Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACAAACTTGGCACTGGTTTGGTTGTTGCCCGAAGGTCAGATGGATCATGGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacataccatctgttatggttcttccattttatggtgccagtcagtgttaccatagttatatgtttttttcttgagaaactagaatcagttttgttc...

Basic information

species Vitis vinifera
transcript Vv11s0016g00400.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM5G872216_T01 (Zea mays), 5'ss of exon 3
TTACAAACTTGGCACTGGTTTGGTTGTTGCCCGAAGGTCAGATGGATCATGGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacata--ccatctgttatggttcttccattttatggtgccagtcagt---gttaccatagttatatgtttttttcttg-agaaactagaatcagttttgttc
|||||||||||| |||||  | || ||||| ||||| || |||||||||||||||||||||||||| ||| | ||||  ||||| |||||||| || |||||    ||   | |  | | ||  |||    |  | ||   | ||     |   ||    | ||   || | |  |    || | |   || | | ||        
TTACAAACTTGGAACTGGCCTAGTAGTTGCTCGAAGATCTGATGGATCATGGTCTGCACCATCTGCTATACTTTCTGCTGGTTTTGGATGGGGAGCACAGgtttgtatggtcaacttctaatacttcgcttaaatcataaaggcaacatatctggtgcttaaaggggtacggtgctcatgtgcacattttaaatttagga------

upper sequence: Vv11s0016g00400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA17G05010.1 (Glycine max), 5'ss of exon 3
TTACAAACTTGGCACTGGTTTGGTTGTTGCCCGAAGGTCAGATGGATCATGGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacataccatctgttatggttcttccattttatggtgccagtcagtgttaccatagttat--atgtttttttcttgagaaactagaatcagttttgttc
||||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||| || || ||||||||  | |||||||||||||||||||||||||  | |  || ||  | | ||  |  ||||   |       ||| |||    ||  | |   || |  |||  | || ||| ||||   ||  |     
TTACAAACTGGGCACTGGTTTGGTTGTTGCTCGAAGATCAGATGGATCATGGTCTGCACCGTCAGCAATATTCTCCCTGGGTTTAGGATGGGGTGCTCAGgtaaggagaatatatgcga-gtttagttaatttgtagaattttctcactgtggttatgttcactgatatggtttgatagaaaaaatagagaaagaatacaa-

upper sequence: Vv11s0016g00400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G17500.1 (Glycine max), 5'ss of exon 3
TTACAAACTTGGCACTGGTTTGGTTGTTGCCCGAAGGTCAGATGGATCATGGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacataccatctgttatggttcttccattttatggtgccagtcagtgttaccatagttatatgtttttttcttgagaaactagaatcagttttgttc-
||||||||| || ||||| ||||||||||| ||||| ||||| ||||||||||||||||| || || ||||||||  | |||||||||||||||||||||||||  | |  || |  ||   |  ||    ||||   |       |  ||||   |   |  || |  |||  | || ||| | ||   ||  |    | 
TTACAAACTGGGTACTGGCTTGGTTGTTGCTCGAAGATCAGACGGATCATGGTCTGCACCGTCAGCAATATTCTCCCTGGGTTTAGGATGGGGTGCTCAGgtaaggaaaatatatactagtttagtttatctttagaattttgactatggttatgctcactg-atatggtttgatagaaaaaatggagaaagaatatacca

upper sequence: Vv11s0016g00400.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G43230.1 (Arabidopsis thaliana), 5'ss of exon 3
TTACAAACTTGGCACTGGTTTGGTTGTTGCCCGAAGGTCAGATGGATCATGGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacataccatctgttat--ggttcttccattttatggtgccagtcagtgttaccatagttatatgtttttttcttgagaaactagaatcagttttgttc-
 |||||||| || |||||| ||||  |  | || ||  |||| || ||||||||||| |||||||||||| | || || ||| | ||||||||||| ||||||||| |    | |   ||      | | ||| |||  ||   ||      || | ||||  | ||              | | | | |    ||||||   
ATACAAACTCGGGACTGGTCTGGTAATATCTCGGAGACCAGACGGGTCATGGTCTGCTCCATCTGCCATACTATCAGTAGGTCTTGGATGGGGTGCACAGgtaaacttcatcttttccattcaagacatgcatgttagagttaaagatgcgttttcaatagccacata----------agaagatttgtactctttttgtcag

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|30321963|gb|CD005225.1|CD005225
EST:     GCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAG                         ATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAAAGCT
genomic: GCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacatac ... cttcccacagATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAAAGCT
EST: gi|22008024|gb|BQ793058.1|BQ793058
EST:     GGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAG                         ATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAAAGCT
genomic: GGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacatac ... cttcccacagATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAAAGCT
EST: gi|110711818|gb|EE088731.1|EE088731
EST:     GGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAG                         ATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAAAGCT
genomic: GGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacatac ... cttcccacagATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAAAGCT
EST: gi|27580296|gb|CB002991.1|CB002991
EST:     GCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAG                         ATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAGAGCT
genomic: GCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacatac ... cttcccacagATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAAAGCT
EST: gi|30321887|gb|CD005149.1|CD005149
EST:     GCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAG                         ATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAAAGCT
genomic: GCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacatac ... cttcccacagATTGGGGGTGAGCTCATGGACTTCATAATTGTGCTTCATGGTTCCAAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACAAACTTGGCACTGGTTTGGTTGTTGCCCGAAGGTCAGATGGATCATGGTCTGCACCATCTGCCATATTCTCTGTCGGTTTAGGATGGGGTGCTCAGgtaaacataccatctgttatggttcttccattttatggtgccagtcagtgttaccatagttatatgtttttttcttgagaaactagaatcagttttgttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgagaaa