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'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccaccttgcctgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG

Basic information

species Vitis vinifera
transcript Vv05s0020g03080.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 17
gtacc-caccttgcc-tgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG
||| |  | |||||  |||  | |||  || | |  | |||    | | | | |||  ||  |       ||||  |  | |||     |||||||||||| |||||||| || || ||| | || || |||||||||||||| ||| | |||||||| ||  |||| || || |||||
gtaacgtatcttgctatgtatttctgtctcctatttaagttca--aatatattaaa--tgagtttcagaaattacatt-tgaaaacatgcagGAGAGAGGTCATTGATGAGGACGGTTGGTTGCACACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G059381_T03 (Zea mays), 3'ss of exon 4
-----gtacccaccttgcctgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG
      |     | || |   |     |   || ||| |||    | |||    | ||| || |||| || |  ||        |||     ||| |||||||| |||||||| ||||| ||| | ||||| |||||||||||||| ||| | |||||||| || ||||| || || |||||
gtaacttgttatcattacacatctatttacatcctttaaataa-atacatcc-attaaactttgataaatgtatttg-------aaaacctgcagAAGAGAGGTCATTGATGAGGATGGTTGGTTACATACTGGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTCTAAAAATTATAGATAG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 8
gtacccaccttgcctgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatc--tgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG
      |  ||   |      ||    | |     |||  || ||  | |  || |   |   |||  | | ||  |  | |||   | ||| | ||| || |||||||||||||| ||| | || || |||||||||||| | ||| |||||||||| ||  |||||||||| |||||
---gtaaatttctatccgtcacttaaacatagctttgtactgaatgatcttcaactgcaacttatcaataaatacattttaaaaacta-cagAAAAGAAGTCATTGATGAAGATGGTTGGTTGCACACTGGAGACATAGGTCTGTGGCTACCTGGAGGACGTTTAAAGATCATCGATAG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 17
gtacccaccttgcctgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG
|||   ||||| ||||||||| || ||||  ||||||   |  |  ||| ||   ||  |   |  ||| | |   |||||||||| ||||||||| || |||||||||||||||||||| ||||| ||||| || ||    ||||||||||| ||||| || || || ||||||||
gtaattacctttcctgttctg-tgcttctaatgaatgaaat-taccttg-catgtttaaaagtaattgaattt-caatcaaattgagcagGAGAGATGTCATTGATGAAGATGGATGGCTACATACTGGAGATATTGGGACGTGGTTACCTGGTGGTCGTCTCAAAATTATTGATAG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 17
gtacccaccttgcctgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG
|||   ||||| ||||||||| || ||||| ||||||   |  |  ||| ||   ||  |   |  ||| | |   |||||||||| ||||||||| || ||||||||||| |||||||| ||||| ||||| || ||   |||||||||||| ||||| || || || ||||||||
gtaattacctttcctgttctg-tgcttcttatgaatgaaatttaccttg-catgtttaaaagtacttgaattt-caatcaaattgagcagGAGAGATGTCATTGATGAAGACGGATGGCTACATACTGGAGATATTGGGACATGGTTACCTGGTGGTCGTCTCAAAATTATTGATAG

upper sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 17
gtacccaccttgcctgttctgctggttctt-ttgaatgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG
|||   ||     |||   ||    ||| | ||  |        | | |  ||||| |  |   || | | ||     |   |||   ||||| |||||| ||||||||||||||||||||||| || ||||| |||||| | ||| | || ||||| || ||||| || ||||| ||
gtataaacacctactgcattggaaattcctctttcactaaccaaagtgtaccaaaagtttaattatttcagtaaaacgtattatttt-cagGAAAGAGGTGATTGATGAAGATGGATGGCTTCACACTGGAGATATAGGTCTGTGGCTGCCGGGAGGACGTCTAAAAATTATTGACAG

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|71889597|gb|DT038652.1|DT038652
EST:     GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGAC                         GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
genomic: GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccacct ... aattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
EST: gi|110414986|gb|EC980854.1|EC980854
EST:     GTTCGGAGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGAC                         GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
genomic: GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccacct ... aattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
EST: gi|46917646|gb|CN546975.1|CN546975
EST:     GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGAC                         GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
genomic: GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccacct ... aattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
EST: gi|71882993|gb|DT032048.1|DT032048
EST:     GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGAC                         GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
genomic: GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccacct ... aattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
EST: gi|161720583|gb|FC069911.1|FC069911
EST:     GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGAC                         GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
genomic: GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccacct ... aattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
EST: gi|46917526|gb|CN546855.1|CN546855
EST:     GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGAC                         GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
genomic: GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccacct ... aattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
EST: gi|71881187|gb|DT030242.1|DT030242
EST:     GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGAC                         GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
genomic: GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccacct ... aattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
EST: gi|161720400|gb|FC069849.1|FC069849
EST:     GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGAC                         GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
genomic: GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccacct ... aattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
EST: gi|71882474|gb|DT031529.1|DT031529
EST:     GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGAC                         GAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT
genomic: GTTCGGGGTCCCATTCTTTTTCTAGGTTACCATAAAGATGAAGTGCAGACgtacccacct ... aattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG
                            atctgat  putative branch site (score: 4)
        attttgtcaaaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacccaccttgcctgttctgctggttcttttgaatgttgtgcattttgtcaaaattggatacatctgattatgtgatcaaattgaacagGAGAGAGGTAATTGATGAAGATGGATGGCTTCATACGGGAGACATAGGTTTATGGTTACCTGGAGGTCGCCTAAAGATCATTGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA