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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAGgttgttattatttaatctattattattgttgtttttattattttgtttttgtggtgaattagtatttttactttttatttcttaatgctttggttagttg...

Basic information

species Vitis vinifera
transcript Vv16s0100g00320.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0100g00320.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G27300.1 (Glycine max), 5'ss of exon 2
GTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAGgttgttattattta----atctattat--tattgttgtttttattattttgtttttgtggtgaattagtatttttactttttatttcttaatgctttggttagttg
| ||| ||||  ||||| || || || || ||||||||||| |||||||| ||||  ||||| ||||  |||||||||||||| || | |||  |||| ||||||| ||     || |||| |  | | |  |  ||| || |||   ||||   || |      |  ||  ||||||  |   ||||| |  | |||    
GCTGTGAGTGCAATTGCCTTTCCCTCTGGTTCTGATAAGCTGTATACTGGAAGCACTGATGAGACTGCAAGGATTTGGGACTGCCAGTGTGGAAAGgtggttattaattggatcatgtattgttttgtagaggcattttttgtttcaattttaaagtta-cagacaccttgtcttttt--tcactaatgttaagcttaa---

upper sequence: Vv16s0100g00320.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT5G51980.2 (Arabidopsis thaliana), 5'ss of exon 2
----GTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAGgttgttattatttaatctattattattgttgtttttattattttgtttttgtggtgaattagtatttttactttttatttcttaat-gctttggttagttg-
     |||| ||||| ||||||||||| || || ||||||||||| || ||||| || |||||||| ||  || |  ||||||| |||   ||||| |||||     ||  | ||   |   | |  | | |  | | |  |    || | |||| |     ||   |  ||||  |      | | | | |   | | || 
GAAGCTTGTTAGTGGTATTGCTTTGCCTTCTGGTTCTGATAAGCTTTACACTGGAAGTAAAGATGAGACCTTGCGTGTTTGGGATTGTGCTTCTGGACAGgtatggtttgctcaaaggaccttaa--gctttcctcagtgatagaattgtttggttaggatatagagtggctttagagaatgcagttgttgtccatggatgt
















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|351049271|gb|FQ429014.1|FQ429014
EST:     CTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAG                         TGCACTGGTGTGGTTAATCTTGGTGGAGAAGTTGGCTGTATGATTAATGAG
genomic: CTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAGgttgttatta ... tcttttgtagTGCACTGGTGTGGTTAATCTTGGTGGAGAAGTTGGCTGTATGATTAGTGAG
EST: gi|349829433|gb|FQ419965.1|FQ419965
EST:     CTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAG                         TGCACTGGTGTGGTTAATCTTGGTGGAGAAGTTGGCTGTATGATTAGTGAG
genomic: CTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAGgttgttatta ... tcttttgtagTGCACTGGTGTGGTTAATCTTGGTGGAGAAGTTGGCTGTATGATTAGTGAG
EST: gi|161721021|gb|FC069636.1|FC069636
EST:     CTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAG                         TGCACTGGTGTGGTTAATCTTGGTGGAGAAGTTGGCTGTATGATTAGTGAG
genomic: CTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAGgttgttatta ... tcttttgtagTGCACTGGTGTGGTTAATCTTGGTGGAGAAGTTGGCTGTATGATTAGTGAG
EST: gi|110698131|gb|EE075789.1|EE075789
EST:     TGGGAGCAA-GATGAAACTGTGAGGGATTTGG-ACTGTCAATCTGGTCAG                         TGCACTGGTGTGGTTA
genomic: TGGGAGCAAAGATGAAACTGTGAGG-ATTTGGGACTGTCAATCTGGTCAGgttgttatta ... tcttttgtagTGCACTGGTGTGGTTA
EST: gi|22009470|gb|BQ794504.1|BQ794504
EST:     GACTGTCAATCTGGTCAG                         TGCACTGGTGT-GTTAATCTTGGTGGAGAAG-TGGCTGTATGATTAGTGAG
genomic: GACTGTCAATCTGGTCAGgttgttatta ... tcttttgtagTGCACTGGTGTGGTTAATCTTGGTGGAGAAGTTGGCTGTATGATTAGTGAG
EST: gi|30305654|gb|CB982448.1|CB982448
EST:     CTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAG                         TGCACTGGTGTGGTTAATCTTGGTGGAGAAGTTGGCTGTATGATTAGTGAG
genomic: CTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAGgttgttatta ... tcttttgtagTGCACTGGTGTGGTTAATCTTGGTGGAGAAGTTGGCTGTATGATTAGTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTCAGTGGGATTGCTTTGCCATCCGGGTCTGATAAGCTATATACTGGGAGCAAAGATGAAACTGTGAGGATTTGGGACTGTCAATCTGGTCAGgttgttattatttaatctattattattgttgtttttattattttgtttttgtggtgaattagtatttttactttttatttcttaatgctttggttagttg

- - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT