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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctctctaaatgaaatgcttccacaaatgtcctggggaatccatgcatgctggattagttcctgttagtccatgactgatttgctggatattgcagTTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTACTCCTTGCAAATTGGTTATGTGATAACCATATGAAGGATCCCTTG

Basic information

species Vitis vinifera
transcript Vv18s0157g00050.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0157g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g05240.1 (Oryza sativa), 3'ss of exon 5
tttttctctctaaatg---aaatgcttccacaaatgtcctggggaatccatgcatgctggattagttcctgttagtccatgactgatttgctggata---ttgcagTTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTACTCCTTGCAAATTGGTTATGTGATAACCATATGAAGGATCCCTTG
     | || |||||    ||||   |    |  |   ||      ||  ||  | |||  |   |  |||| | |   |||   ||||  || | |   ||||||| | |||| ||||| ||||| ||||||||||||||  | ||| ||||  ||   |||||||||||| | ||||||||| || ||||||||||||||
----acactataaatctgtaaataaatatctaggttatctatttcgtcagtg-gttctgattatatatctgtgaattt-tgatgtattttttgtacaaacttgcagTATGTTGGTAATGTCCATGGTGATGAACCTGTTGGAAGGGAGGTTCTTATAAAGCTTGCAAATTGGCTGTGTGATAACTATTTGAAGGATCCCTTG

upper sequence: Vv18s0157g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G31000.1 (Glycine max), 3'ss of exon 5
---------tttttctctctaaatgaaatgcttccacaaatgtcctggggaatccatgcatgctggattagttcctgttagtccatgactgatttgctggatattgcagTTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTACTCCTTGCAAATTGGTTATGTGATAACCATATGAAGGATCCCTTG
         ||| |   |||   | |   |  |     |||  ||||  |||| |     ||     ||   | | |  | |   ||||    ||  |   |  |||||||||||||||||||||| || ||||||||||| || |||||||| ||  || |  | || ||||||||||||||||||||| |||||||||| |||
tatgccatatttatacttctgcttta---gtgttagttaattccctgaagaatgctc---tgtaatcttgaattcagcaattttgtgacca--ttaatac-tgctgcagTTTATTGGAAATGTGCACGGTGATGAACCTGTGGGACGTGAGCTGCTTATATTTTTGGCCAATTGGTTATGTGATAACCATTTGAAGGATCCTTTG

upper sequence: Vv18s0157g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G36590.1 (Glycine max), 3'ss of exon 5
--------tttttctctctaaatgaaatgcttccacaaatgtcctggggaatccatgcatgctggattagttcctgttagtccatgactgatttgctggatattgcagTTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTACTCCTTGCAAATTGGTTATGTGATAACCATATGAAGGATCCCTTG
        |||    ||     |  | || |      |||  ||||  ||||       ||  |  ||   | | |  | ||  ||||    ||  |   |  |||||| ||||||||||||||| || ||||||||||| || |||||||| ||  || |  | || ||||||||||||||||||||| |||||||||| |||
atgtcatatttaatacttctgctttagtgtta--gttaattgcctgaagaatgttc---tgtagtcttgaattcagcaattctgtgacca--ttaatac-tgatgcagTATATTGGAAATGTGCACGGTGATGAACCTGTGGGACGTGAGCTGCTTATATTTTTGGCCAATTGGTTATGTGATAACCATTTGAAGGATCCTTTG

upper sequence: Vv18s0157g00050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G71696.2 (Arabidopsis thaliana), 3'ss of exon 5
-tttttctctctaaatgaaatgcttccacaaatgt--cctggggaatccatgcatgctggattagttcctgttagtcca--tgactgatttgctggatattgcagTTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTACTCCTTGCAAATTGGTTATGTGATAACCATATGAAGGATCCCTTG
 ||       || ||| |  ||   | | | |||    ||  |  ||    |  ||  |   |||      | | || |  |   ||| |   |||  || |||||  ||||| ||||| ||||||||||||||||| || ||||||||  | |||| ||||||||| ||| | ||||||||| ||| ||||||||| |||
gttaaaactgctcaattatttgtgcctatacatgcaatctttgagatattagattgtggtgatagcctagatgaatctaaatagttgaatatttggtcat-gcagTACATTGGGAATGTACATGGAGATGAACCTGTAGGGCGTGAGCTCTTATTACGCCTTGCAAACTGGATTTGTGATAACTATAAGAAGGATCCATTG

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|71855520|gb|DT004575.1|DT004575
EST:     TGGAAATTTCTGACAAACCAGGGGAGGAAGAAGCGGAACCTGCATTTAAG                         TTTATTGGAAA
genomic: TGGAAATTTCTGACAAACCAGGGGAGGAAGAAGCAGAACCTGCATTTAAGgtgaatgatc ... gatattgcagTTTATTGGAAA
EST: gi|71856642|gb|DT005697.1|DT005697
EST:     TGGAAATTTCTGACAAACCAGGGGAGGAAGAAGCAGAACCTGCATTTAAG                         TTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTA
genomic: TGGAAATTTCTGACAAACCAGGGGAGGAAGAAGCAGAACCTGCATTTAAGgtgaatgatc ... gatattgcagTTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcatgctggattagttcctgttagtccatgactgatttgctggatattgcagTTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTACTCCTTGCAAATTGGTTATGTGATAACCATATGAAGGATCCCTTG
                                gactgat  putative branch site (score: 3)
            attagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctctctaaatgaaatgcttccacaaatgtcctggggaatccatgcatgctggattagttcctgttagtccatgactgatttgctggatattgcagTTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTACTCCTTGCAAATTGGTTATGTGATAACCATATGAAGGATCCCTTG

- - tctctct
- - - - - -aaatgaa
- - - - - - - - - - - - ccacaaa
- - - - - - - - - - - - - - - - - - - - - - ccatgca
- - - - - - - - - - - - - - - - - - - - - - - - - -tgctgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgctg