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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgcgcaggcataattactgcatatggcagctcaattgaaaattttaaatgattgtttgtttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCTGAGTGCCGTCATCTGATCTCAAGGATTTTTGTAGCTGATCCTGCAACG

Basic information

species Vitis vinifera
transcript Vv03s0063g01080.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 3'ss of exon 5
-----------------gtatttgcgcaggcataattactgcatatggcagctcaattgaaaattttaaatgattgt-ttgtttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCTGAGTGCCGTCATCTGATCTCAAGGATTTTTGTAGCTGATCCTGCAACG
                   |    | | | |  ||  | | ||||   ||  |  |||  |||   | |  |||  | ||  || | ||||||||| |||   || ||||| ||||||||||||||||| || |||||||| ||||||||  |||| ||  | ||||||||||| ||  | || || || 
gtttccattgcggtcatccaacatcacggtctcaaa-atttcata-accattttgattacaaaaactgatcgatgatcttcattttcgcagAGAATATTGGGTGTGCAGTACTCTATTCCAGATTATGTCCACATATCTCCAGAGTGCCGAGATCTTATTGCGAGGATTTTTGTGGCCAACCCAGCCACT

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G01240.1 (Glycine max), 3'ss of exon 7
gta-tttgcgcaggcataattactgca-tatggcagctcaattgaaaattttaaatgattgtttgtttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCTGAGTGCCGTCATCTGATCTCAAGGATTTTTGTAGCTGATCCTGCAACG
|||   | |     |||  |||   ||   | | |     ||||||    |||||   |||  | || ||||||||| ||||||||||||||||| || ||||| |||||||||||||||||||| |||||||||||||| ||||||||||| ||||| || || ||||||  |
gtaacctactgcaccatttttaggtcaacgtagtaataatattgaattacttaaactgttggattttgcttgcagAGGATTTTGAAAGTCCAGTACTCAATTCCTGATTATGTTCATATATCTCCCGAGTGCCGTCATCTAATCTCAAGGATCTTTGTGGCAGACCCTGCACAG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G15330.1 (Glycine max), 3'ss of exon 7
----gtatttgcgcaggcat---aattactgcat-atggcagctcaattgaaaattttaaatgattgtttgtttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCTGAGTGCCGTCATCTGATCTCAAGGATTTTTGTAGCTGATCCTGCAACG
     || |||| |     |   ||| | ||  | |       | ||||     |  ||||    ||  || || |||||||| |||||||| || ||||| || ||||| || ||||||||||||||| | ||||||||||||||||| |||||||||||||| ||||||||||||| |
gtaactaattgcacctttttttcaatcagtgtgttactttgattgaattagttttcctaaactgatgcatgcttgttgcagAGGATTTTGAATGTTCAGTACTCAATTCCTGACTATGTTCATATATCTTCCGAGTGCCGTCATCTGATATCAAGGATTTTTGTTGCTGATCCTGCAAAG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G29500.1 (Glycine max), 3'ss of exon 7
gta-tttgcgcaggcataattactgca-tatggcagctcaattgaaaa-----ttttaaatgattgtttgtttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCTGAGTGCCGTCATCTGATCTCAAGGATTTTTGTAGCTGATCCTGCAACG
|||   | |     |||  |||   || | | | |     ||||||       | |||||   |||  |  | ||||||||| ||||||||||||||||| || ||||| |||||||||||||||||| |||||||||||||||| ||||| ||||| ||||| || || ||||||  |
gtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttcttaaactgttggattatgcttgcagAGGATTTTGAAAGTCCAGTACTCAATTCCTGATTATGTTCATATATCTTCTGAGTGCCGTCATCTAATCTCTAGGATCTTTGTGGCAGACCCTGCACAG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G33120.1 (Glycine max), 3'ss of exon 7
gtatttgcgcaggcataattactgc--atatggcagctc-aattgaa--aatttt---aaatgattgtttgtttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCTGAGTGCCGTCATCTGATCTCAAGGATTTTTGTAGCTGATCCTGCAACG
|||  |    |  | |  || |  |  || ||| |  |   ||||||  | ||||   ||||   ||  ||||  |||||||| |||||||| || ||||| || ||||| || || ||||| |||||| | ||||||||||||||||| |||||||||||||| ||||||||||||| |
gtaactaatgacactttttttcaaccaatgtggtacttttgattgaattagttttcctaaattgatgaatgttggttgcagAGGATTTTGAATGTTCAGTACTCAATTCCTGACTACGTTCACATATCTTCCGAGTGCCGTCATCTGATATCAAGGATTTTTGTCGCTGATCCTGCAAGG

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------------------gtatttgcgcaggcataattactgcatatggcagct--caattgaaaattttaaatgattgtt----tgtttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCTGAGTGCCGTCATCTGATCTCAAGGATTTTTGTAGCTGATCCTGCAACG
                             || |||   |    ||||||  |  | |   |  |   |  | ||   | |      ||||     | |||  | ||||||||  |||| || |||||| ||||||| ||||||||||| ||||||||||| || || ||| ||||||| || || ||||| ||||| ||||||| |
gtgagcctttcactttcttcatgcttcaatagttgaa-aaatgtaattatggattttattacttgctagctaaactatctgttctcttgtgaaaatatttgct-cagAGAATCCTGAATGTTCAGTATGCTATTCCGGATTATGTTCACATATCTCCTGAATGTCGCCATTTGATCTCCAGAATATTTGTTGCTGACCCTGCAAAG

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|71872877|gb|DT021932.1|DT021932
EST:     ACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAG                         AGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCT
genomic: ACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgtatttgcgc ... tttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgcatatggcagctcaattgaaaattttaaatgattgtttgtttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCTGAGTGCCGTCATCTGATCTCAAGGATTTTTGTAGCTGATCCTGCAACG
                                         tttgtttctt  CT-rich tract
                   aattgaaaattttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgcgcaggcataattactgcatatggcagctcaattgaaaattttaaatgattgtttgtttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCTGAGTGCCGTCATCTGATCTCAAGGATTTTTGTAGCTGATCCTGCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT