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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc...

Basic information

species Vitis vinifera
transcript Vv06s0004g04090.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os04g42270.1 (Oryza sativa), 5'ss of exon 3
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc
|||| |||||||||||| ||   ||  ||||||||||||| |||| |||||| || |||||||| || || ||| | ||||||||||| || ||||||||||   |  | |||  |||     ||| ||  | ||||| ||   | | |   || || ||  ||||  |   |     |     || ||           
TGGTCTTCATTGTTGACCTTAAGGCTGACAAGAAGAAGATCAAGGCTGCTGTCAAGAAGATGTACGACATCCAGGCAAAGAAAGTGAACACTCTGATCAGgt--tagcactttccttc-----atacttcattttatcgcttgatttgc--taggtagtg--tagttaactgaccctacttgtcttccag----------

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os01g24690.3 (Oryza sativa), 5'ss of exon 2
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcga-taaagatatcagacttttcaaagttagattc
| || ||||| || ||| |    ||  ||||||||||||| ||||  ||||| || ||||||||||| || ||| | |||||||| || || ||||||||||        | |||   ||  |   ||| ||   ||  |||| ||  |  || |   |   | | | | |     ||||    || |  ||   ||    
TTGTCTTCATCGTCGACCTCAAGGCAGACAAGAAGAAGATCAAGGCAGCTGTCAAGAAGATGTATGACATCCAGGCAAAGAAAGTTAACACTCTGATCAGgt--------tattaactcaccttcctttgtt--catggctgaatacgcttcattctgtatgttgacaacttggtgtatcgattttctgtaatacag----

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G124411_T04 (Zea mays), 5'ss of exon 3
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgt-atcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc
| || |||||||| ||| |    ||  ||||||||||||| |||| |||||| || ||||||||||| |||||| ||||||| || || ||||||||||||| | || |   |  | |   ||| | || |  || ||   | | | |   |||  | |  | || ||  | |   | || | | | || |          
TTGTCTTCATTGTCGACCTCAAGGCAGACAAGAAGAAGATCAAGGCTGCTGTCAAGAAGATGTATGACATTCAGGCCAAGAAGGTCAACACCCTGATCAGgttagcatttggtccagtgttattttcttgtgcataatttatta-tgttgtgcaactgtgagttattct-tgattgtgtctgtcctgtccag---------

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G40780.2 (Glycine max), 5'ss of exon 2
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc---
||||||||||||||||| | || ||| ||||||||||||| |||||||| || || |||||||||||||||||| |||||||||| || ||| |||||||||   |   ||| ||     ||  |  |     || |   |   |  |     | ||||   || | || || | |||        | ||  | | |||    
TGGTTTTCATTGTTGACTTGCGGGCCGACAAGAAGAAGATCAAGGATGCAGTCAAGAAGATGTATGATATTCAGGCCAAGAAAGTAAACACCTTGATCAGgtg--agcctttataaagtgatgcttatagaatttgtttgttgattcattattgctattttctaat-gacaatggtatgcttgcagtgaatttgatattgcag

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G10550.1 (Glycine max), 5'ss of exon 2
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattccaattatattttttat---tatccctgagt-atacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc
||||||| ||||||||| ||||||| |||||||| ||||| ||||||||||| || ||||||||||| |||||| | |||||||| |||||  | ||||||||     | |   |   || ||| || |  ||    |||   ||| |  |  |  |   |    |  || || ||| |   |  | |  | |   ||| |   
TGGTTTTTATTGTTGACCTTCGTGCAAACAAGAAAAAGATTAAGGATGCTGTGAAGAAGATGTATGACATTCAGGCAAAGAAAGTCAATACATTAATCAGgtaatggaaatgacaacgcatttacatctgctacatgtatatttgatttgttgaaaaaaaaaacaaatgtagagaaaaaggactaattggttagc-ttaca---

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA15G04670.2 (Glycine max), 5'ss of exon 3
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcgataaagatatcagacttt-tcaaagttagattc-
|||||||||| || ||| | || ||  ||||||||||||| |||||||| || || ||||||||||||||||||||||||||||| || ||| | |||||||   | | ||| | |    ||  | ||     || |       | |      | || ||   |    ||      |    | ||| | |  |  | || | 
TGGTTTTCATAGTCGACTTGCGGGCTGACAAGAAGAAGATCAAGGATGCAGTCAAGAAGATGTATGATATTCAGACCAAGAAAGTAAACACCTTAATCAGgtg--agtctttatgtagtgatgcttttagaatttgtttgatgattttttattgctaatgacaatggtatgcttgcagtgaattttattactgagacataca

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G15230.2 (Glycine max), 5'ss of exon 3
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgt-atcaatatttttat-----tccaattatattttttattatccctgagtatacagcagttattggatagtcgataaa-gatatcagacttttcaaagttagattc
||||||||||||| ||| | |||||| ||||||||||||| |||||||| || || || |||||||| || ||| |||||||||| || ||| ||||||||| | |||   ||| ||     | || || |  |  | ||  |  |  | |  |     | |  || | | | |||    | ||    |  || |    | ||    
TGGTTTTCATTGTCGACCTGCGTGCCGACAAGAAGAAGATCAAGGATGCCGTGAAGAAAATGTATGACATCCAGGCCAAGAAAGTTAACACCTTGATCAGgtgagcaactatttaatgactattcagttttgatagtaatggtttcataatgcattattgctgatgaa-atttgatgggtggtagtgaa--ttccgttttcag----

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA12G07160.2 (Glycine max), 5'ss of exon 3
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgt----atcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc
||||||||||||| ||| | |||||| ||||||||||||| |||||||| || || || |||||||| || ||| |||| |||||||| ||| |||||||||    ||| ||    | ||| || || |  |  | || ||  |  | |  |     | |  || | | | | | |   |   ||   ||||    ||   || 
TGGTTTTCATTGTCGACCTGCGTGCCGACAAGAAGAAGATCAAGGATGCGGTGAAGAAAATGTATGACATCCAGGCCAAAAAAGTGAACACCTTGATCAGgtgagcatctatgcaatgattgcagttttgatagtaatgatttcatattgcattattgctgatgaa-atttgttgat--tggtagtgatttccgtattcactt-

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G52310.1 (Glycine max), 5'ss of exon 3
-TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgta-tcaatatttttattccaattatattttttat---tatccctgagtatacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc
 ||||||| ||||||||| | |||||  |||| |||||||| || |||||||| || ||||||||||| |||||| | ||||||||||||||  | |||||||| |  | ||    | |  | ||| || |  ||    ||    ||| |       |   |    |  || || |||||   |  | |  | |   |||     
CTGGTTTTTATTGTTGACCTCCGTGCTGACAAAAAGAAGATTAAAGATGCTGTGAAGAAGATGTATGACATTCAGGCGAAGAAAGTGAATACTTTAATCAggtaatggaaatgaaaaatgtatttagatctgctacatgtaattttgaattgttgataaacaaccaaatgtagagaaagaggaccaattgcttagc-ttac----

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G39460.1 (Arabidopsis thaliana), 5'ss of exon 2
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgta--tcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc
| |||||||||||||||||||||||  ||||||||||||| |||||||||||||| ||||||||||| || ||||||||||||||||| || || ||||||||  | ||    | | || | || |    || |  |     ||| |||     |  |||| || | |     | | | |  |  || | | ||        
TTGTTTTCATTGTTGACATTCGTGCTGACAAGAAGAAGATTAAGGATGCTGTTAAGAAGATGTATGACATCCAGACCAAGAAAGTGAACACACTCATCAGgtactttaaagagtatttttctatgaagccttgttgtgagattgattatgttcaatatatttgacact-----atggt-ttggttttgttacag--------

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G55280.1 (Arabidopsis thaliana), 5'ss of exon 3
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcg-ataaagatatcagacttttcaaagttagattc
| || |||||||||||||| |||||  ||||||| ||||| || |||||||| || ||||||||||| ||||||||||||||||| || ||||| || |||||  || | |   | | || | | || |    ||||   | |  ||  ||   | | || ||  | | ||  ||                          
TAGTCTTCATTGTTGACATCCGTGCTGACAAGAAAAAGATCAAAGATGCTGTCAAGAAGATGTATGACATTCAGACCAAGAAAGTCAACACCCTCATTAGgta--aacactaaaacttcactgagatatgggtttatg--taaacatggagtgatgagtgtatgtttgtatgcag--------------------------

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S459_11V6.1 (Physcomitrella patens), 5'ss of exon 1
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattccaattatattttttattatccctg-agtatacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc--
|||||||||| || ||  | || ||| ||||||||||||| || || || || || |||||||| || |||||||||||||| || |||||  |||||||||    || ||||        |||| | |      | | ||  ||  |   | |   | ||| |  | |  ||     ||    | |  |     |||||   
TGGTTTTCATCGTGGATGTGCGCGCCGACAAGAAGAAGATCAAAGAGGCCGTCAAGAAGATGTACGACATTCAGACCAAGAAGGTCAATACTTTGATCAGgtgattatgttttcccatgctttatttctcggggcaacactctagggtttgggaa--actgggtttttg-caattgcgtcgtgttgtgtagctccagattttc

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: PP1S146_96V6.1 (Physcomitrella patens), 5'ss of exon 1
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgta-tcaatatttttattccaattatattttttattatccctgagtatacagcagtt-attggatagtcgataaagatatcagacttttcaaagttagattc
||||||||||||||||  | || ||  ||||||||||||| ||||| ||||| || ||||||||||| || ||||||||||| || || ||  |||||||||| ||| |||      |    |  ||| |  |    | | | ||  |  |||  || | |   |   ||||  |  |   |   | |||  |  | | |  
TGGTTTTCATTGTTGATGTGCGGGCTGACAAGAAGAAGATCAAGGAGGCTGTCAAGAAGATGTATGACATCCAGACCAAGAAGGTCAACACATTGATCAGgtactcattatcccccctttgttgttatgtcctccagtgcgttagggttaagcgtttcagtctcttcgcgattgaattgatatgttattcccacatgggt--

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ09823 (Selaginella moellendorffii), 5'ss of exon 2
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattc----------------caattatatttttta---ttatccctgagtatacag------cagttattggatagtcgat---aaagatatcagacttttcaaagttagattc----------------------------------------
|||| ||||| || ||||| || ||| ||||||||||||| ||| | || || || | |||||| ||||| ||||||||||| ||||| || |||||||||||    |  |||  |||                | | | | | ||||    | |   ||  || |   |      || || |||| | ||   |   |  ||| |  | |||| ||   |   |||                                         
TGGTCTTCATCGTCGACATCCGGGCCGACAAGAAGAAGATCAAGAACGCCGTGAAGATGATGTACGATATCCAGACCAAGAAGGTGAACACGCTGATCAGgtaatctttctttctttctttcctcggtggtagtctagtgtgtcttttcgattcacttcttcgtgtgtgggcttaccatttcttggttcgtttgtctgattgatttttggctttccagcttctcattgttttcattcatgggcttaccactttcgtttttttttccag

upper sequence: Vv06s0004g04090.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ15194 (Selaginella moellendorffii), 5'ss of exon 2
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattc------caattatattttttattatccctgagtatacagcagttattggatagtcgataaagatatcagacttttcaaa-gttagattc------------------------------------------------------------
|||| ||||| || ||||| || ||| ||||||||||||| ||| | || || || | |||||| ||||| ||||||||||| ||||| || |||||||||||    |  |||  |||      |  |  || | |   || ||  |    || ||    ||  ||  | | |        | |  |   |||     | | ||||                                                             
TGGTCTTCATCGTCGACATCCGGGCCGACAAGAAGAAGATCAAGAACGCCGTGAAGATGATGTACGATATCCAGACCAAGAAGGTGAACACGCTGATCAGgtaatctttctttctttctttcctcggtggtagtctcgtttgtcttttca-attcacttcttcgtgtgtgggcttaccgtttcttggttcttttgtctgattgattttggctttctagcttctcattgttttcattcatgggcttaccactttcttcttttttccag

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|110693591|gb|EE069954.1|EE069954
EST:     GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAG                         GCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
genomic: GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatat ... tgtgatccagGCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
EST: gi|30302847|gb|CB979641.1|CB979641
EST:     GTTAAAAAGATGTATGATATTCACACCAATAAAGTGAATACCCTGATCAG                         GCCTGATGGTACCTAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
genomic: GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatat ... tgtgatccagGCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
EST: gi|110723721|gb|EE101359.1|EE101359
EST:     GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAG                         GCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
genomic: GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatat ... tgtgatccagGCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
EST: gi|110383279|gb|EC947641.1|EC947641
EST:     GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAG                         GCCTGATGGTACCAAGAAGGCATATGTTAGGTTGACCCCAGACTATGATGC
genomic: GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatat ... tgtgatccagGCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
EST: gi|110689147|gb|EE065119.1|EE065119
EST:     GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAG                         GCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
genomic: GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatat ... tgtgatccagGCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
EST: gi|110708203|gb|EE085476.1|EE085476
EST:     GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAG                         GCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
genomic: GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatat ... tgtgatccagGCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
EST: gi|110377848|gb|EC942944.1|EC942944
EST:     GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAG                         GCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC
genomic: GTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatat ... tgtgatccagGCCTGATGGTACCAAGAAGGCGTATGTTAGGTTGACCCCAGACTATGATGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTTCATTGTTGACATTCGTGCCAACAAGAAGAAGATAAAGGATGCTGTTAAAAAGATGTATGATATTCAGACCAAGAAAGTGAATACCCTGATCAGgtatcaatatttttattccaattatattttttattatccctgagtatacagcagttattggatagtcgataaagatatcagacttttcaaagttagattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaag