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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTATTTTATCCACAATCATTTGATATTTACCGTCAAGTTTCATAAAGATTTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttcttgctggtcgttgactattgaagttgatctttccccccagtagtatatatactgatgacattataatatttgctattggatgcatccag

Basic information

species Vitis vinifera
transcript Vv04s0008g06640.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g06640.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G180575_T01 (Zea mays), 5'ss of exon 5
AGTATTTTATCCACAATCATTTGATATTTACCGTCAAGTTTCATAAAGATTTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttct-----tgctggtcgttgactattgaagttgat--ctttccccccagtagtatatatactgatgacattataatatttgctattggatgcatccag----
|||  ||||||||||| || |||  ||||   || || |  ||||| |||      || ||     | || ||||| ||||||||||||||||||||||||| |||| |     |||| | | |    | |||    ||||  ||||| | |    | ||| |    |  | || ||||| | |||  | ||  ||   ||  |    
AGTCCTTTATCCACAACCACTTGGCATTTTTAGTAAAATACCATAAGGATGAAACTACAGATCTCTCTAGAATTGTTGGATTTGAGGTCAAACCATTCAGgttagttttagttatgcttgccctattttgttgggtatgatgcctttcacgctgacactatcttgtttactaac-ttatacttttt-ttgttaaatttctcatgccag

upper sequence: Vv04s0008g06640.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G046005_T01 (Zea mays), 5'ss of exon 5
AGTATTTTATCCACAATCATTTGATATTTACCGTCAAGTTTCATAAAGATTTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttcttgctggtcgttgactattg----aagttgat--ctttccccccagtagtatatatactgatgacattataatatttgctattggatgcatccag----
|||  |||||||||||||| |||  ||||   || || |  || || |||      || ||     | || ||||| ||||||||||||||||||||||||| |||| | | |   | |   |||||     |   ||||  ||||| | |    | ||| |    |  | || ||||| | |||  | ||  ||   ||  |    
AGTCCTTTATCCACAATCACTTGGCATTTTTAGTAAAATACCACAAGGATGAAACTACAGATCTCTCTAGAATTGTTGGATTTGAGGTCAAACCATTCAGgttagttttagttatgcttgccctattttgttagtatgatgcctttcacgctgacactatcttgtttactaac-ttatacttttt-ttgttaaatttctcatgccag

upper sequence: Vv04s0008g06640.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA04G06420.1 (Glycine max), 5'ss of exon 5
AGTATTTTATCCACAATCATTTGATATTTACCGTCAAGTTTCATAAAGATTTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttcttgctggtcgttg-actattgaagttgatctttccccccagtagtatatatactgatgacat-tataatatttgctattggatgcatccag---------------------------------------------------
| || ||||| ||||| ||||||  |||||| || ||||  ||||||||  ||| |||||| || || || |||||||| |||||||| | ||||||||||| | |  ||  | || ||   | || |  | |  || |      | |  | |   ||||   ||  ||| |||    ||| |  ||  ||   | ||                                                    
AATACTTTATTCACAACCATTTGGCATTTACTGTTAAGTACCATAAAGACATGCTAACTGAATCTGCTAGAATTGTGGGCTTTGAGGTTACACCATTCAGgtcattatttttttgttgtcatattaatttattccatttaattttctacaaat---tataggaatctcatgtattgggtttcccttttaattgtttcatccttttgtgatgtttagtagtgatttttcaaatctggatgttgatctgcag

upper sequence: Vv04s0008g06640.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G25100.1 (Arabidopsis thaliana), 5'ss of exon 5
AGTATTTTATCCACAATCATTTGATATTTACCGTCAAGTTTCATAAAGATTTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtg-agttcttgctggtcg--ttgactattgaagttgatctttccccccagtagtatatatactgatgacattataatatttgctattggatgcatccag
|||||||||| |||||||| |||  ||| || |||  || ||||| |||| ||||||| ||  | ||||||||||||||||||||||||||||||| |||||| | || ||| |    |  | |||| |||   |      |      ||| | || ||||  |    | | | | || | |                  
AGTATTTTATGCACAATCACTTGGCATTCACTGTCCGGTATCATAGAGATATGCAAACCGATGCTGCAAGGATTGTGGGATTTGAGGTCAAACCATACAGgtgcaatttttgttaacagattggactcttgggatctcctctattttgcagaactaaatatttt----atact-tgatttgtag----------------

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|71867874|gb|DT016929.1|DT016929
EST:     TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAG                         TATTAAACATGAATACGATGGGGAATGGAATGGCAAGAATCGTCTATTGAC
genomic: TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttctt ... atgcatccagTATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
EST: gi|71868110|gb|DT017165.1|DT017165
EST:     TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAG                         TATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
genomic: TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttctt ... atgcatccagTATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
EST: gi|349833321|gb|FQ416699.1|FQ416699
EST:     CAAACCATTCAG                         TATTAAACATGAATACCATGGGGAATGGAATGGCAAGAATCGTCTATTGAC
genomic: CAAACCATTCAGgtgagttctt ... atgcatccagTATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
EST: gi|33409925|gb|CF215552.1|CF215552
EST:     TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAG                         TATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
genomic: TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttctt ... atgcatccagTATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
EST: gi|110699448|gb|EE076454.1|EE076454
EST:     TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAG                         TATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
genomic: TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttctt ... atgcatccagTATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
EST: gi|110723814|gb|EE099106.1|EE099106
EST:     TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCCAACCATTCAG                         TATTAAACATGAATACTAAGGGGGAATGGAATGGCAA
genomic: TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttctt ... atgcatccagTATTAAACATGAATACGAAGGGG-AATGGAATGGCAA
EST: gi|110700412|gb|EE078424.1|EE078424
EST:     TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAG                         TATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
genomic: TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttctt ... atgcatccagTATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
EST: gi|110699772|gb|EE077065.1|EE077065
EST:     TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAG                         TATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC
genomic: TTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttctt ... atgcatccagTATTAAACATGAATACGAAGGGGAATGGAATGGCAAGAATCGTTTATTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTATTTTATCCACAATCATTTGATATTTACCGTCAAGTTTCATAAAGATTTGCAAACTGACTCAGCAAGGATTGTGGGATTTGAGGTCAAACCATTCAGgtgagttcttgctggtcgttgactattgaagttgatctttccccccagtagtatatatactgatgacattataatatttgctattggatgcatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG