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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttctacctcttcattttcctagtgtaccaagctcatcttattggcatgctcatgtttttggttgatatttttttcttgttctttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGTAGATCTATTTTTCAGAAAGGAACTTCCATTAAG

Basic information

species Vitis vinifera
transcript Vv05s0051g00870.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os02g56850.2 (Oryza sativa), 3'ss of exon 6
gtgtgtttctacctc----ttcattttcctagtgtaccaagct-catcttattggcatgctcatgtttttggttgat-atttttttcttgttctttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGTAGATCTATTTTTCAGAAAGGAACTTCCATTAAG
|| ||| | || | ||||| || | || | | || | | |||| || ||| | || | | | | | || || ||||||||||| |||||||| |||||||| |||||||||| ||||| | |||| |||| || ||||| ||||
gtatgtctacactctagggtgcatttatgtactatatattgttatgtcattccaactatctcagacttgcatttgttcatgtggtggctatattgcagATATATTGCTGTTGAATTTGCTTCTATATGGAAAGGGATGGGTGCGCACGTAGACTTGTTTTATCGAAAAGAGCTTCCTCTAAG

upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G08180.1 (Glycine max), 3'ss of exon 6
gtgtgtttctacctcttcattttcctagtgtaccaagctcatcttattggcatgctcatgtttttggttgatatttttttcttgttctttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGTAGATCTATTTTTCAGAAAGGAACTTCCATTAAG
|||| | | || | || |||| || | | || || | || |||||| | | || || || | | ||||| || || || ||||| ||||||||||| || |||||| |||||||||| | || |||||| |||||||||||||||||||| | ||
--gtgtgtatgtcttcttat-------gtgtttttagtttaactacttagtat-ctcatggt---gattaat--ttatattttgtttttcagTTATATTGCAGTTGAGTTTGCATCTATATGGCGTGGGATGGGTTCCACAGTTGATCTAGTTTTCAGAAAGGAACTTCCACTGAG

upper sequence: Vv05s0051g00870.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G24170.2 (Arabidopsis thaliana), 3'ss of exon 7
gtgtgtttctacctcttcattttcctagtgtaccaagctcatcttattggcatgctcatgtttttggttgatattttt-ttcttgttct--ttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGTAGATCTATTTTTCAGAAAGGAACTTCCATTAAG
|| | ||| |||| ||||||| || | | | | | || ||| ||| | ||| | || ||| | ||||||| |||||||| |||||||| ||||||||| ||| ||||||| | |||||||| |||| ||||| ||||||||||| ||||
gta-atgtcttcctcaatgttttcctcctg--ctgtacctaacatgccagctgtttcaatggtttaatcctcgtttctatttacgttttaattagGTATATTGCTGTGGAGTTTGCATCAATATGGCGTGGAATGGGTGCTACTGTAGATTTATTCTTCAGGAAGGAACTTCCGCTAAG

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|46917982|gb|CN547311.1|CN547311
EST:     GCTTTGAGTTTGGATGAGTTGCCCAAGCGTGCTGTAATACTAGGGGGAGG                         GTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGT
genomic: GCTTTGAGTTTGGATGAGTTGCCCAAGCGTGCTGTAATACTAGGGGGAGGgtgtgtttct ... tgttctttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGT
EST: gi|294967112|gb|GW839987.1|GW839987
EST:     GCTTTGAGTTTGGATGAGTTGCCCAAGCGTGCTGTAATACTAGGGGGAGG                         GTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGT
genomic: GCTTTGAGTTTGGATGAGTTGCCCAAGCGTGCTGTAATACTAGGGGGAGGgtgtgtttct ... tgttctttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGT
EST: gi|110729876|gb|EE106312.1|EE106312
EST:     GCTTTGAGTTTGGATGAGTTGCCCAAGCGTGCTGTAATACTAGGGGGAGG                         GTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGT
genomic: GCTTTGAGTTTGGATGAGTTGCCCAAGCGTGCTGTAATACTAGGGGGAGGgtgtgtttct ... tgttctttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGT
EST: gi|110699093|gb|EE077335.1|EE077335
EST:     GCTTTGAGTTTGGATGAGTTGCCCAAGCGTGCTGTAATACTAGGGGGAGG                         GTACATTGCTGTTGAGTTTGCTTCA-TATGGAATGGGATGGGTGTTGCTGT
genomic: GCTTTGAGTTTGGATGAGTTGCCCAAGCGTGCTGTAATACTAGGGGGAGGgtgtgtttct ... tgttctttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatcttattggcatgctcatgtttttggttgatatttttttcttgttctttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGTAGATCTATTTTTCAGAAAGGAACTTCCATTAAG
                            ggttgat  putative branch site (score: 5)
 tatttttttcttgttc  CT-rich tract
 atatttttttcttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtttctacctcttcattttcctagtgtaccaagctcatcttattggcatgctcatgtttttggttgatatttttttcttgttctttagGTACATTGCTGTTGAGTTTGCTTCAATATGGAATGGGATGGGTGTTGCTGTAGATCTATTTTTCAGAAAGGAACTTCCATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA