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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattcttgtcctcatctgtcttatgatgctttaattcatatttttgctcatgtatttggatgtaattctttttcag

Basic information

species Vitis vinifera
transcript Vv01s0011g05790.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os02g50320.1 (Oryza sativa), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgt-tggtattcttgtcctcatctgtcttatgat-gctttaattcatatttttgctcatgtatttgg-atgtaattctttttcag--
 || ||  | ||||| ||||||||||| |||||| |||| ||||| || ||  | ||||| ||||||||||| || ||||| ||||||||||| |||||||| ||| | |    | |   | | |  |    |   |   |   ||  | | | |||||  ||||  |  |   |||| || |   
TGGTGTACTCTATGACATGCTGCAAAAGGAGGTCATTTCATTGAGAAAGGCATGCCATGAGAAAGATCAAAGTCTAAAAGACAAGGATGATGCAATTGAGgtatggcactagaattcctgtttattatggatttaatgggaccaatgctgtgggtcatgcctttgctaactgcctcttgtttacag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgt-tggtattcttgtcctcatctgtcttatgatgcttt----aattcatatttttgctcatgtatttggatgtaattctttttcag
 ||  |  | ||||||||| |||| || |||||  |||||||||| || ||  | |||||||||||||| || || |||||||| |||||||| |||||||| ||| | | || | || || |||   |    | |      ||     || || |   || ||  ||  | |  || |  | |||
TGGTTTTCTTTATGATATGTTGCAGAAGGAGGTAATTTCTTTGAGAAAGGCATGCCATGAAAAAGATCAGAGTCTAAAAGATAAAGATGATGCGATTGAGgtatggaaatattttgcttatttgttgcactgagttcataggaagctcgatattagaaaatttacctgtttcttcttgtcctacag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G039325_T01 (Zea mays), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggt----attcttgtcctcatctgtcttat------gatgctttaattcatatttttgctcatgta-tttggatgta-attctttttcag---
 ||  |  |||||||||||||||||||||||||  |||||||||| ||  |  | |||||||| ||||| |  || |||||||| |||||||||||||||||  |     |||  | |||| ||  ||    |      |||  ||   |  ||| |  |  | ||| | ||||  | |  ||| || |   |   
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGTCATGCCATGAAAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtatgcgtccatttctttccttattcgttcactttagtggatagttagctaaatactgattattatgaagtttgcttatctattgttgtctggcag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GRMZM2G008556_T01 (Zea mays), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattcttgtcctcatctgtcttatgatgctttaattcatattt--ttgctcatgtatttggatgtaatt--ctttttcag-------------
 ||  |  |||||||||||||||||||||||||  |||||||||| ||  |  | ||||| || ||||| |  || |||||||| |||||||||||||||||  || | | | || |  |||   || |    ||||| |  ||| ||   |    |   |||   ||| ||||  ||| |  |              
TGGTTTCCTATATGATATGCTGCAAAAAGAGGTAATTTCTTTGAGAAAGACATGCCATGAGAAGGATCAGATTCTAAAAGATAAAGATGATGCTATTGAGgtctgtgtccatttcttt-tcttctttgtt-cactttagtggatagttagctatatactgattattatgaaatttgcttatctactgctgtctggcag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA02G09390.1 (Glycine max), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattct-tgtcctcatc-tgtct---tatgatgctttaattcatattt--------------ttgctcat-gtatttggatgtaattctttttcag
  | || ||||||||  | ||||||||||||||| |  | ||||||||||||||||| || |||||||||||||| |||||||| |||||||||||||||||  || ||   | |  | ||  ||| |   ||| || ||| | ||| ||| |              ||||| || || |      || ||  | | ||||
CAGTGTTTTATATGACTTTCTGCAAAAAGAGGTCATAGCCTTGAGGAAAGCTGGTCACGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCTATTGAGgtaagtgtttggtctatttattgtgtttggatataatccttgacttcttatgtataaatgatagtccttgctaattgtttccaatggtcatcatctatcag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA05G34560.1 (Glycine max), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtatt--cttgtcctc----atctgtcttatgatgct--ttaat--tcatatttttgctcatgtatttggatg-taattctttttcag
 || || || |||||| ||||||| ||||||||| |  | |||||||||||||||||||| |||||||||||||| |||||||| |||||||| ||||| ||| |||||   ||||  |     ||   |||||   | ||  || ||  | ||| | ||    |  | ||   ||| |  || | | ||||
GGGAGTTTTGTATGATTTGCTGCAGAAAGAGGTCTTAGCCTTGAGGAAAGCTGGTCATGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCCATTGAAgttagtatttatttgtttttggatattaatcttagatttctaattgataattataatcttagctaactgttgcaatggttgttatctgtcag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA07G26540.1 (Glycine max), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattct-tgtcctcatc-tgtct---tatgatgctttaattcatatttttgctcatgtatttggatgtaattctttttcag----------------
 || || ||||||||  ||||||||||||||||  |  | |||||||||||||||||||| |||||||||||||| |||||||| |  ||||||||||||||   | ||   | |  | ||  | | |   ||| || ||| | ||| ||||| |       || |      ||||| |||   |                 
TGGTGTTTTATATGACTTGCTGCAAAAAGAGGTGATAGCCTTGAGGAAAGCTGGTCATGAGAAAGATCAAAGCCTAAAAGATAAAGGCGATGCTATTGAGgtaaatgtttggtctatttattgtatttggatataatccttgacttcttatttataaatg-atagtccttgctaattgtttccaatggccatcatctatcag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA08G05100.1 (Glycine max), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattcttgtcctc------atctgtcttatgatgct--ttaat--tcatatttttgctcatgtatttggatg-taattctttttcag
||| || || |||||| ||||||| ||||||||| |  | |||||||||| ||||||||| |||||||||||||| |||||||| |||||||| ||||| ||| ||||| || |  ||      ||   |||||   | ||  || ||  | ||| | ||    |  | ||   ||| |  || | | ||||
AGGAGTTTTGTATGATTTGCTGCAGAAAGAGGTCTTAGCCTTGAGGAAAGTTGGTCATGAGAAAGATCAAAGCCTAAAAGATAAAGATGATGCCATTGAAgttagtatttttttgttcttggatattaatcttagatttctaattgataattataatcttagctaattgttgcaatggttgttatctgtcag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattcttgtcctcatctgtcttatgatgctttaattcatatttttgctcatgtatttggatgtaattctttttcag---------------------------------
 || || || |||||| | || || ||||| || |||||||||||||||||   | ||||||| ||||||||||||||||| || |||||||| || |||||  |  ||||  | ||    |   || || | |||||   ||||||  | ||  | ||         | |  | ||  |                                  
TGGTGTTTTGTATGATTTACTACAGAAAGAAGTAGTTTCTTTGAGGAAAGCCTCTAATGAAAAGGATCAAAGCCTCAAAGACAAAGATGATGCCATCGAGgtaagagttctgtttctt---taagttctgtttctttatgccatattaat-cttgtttaaagaagaacattcttgttgtaaacggaggaagtaatgatacgttgatgttcgtag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattcttgtcctcatctgtcttatgatgctttaattcatatttttgctcatgtatttggatgtaattctttttcag---
|||||| || |||||| | || || || || || ||  | ||||| ||| ||   |||||||| ||||||||||||||||| ||||||||||| || |||||      |||   |   || |  | ||| |    ||  |  | |    || |  |       |   | ||  ||||   |   
AGGGGTTTTGTATGATTTACTACAGAAGGAAGTAGTCGCCTTGAGAAAATCTTCGCATGAAAAGGATCAAAGCCTCAAAGACAAGGATGATGCCATAGAGgtaaaatctct---ctgaatgtaccatataaaatgttgttaaaaagacgtgtttgtaatggaagtcttgatatttttcttgtag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 5'ss of exon 10
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattcttgtcctcatctgtcttatga-----tgct----ttaattcatatt-tttgctcatg-tatttggatgta-attctttttcag
||| || ||| ||||| |||| ||||| |||||  |  |||| |||||||||| | |||| |||||||||||||| | |||||| || || |||||||||||| ||  |    |   || || ||  |  |     ||||    || ||| ||||| | || |||   || ||||   |   ||   ||| ||
AGGAGTATTACATGATTTGCTTCAAAAGGAGGTGATAACTTTAAGGAAAGCTGCTAATGATAAAGATCAAAGCCTTAGAGATAAAGACGAAGCTATTGAGgttagtcattagttttacacctttccaagaaacgtttgcttatatttatttatattctctgatcaaaatacttgggcttgtgtttgcttttag

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S31_77V6.1 (Physcomitrella patens), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtatt--cttgtcctcatctgtct--tatgatgctttaattcatatttttgctcatgtatttggatgt---aattctttttcag-------------
||| ||||| || ||  | || || |||||||| ||     ||||||| ||  | | ||||||||||||||| || || || ||||||||||||||||||||| ||||   |    |   ||||   |   ||       ||| ||| |     |    || || || | ||   ||  | ||    |             
AGGTGTGTTGTACGACCTTCTCCAGAAAGAGGTTGTCAACCTGAGGAAGGCGAGCCTTGAAAAAGATCAAAGTCTGAAGGACAAGGATGATGCTATTGAGgttcgtatgggccaaactatatctcattagcatatcaacataactcaaaggaaggaa-gtggatctgaaggtttgaacaccttgatggtgaccacttgctg

upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: PP1S136_188V6.1 (Physcomitrella patens), 5'ss of exon 9
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattc--ttgtcctcatctgtct----tatga----tgctttaattcat-atttttgctcatgtatttggatg---taattctttttcag-------------------------------------------------------------------------------------------------------
||| ||||| |||||  | || || ||||| || ||     ||||||| ||  |  |||||||||||||||| ||||| |||||||||||||||||||||||  ||||    |   |  |||||  ||    |||||    | || |  ||  | | ||||||     | |||| |     | ||| | |||                                                                                                          
AGGTGTGTTGTATGACCTTCTACAGAAAGAAGTTGTCAACCTGAGGAAGGCAAGCTATGAAAAAGATCAAAGTCTCAAGGATAAGGATGATGCTATTGAGgtgcgtatagggtaaactacatcttactagcatatgaatacttctctgcttagtgagttttgcattgatttttgaacaacttgattatatttatcgactgcagatattgttgttacctcgtaccttcccggtttgctgtttttgacatgtattcacgctggcttcgtggctgcttctaatgtgttctgatatgtgcag

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|87585995|gb|DY474485.1|DY474485
EST:     CTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAG                         ATGCTAGCTAAGAAGGTAGATACATTAACCAAGGCAATGGAAGTTGAGGCT
genomic: CTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattc ... tctttttcagATGCTAGCTAAGAAGGTAGATACATTAACCAAGGCAATGGAAGTTGAGGCT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGGGTGTTATATGATATGCTGCAAAAAGAGGTCGTTTCTTTGAGGAAAGCTGGTCATGAAAAAGATCAAAGCCTCAAAGATAAGGATGATGCTATTGAGgttggtattcttgtcctcatctgtcttatgatgctttaattcatatttttgctcatgtatttggatgtaattctttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG