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

AAACAAGATGAATCTCTTCTAGAAGATGTCTGGACTCTATTAAGGGCAGGAAGGCTGGAAGAGGCTTGTGACCTTTGCCGGTCTGCTGGACAAgtatgctaatctcccaagtgtgagtttatggaccactgtttttttatttcttttttgttttcctgacatataattctttctgttag

Basic information

species Vitis vinifera
transcript Vv09s0002g00840.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00840.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os11g42420.1 (Oryza sativa), 5'ss of exon 8
AAACAAGATGAATCTCTTCTAGAAGATGTCTGGACTCTATTAAGGGCAGGAAGGCTGGAAGAGGCTTGTGACCTTTGCCGGTCTGCTGGACAAgtatgctaatctcccaagt---gtgagtttatggaccactgtttttttatttcttttttgttttc--ctgacatataattctttctgttag
|| ||||||||||  ||| |||| ||| |||||||||| || || ||||||||| | |||||||| | ||| || || ||||||||||| || ||| || | |        |    || |||| |       | | ||| ||  |  |||| ||| |    |||    | | | | | | | ||
AAGCAAGATGAATTGCTTTTAGAGGATATCTGGACTCTCTTGAGAGCAGGAAGGTTAGAAGAGGCATCTGAACTGTGTCGGTCTGCTGGTCAGgtaggccagttagttgtatcccatgtgtttcttataatgtatctttctaccttcttttggttgtgtattgatccttgagtatgttt-tcag

upper sequence: Vv09s0002g00840.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G348675_T02 (Zea mays), 5'ss of exon 32
AAACAAGATGAATCTCTTCTAGAAGATGTCTGGACTCTATTAAGGGCAGGAAGGCTGGAAGAGGCTTGTGACCTTTGCCGGTCTGCTGGACAAgtatgctaatctcccaagtgtgagtttatggaccactgtttttttatttcttttttgttttcctgacatataattctttctgttag
|| ||||||||||  |||||||||||| | |||||||| ||||| ||||||||  | |||||||| | |||| | ||||| |||||||| || |||      |||    ||  ||  ||  |     | | || | |   || |||| || |   ||||| |||      | || | ||
AAGCAAGATGAATTGCTTCTAGAAGATATATGGACTCTTTTAAGAGCAGGAAGATTAGAAGAGGCATCTGACTTGTGCCGTTCTGCTGGCCAGgtagatcggtctgtgtagattgcattattt--ttattattctctctattgttttctgatg--ctgac-tattgagtatactttcag

upper sequence: Vv09s0002g00840.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G04680.1 (Glycine max), 5'ss of exon 5
AAACAAGATGAATCTCTTCTAGAAGATGTCTGGACTCTATTAAGGGCAGGAAGGCTGGAAGAGGCTTGTGACCTTTGCCGGTCTGCTGGACAAgt--atgctaatctcccaagtgtgagtttatggaccactgtttttttatttcttttttgttttcctgacatataattctttctgttag
||||||||||||||||||||||||||||| |||| ||| |||||||| |||||||| |||||||||||||  ||||||||||| |||||||| ||       | | |  | |   | ||||| |||||      ||  ||  |   |  ||    |  | |||| |  || ||| ||  ||
AAACAAGATGAATCTCTTCTAGAAGATGTATGGATTCTTTTAAGGGCTGGAAGGCTAGAAGAGGCTTGTGGACTTTGCCGGTCCGCTGGACAGgtcgccataactttgaccatgataagtttctggac------ttcattgatctatgcttcccatattaacatcttgttattt-tggcag

upper sequence: Vv09s0002g00840.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G14120.3 (Arabidopsis thaliana), 5'ss of exon 9
AAACAAGATGAATCTCTTCTAGAAGATGTCTGGACTCTATTAAGGGCAGGAAGGCTGGAAGAGGCTTGTGACCTTTGCCGGTCTGCTGGACAAgtatgctaatctcccaagtgtgagtt-----tatggaccactgtttttttatttcttttttgttttcctgacatataattct-ttctgttag
||||||||||||||| |||| || ||||| |||||| |  ||||||| || ||  | |||||||| ||||| || ||| |||||||||| || |||  ||  | |      | | | ||     || ||   |   ||       |   |  |  |  |   ||  || | | || || ||  ||
AAACAAGATGAATCTGTTCTTGAGGATGTATGGACTTTGATAAGGGCTGGGAGAATAGAAGAGGCATGTGATCTCTGCAGGTCTGCTGGGCAGgtaatctt-tataagggatataaattctttataagggtaatgattagaaaggtgtgtactgataatgtcgatttaaattactattttgccag

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|352781037|gb|FQ466350.1|FQ466350
EST:     GGGCAGGAAGGCTGGAAGAGGCTTGTGACCTTTGCCGGTCTGCTGGACAA                         CCATGGCGAGCTGCAACTCTATGCCCATTTGGAGGATTGGACCAATTTCCT
genomic: GGGCAGGAAGGCTGGAAGAGGCTTGTGACCTTTGCCGGTCTGCTGGACAAgtatgctaat ... tttctgttagCCATGGCGAGCTGCAACTCTATGCCCATTTGGAGGATTGGACCAATTTCCT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACAAGATGAATCTCTTCTAGAAGATGTCTGGACTCTATTAAGGGCAGGAAGGCTGGAAGAGGCTTGTGACCTTTGCCGGTCTGCTGGACAAgtatgctaatctcccaagtgtgagtttatggaccactgtttttttatttcttttttgttttcctgacatataattctttctgttag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA