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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGTCTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAGgtaaaattctcaatataatggttcacagctattgattacagaagcatatattgacatggtgagtttttgatgcatgaacacatccaaaactagcttggtt...

Basic information

species Vitis vinifera
transcript Vv15s0046g03390.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os04g58620.1 (Oryza sativa), 5'ss of exon 14
TTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGTCTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAGgtaaaat--tctcaatataatggttcacagctattgattacagaagcatatattgacatggtgagtttttgatgcat--gaacacatccaaaactagcttggtt
||| ||||| || || ||||||||||||||||| || || ||  | || ||    |||||||||||||||||| ||||||| |||||||| || |||||||||   |  | ||| | | || |  || | | ||   ||||       |    |||| |  |   |||||| ||||   ||  ||||    ||  | ||| || 
TTCAATGGCTCTTACACCATGGTTAGCTGCTGGTGGCCAGTTTTTGGCATCAAAATTTGAGCAGCATGATGTGAGAAGTTTATTACCTGTGGAAAGTGAGgtatcttcttttcactctcatagacca-acccatgttttaccttctgtttcgatgacctttttt-tttttgctgcaatagaggacatttgcaaa-aacttagt-

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA18G46420.1 (Glycine max), 5'ss of exon 21
TTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGTCTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAGgtaaaattctcaatataatggttcacagctattgattacagaagcatatattgac--atggtgagtttttgatgcatgaacacatccaaaactagcttggtt--
 || |||||| | || |||||| ||||||| ||||| || || ||||| || |||||||||||| |||||||  ||||||| || || || || |||||||||||||     | || |  |||     ||| | |||  | ||  | ||| | |   ||  | || ||   | | ||  |    |    |       ||||   
-TCAATGGCCATCACACCATGGCTAGCTGCAGGAGGCCAGTTGATTGCTTCCCGTTTTGAGCAGAATGATGTTAGAAGTTTATTGCCGGTAGAAAGTGAGGtaaaatctcttaaatga--gttgctgactagtaattttataaata-atagtcatgaatttttagcttcaaaagtatctatgattgggcactcttactggtgca

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA09G39770.1 (Glycine max), 5'ss of exon 17
TTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGTCTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAGgtaaaattctcaatataatggttcacagctattgattacagaagcatatattgac--atggtgagtttttgatgcatgaacacatccaaaact-agcttggtt
||| |||||| | || |||||| ||||||| ||||| ||  | ||||| || || ||||||||| |||||||  ||||||| |||||||| || |||||||||||||       || |  |||     ||| | |||  | ||  | ||| | |   ||  | || ||  || | || |  | |   |    | |  |  |||
TTCAATGGCCATCACACCATGGCTAGCTGCAGGAGGCCAGCTGATTGCTTCCCGCTTTGAGCAGAATGATGTTAGAAGTTTATTACCTGTAGAAAGTGAGgtaaaatctcttgaatga--gttgctgactagtaatttaataaata-atagtcatgaatttttagcttcagaagtatcagaaaaggaagggatgaaataagtt

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 5'ss of exon 14
TTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGTCTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAGgtaaaattctcaat-ataatggttcacagcta---ttgattacagaagcatatattgacatggtgagtttttgatgcatgaacacatccaaaactagc--ttggtt----------------------------------------------
 || |||||  | || || |||||||||||||| || || |||||||| ||||||||||||  ||||||||| |||||||| || || || ||||||||||||  | ||| ||| ||     |  | |  |    |  ||||   ||  || |||  |    |  |    |||  ||    |||    | |    ||    |  ||                                              
CTCAATGGCTATCACACCCTGGTTAGCTGCTGGTGGCCAGTTAATTGCATCTCGTTTTGAGTTGCATGATGTTCGAAGTTTATTGCCCGTCGAGAGTGAGgtaggaatcttaatgattcaaatatagaatttacctctattaggcaataatttatcaatcatggaaccacttgtagctcacacattctctagttgaggaaatcattacaaggccgactgatgagaatttttcttgtctgattttatttgcag

upper sequence: Vv15s0046g03390.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT4G00630.2 (Arabidopsis thaliana), 5'ss of exon 13
TTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGTCTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAGgta---------aaattctcaatataa-tggttcacagctatt---gattacagaagcatatattgacatggtgagtttttgat--gcatgaaca--catccaaaactagcttggtt----------------------------------------------
 || ||||| || || || |||||||||||||| || ||||||||||||||||| ||||||   || ||||| |||||||| ||||| ||||| || ||||||         ||    | || |||| |  || |   | |||     || ||   | | || || | |   | |     ||||   | | || |  | ||| || ||       |                                               
ATCAATGGCTCTTACTCCTTGGTTAGCTGCTGGCGGCCAATTAATTGCGTCTCGATTTGAGTTACAAGATGTTCGAAGTTTATTACCAGTTGAAAGCGAGgtactccttcacaacactttaaaataagtcatttatcaccattcctagtttcaattgtaaat-ttaaaacaataaagccatgattgacctcaatatccttccgaagctcatgcattcttggggtaaaaatgactgatcctttactttctgaatttacttgcag

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|110389557|gb|EC954408.1|EC954408
EST:     CTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAG                         ACAGATGATTTGCAAGATCATATTATCATTTGTGGATTTGGACGTGTTGGA
genomic: CTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAGgtaaaattct ... ttgtttccagACAGATGATTTGCAAGATCATATTATCATTTGTGGATTTGGACGTGTTGGA
EST: gi|34546770|gb|CF515002.1|CF515002
EST:     CTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAG                         ACAGATGATTTGCAAGATCATATTATCATTTGTGGATTTGGACGTGTTGGA
genomic: CTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAGgtaaaattct ... ttgtttccagACAGATGATTTGCAAGATCATATTATCATTTGTGGATTTGGACGTGTTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTATGGCCCTGACCCCATGGTTAGCTGCTGGAGGACAATTAATTGCGTCTCGTTTTGAGCAGCATGATGTGCGAAGTTTGTTACCTGTTGAGAGTGAGgtaaaattctcaatataatggttcacagctattgattacagaagcatatattgacatggtgagtttttgatgcatgaacacatccaaaactagcttggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaactag