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACGGATCCATTACCATGTGATCCTAAGAGgtatgacctcccaatcccatgatattgaatatttactaaatattgattttccttcgaggaaatatgtgatcttcataggattaattgcttatctcatttgttctttccccatatgtttgttgtttcaatcaactatcatttactattttttatttttgaactcaccaagtcactattactcctatgtttggcttag

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA14G04410.1 (Glycine max), 5'ss of exon 11
AGAATATCTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtttgat-ttccatggttgccacaattttcttttcctgtttgtttttctaaactattcagtttaaata-----atta-----ctgattcttaatattcttccattttaattatatcattaac-tacagctacttttccttggatcag-----------------------------------
|||||  |||| || ||||||||||||||||||||||||||||| || || || || || |||||||||||||| ||  |||||||      |    ||| ||||     |  |  ||  ||| |||    | | ||||     ||||     |||  || |    | ||| | |||| | | |||  ||      || ||| |  |  |  | |||                                    
AGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCGTGCGATCCCAAGAGgttagaccttccatgtacattagttatttattttgagaatgttactttgaaattatgtgatcttaataggaggattaaatgtctgtctcattgattcctttcctttttactttattgtttctactcaactaatccttttctggtcaatacctttcaacttcatactcttctgtatggcttag

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA02G44400.1 (Glycine max), 5'ss of exon 12
AGAATATCTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtttgat-ttccatggttgccacaattttcttttcctgtttgtttttctaaactattcagtttaaataattactgattcttaatattcttccattttaattatatcattaactacagctacttttccttggatcag
|||||  |||| || ||||||||||||||||||||||||||||| || || || || || |||||||||||||  ||  |||||||      |   | ||  |||   |  ||||  | | || |    |  | |||||   | | | |  ||  |  |    |  ||  | ||                                 
AGAATTACTGCGAAAGATGCACTTGATGCTGAGTATTTCTGGACAGATCCATTACCATGCGATCCCAAGAGgtaagaccttccatgtacattaagttatttattttgagaatgttactttgaaat---tatgtgaaatagg-attaaatgctatgaagcacggacattgctcatc--------------------------------

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|110707937|gb|EE084906.1|EE084906
EST:     CTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAG                         TTTACCAAAATATGAATCTTCCCATGAGTTCCAGACAAAGAAGAAGCGCCA
genomic: CTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtttgatttc ... cttggatcagTTTACCAAAATATGAATCTTCCCATGAGTTCCAGACAAAGAAGAAGCGCCA
EST: gi|71869733|gb|DT018788.1|DT018788
EST:     CTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAG                         TTTACCAAAATATGAATCTTCCCATGAGTTCCAAACAAAGAAAAAGCGCCA
genomic: CTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtttgatttc ... cttggatcagTTTACCAAAATATGAATCTTCCCATGAGTTCCAGACAAAGAAGAAGCGCCA
EST: gi|110702769|gb|EE079031.1|EE079031
EST:     CTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAG                         TTTACCAAAATATGAATCTTCCCATGAGTTCCAGACAAAGAAGAAGCGCCA
genomic: CTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtttgatttc ... cttggatcagTTTACCAAAATATGAATCTTCCCATGAGTTCCAGACAAAGAAGAAGCGCCA
EST: gi|110689298|gb|EE065410.1|EE065410
EST:     CTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAG                         TTTACCAAAATATGAATCTTCCCATGAGTTCCAGACAAAGAAGAAGCGCCA
genomic: CTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtttgatttc ... cttggatcagTTTACCAAAATATGAATCTTCCCATGAGTTCCAGACAAAGAAGAAGCGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATATCTGCCAAGGATGCACTTGATGCTGAGTATTTCTGGACTGACCCTTTGCCTTGTGATCCCAAGAGgtttgatttccatggttgccacaattttcttttcctgtttgtttttctaaactattcagtttaaataattactgattcttaatattcttccattttaattatatcattaactacagctacttttccttggatcag

- - - - - - - - - - - -  ATGCTG