Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaattcatatgattatcattttttgttggca...

Basic information

species Vitis vinifera
transcript Vv08s0040g02630.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G124411_T04 (Zea mays), 5'ss of exon 3
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatc-ttctcagcagttcaattgaaattattg-gcatttttttttcagttgcaacaattcatatgattatcattttttgttggca
||||||||||||| ||| ||   || ||||| |||||||| |||| |||  | ||||| ||||||||||||||| ||||||| || || ||| ||||||||| |  | ||  |   |  |  || ||    |   |||| |   | ||| |||  | |   | | |    |   |   | |  |   ||             
TTGTCTTCATTGTCGACCTCAAGGCAGACAAGAAGAAGATCAAGGCTGCTGTCAAGAAGATGTATGACATTCAGGCCAAGAAGGTCAACACCCTGATCAGgttagcatttggtccagtgttattttcttgtgcataatttattatgttgtgcaactgtgagttattcttgattgtgtctgtcctgtccag------------

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G083253_T04 (Zea mays), 5'ss of exon 3
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaattcatatgattatcattttttgttggca
| ||||||||||||||| ||   || ||||| |||||||| |||| |||  | ||||| ||||||||||| ||| | ||||| || || ||||||||||||| |  ||||      |  |  | |      | |      | |||||      | || | ||  |  || | ||   ||  ||||| | | |     |  
TGGTCTTCATTGTTGACCTCAAGGCAGACAAGAAGAAGATCAAGGCTGCCGTCAAGAAGATGTATGACATCCAGGCAAAGAAGGTCAACACCTTGATCAGgttagcacttgccccagtgtaattttt----tcctgcacgatttatta-----tgttgtgcaacta-aagagtt---attcttatcgtgtctgtgcag--

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA18G52310.1 (Glycine max), 5'ss of exon 3
-TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaattcatatgattatcattttttg-ttggca---
 | || || ||||||||| |||||||||||||||||||||| || |||||  ||||||| ||||||||||||||| | |||||||||||||| || ||||||||| |     ||    ||| |  | ||   |    |  |  | |||   | || ||  | |    | | |||  | |  |  |  |    ||| || ||    
CTGGTTTTTATTGTTGACCTCCGTGCTGACAAAAAGAAGATTAAAGATGCTGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaa--atgaaaaatgtatttag--atctgctacatgtaattttgaattgttgataaacaacca-aatgtagagaaagaggaccaattgcttagcttac

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA11G15230.2 (Glycine max), 5'ss of exon 3
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattgaaattattg-gcatttttttttcagttgcaacaattcatatg-attatcattttttgttggca-
| || |||||||| ||| | ||||| ||||| |||||||| ||||||||  ||||||||||||||||||| ||| |||||||||| || ||||||||||||| |  |  | ||||     ||  ||||   ||  || | |||  ||    | |   || |   |    | | || ||  |   ||     ||  |||  || 
TGGTTTTCATTGTCGACCTGCGTGCCGACAAGAAGAAGATCAAGGATGCCGTGAAGAAAATGTATGACATCCAGGCCAAGAAAGTTAACACCTTGATCAGgtgagcaact-atttaatgactattcagt--tttgatagtaatggtttcataatgcattattgctgatgaaatttgatgggtggtagtgaattccgttttcag

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA12G07160.2 (Glycine max), 5'ss of exon 3
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaattcat--atgattatcattttttgttggca---
| || |||||||| ||| | ||||| ||||| |||||||| ||||||||  ||||||||||||||||||| ||| |||| |||||||| ||||||||||||| |  |  |    |  |||  |  |||   ||  || | ||| |||     ||   ||   | ||    ||||  |  ||   ||    |||  ||   ||   
TGGTTTTCATTGTCGACCTGCGTGCCGACAAGAAGAAGATCAAGGATGCGGTGAAGAAAATGTATGACATCCAGGCCAAAAAAGTGAACACCTTGATCAGgtgagcatcta---tgcaatgattgcagt--tttgatagtaatgatttcatattgcattattgctgatgaaatttgttgattggtagtgatttccgtattcactt

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G40780.2 (Glycine max), 5'ss of exon 2
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattg--aaattattggcatttttttttcagttgcaacaattcatatgattatcattttttgttggca
| || |||||||||||| | || || ||||| |||||||| ||||||||| | ||||| |||||||| |||||| |||||||||| || ||||||||||||| | | ||| ||   |       |    | ||   |||   | | |||     | |||| | | |  |||   |     ||      ||||  | |||   
TGGTTTTCATTGTTGACTTGCGGGCCGACAAGAAGAAGATCAAGGATGCAGTCAAGAAGATGTATGATATTCAGGCCAAGAAAGTAAACACCTTGATCAGgtga-gcctttataaagtgatgcttatagaatttgtttgttgattcattattgctattttct-aatgacaatggtatgcttgcagtgaatttgatattgcag

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA15G04670.2 (Glycine max), 5'ss of exon 3
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttg-aatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaattcatatg-attatcattttttgttggca------
| || ||||| || ||| | || |||||||| |||||||| ||||||||| | ||||| |||||||| ||||||||||||||||| || ||||| ||||||| | | ||| || | |  ||  | | || | ||   ||||      ||   |||| ||   | |  |||   |     || | |    ||| ||  ||  |      
TGGTTTTCATAGTCGACTTGCGGGCTGACAAGAAGAAGATCAAGGATGCAGTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtga-gtctttatgtagtgatgcttttag-aatttgtttga------tgattttttattgctaatgacaatggtatgcttgcagtgaattttattactgagacataca

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G10550.1 (Glycine max), 5'ss of exon 2
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaa-agacttcattttgaatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaattcatatgattatcattt-tttgttggca----
| || || ||||||||| | |||||  |||| || ||||| ||||||||  ||||||| ||||||||||||||| | |||||||| ||||| || |||||||||  ||  | |    | || | |  | | | |  ||  | |||  ||  |||| ||    |     |  |||  | |  |  |  | |  || ||| ||     
TGGTTTTTATTGTTGACCTTCGTGCAAACAAGAAAAAGATTAAGGATGCTGTGAAGAAGATGTATGACATTCAGGCAAAGAAAGTCAATACATTAATCAGgtaatggaaatgacaacgcatttac--atctgctacatgtatatt--tg--atttgttgaaaaaaaaaacaaatgtagagaaaaaggactaattggttagcttaca

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT2G39460.1 (Arabidopsis thaliana), 5'ss of exon 2
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctca-gcagttcaattgaaattattggcatttttttttcagttgcaacaattcatatgattatcattttttgttggca
|||| |||||||||||||| ||||||||||| |||||||| ||||||||  | ||||| ||||||||||| ||||||||||||||||| ||  | ||||||||    ||| |    | || ||   | | ||     |||  |  ||||     || | |||| |    | | || | |  ||  |    |||||||    
TTGTTTTCATTGTTGACATTCGTGCTGACAAGAAGAAGATTAAGGATGCTGTTAAGAAGATGTATGACATCCAGACCAAGAAAGTGAACACACTCATCAGgta----ctttaaagagtatttttctatgaagccttgttgtgag-attga----ttatgttcaat----atatttgacactatggtttggttttgttacag

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattgaaatt-attggc-atttttttttcagttgcaacaattcatatgattatcattttttgttggca
| ||||||||||||||||||||||||||||| || ||||| || |||||  | ||||| |||||||||||||||||||||||||| || ||| | || ||||||| |||  |  || | |    |  |   ||   |  | ||  | ||   | | | | ||    ||||                                
TAGTCTTCATTGTTGACATCCGTGCTGACAAGAAAAAGATCAAAGATGCTGTCAAGAAGATGTATGACATTCAGACCAAGAAAGTCAACACCCTCATTAGgtaaacactaaaacttcactgagatatgggtttatgtaaacatggagtgatgagtgtatgtttgtatgcag-------------------------------

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S459_11V6.1 (Physcomitrella patens), 5'ss of exon 1
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatctt----ctcagcagttcaattgaaattattggcattt---ttttttcagttgcaacaattcatatgattatcattttttgttggca
| || ||||| || ||  | || || ||||| |||||||| || || ||  | ||||| ||||| ||||||||||||||||| || ||||| |||||||||| |  |  |  |        ||    ||| |     || |  |   | | || |  |   ||||| || ||||  |   |  | |   |     ||||        
TGGTTTTCATCGTGGATGTGCGCGCCGACAAGAAGAAGATCAAAGAGGCCGTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgttttcccatgctttatttctcggggcaacactctagggtttgggaaactgggtttttgcaattgcgtcgtgttgtgtagctccagattttc-------

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S47_274V6.1 (Physcomitrella patens), 5'ss of exon 1
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaa-gacttcatttt-----gaatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaat-tcatatgattatcattttttgttggca
| || ||||| || ||| | ||||| ||||| |||||||| ||| | ||  ||||||||||||| ||||| ||||||||||| || || || |||||||||| |  | | || | |      | || | ||  | ||| |  ||    || | |   | || | | |  ||| ||  |  ||   ||  | |  ||   |   ||  
TGGTGTTCATCGTGGACGTGCGTGCGGACAAGAAGAAGATCAAGCAGGCTGTGAAGAAAATGTACGACATCCAGACCAAGAAGGTCAACACATTGATCAGgtgattgtcctcctctctgttgggatttccttcgaagtgcc-ttagggttttcgaactgttgtctcc--ttgtaattacgtcgggtgcctgt--ttcagtcccgg--

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S146_96V6.1 (Physcomitrella patens), 5'ss of exon 1
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaattcatatgat-tatcattttttgttggca
| || |||||||||||  | || |||||||| |||||||| ||||| ||  | ||||| ||||||||||| ||||||||||| || || || |||||||||||   | |          | || | |     || | ||   |||  |  |    |||     |     | ||| |  |||| | | |||      |||  
TGGTTTTCATTGTTGATGTGCGGGCTGACAAGAAGAAGATCAAGGAGGCTGTCAAGAAGATGTATGACATCCAGACCAAGAAGGTCAACACATTGATCAGgtactcattatcccccctttgttgttatgtcctccagtgcg-ttagggttaagcgtttcagtctcttcgcgattgaattgatatgttattcccacatgggt

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S46_72V6.1 (Physcomitrella patens), 5'ss of exon 1
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaat--tcatatgattatcattttttgttggca
| ||||||||||| ||| | || |||||||| |||||||| ||||| ||  | ||||||||||| |||||||| |||||||| || || || ||||||||||      |||  |      |   |   |  ||       ||| |  |    ||  ||||  ||| |  |  |  |  | |  ||  |     |||   |  
TGGTCTTCATTGTGGACGTGCGCGCTGACAAGAAGAAGATCAAGGAGGCTGTCAAGAAAATGTACGACATTCAAACCAAGAAGGTCAACACATTGATCAGgtctttgtttctctcctctcccctttttccttttttaatgaatcagggtttgttgattttttgtttcttcggtggtggtctcgtttgcgcaaattgcgtg--

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ09823 (Selaginella moellendorffii), 5'ss of exon 2
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagt--tcaattgaaattattggcatttttttttcagttgca-----acaattc----atatgattatc--attttttgttggca--------------------------------------------------------
| |||||||| || |||||||| || ||||| |||||||| ||| | ||  ||||||  ||||| || || ||||||||||| ||||| ||  |||||||||||    ||| || |   | | ||| |  ||  || | ||    | || |  |   || |||   ||       || |||      |  | || ||  |||  || |||||                                                         
TGGTCTTCATCGTCGACATCCGGGCCGACAAGAAGAAGATCAAGAACGCCGTGAAGATGATGTACGATATCCAGACCAAGAAGGTGAACACGCTGATCAGgtaatc-tttctttctttctttcctcggtggtagtctagtgtgtcttttcgattcacttcttcgtgtgtgggcttaccatttcttggttcgtttgtctgattgatttttggctttccagcttctcattgttttcattcatgggcttaccactttcgtttttttttccag

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: EFJ15194 (Selaginella moellendorffii), 5'ss of exon 2
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagt----tcaattgaaatt---attggcatttttttttcagttgcaacaattcatatgattatcattttttgttggca-------------------------------------------------------------
| |||||||| || |||||||| || ||||| |||||||| ||| | ||  ||||||  ||||| || || ||||||||||| ||||| ||  |||||||||||    ||| || |   | | ||| |  ||    ||  |||   ||   |||  | | ||  | |  |     ||  ||  | || || |  | | |  |||                                                                
TGGTCTTCATCGTCGACATCCGGGCCGACAAGAAGAAGATCAAGAACGCCGTGAAGATGATGTACGATATCCAGACCAAGAAGGTGAACACGCTGATCAGgtaatc-tttctttctttctttcctcggtggtagtctcgtttgtcttttcaattcacttcttcgtgtgtgggcttaccgtttct-tggttcttttgtctgattgattttggctttctagcttctcattgttttcattcatgggcttaccactttcttcttttttccag

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|37187636|gb|CF606989.1|CF606989
EST:     ATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAG                         GCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGC
genomic: ATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagactt ... tttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGC




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCTTCATTGTTGACATCCGTGCTGACAAAAAGAAGATAAAGGATGCAATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagacttcattttgaatcttctcagcagttcaattgaaattattggcatttttttttcagttgcaacaattcatatgattatcattttttgttggca

- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaacaa