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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATGGTTTCGTCTAAAGTTCCCACATTTAACATGTGGAAGTCTTGCCAGTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataatcatattatttttcatgtatgctgattaaaacgatatatcctgtcaatttggagttgaacgttcatgctagcaaacttttattgcctctcagttatgtgttgcttttactcatcttacaggtgtttcttttatgtgctatttgagaagtcctatcaatttagtttttttagtgcag

Basic information

species Vitis vinifera
transcript Vv04s0023g03020.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os10g36760.1 (Oryza sativa), 5'ss of exon 4
TGCATGGTTTCGTCTAAAGTTCCCACATTTAACATGTGGAAGTCTTGCCAGTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataatcatattatttttcatgtatgctgattaaaacgatatatcctgtcaatttggagttgaacgttc-atgctagcaaacttttattgcctctcagttatgtgttgcttttactcatcttacaggtgtttcttttatgtgctatttgagaagtcctatcaatttagtttttttagtgcag
||| |||||  |  | |||||||| || || ||||||||||||||||| ||||| | |||||| ||| || ||||||||| |||||| ||||||   ||||| |  | |     |  ||  || ||  |||    ||| || | |||  | | |     || |  | || |||| |   |     |   ||     |||| |                                                                                     
TGCTTGGTTCAGATTGAAGTTCCCTCACTTGACATGTGGAAGTCTTGCGAGTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAGgtaactacaggtgcag-atccttaat-catg----ttataatgttatcgcattttggcatgcacctaaaagttctacctttctgcatgattcacatctctgaag-----------------------------------------------------------------------------------

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G24290.1 (Glycine max), 5'ss of exon 4
TGCATGGTTTCGTCTAAAGTTCCCACATTTAACATGTGGAAGTCTTGCCAGTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataatcatattatttttcatgtatgctgattaaaacgatatatcctgtcaatttggagttgaacgttc--atgctagcaaacttttattgcctctcagttatgtgttgcttttactcatcttacaggtgtttcttttatgtgctatttgagaagtcctatcaatttagtttttttagtgcag
||||||||| ||||| ||||| || |||||||||||||||||||| || |||||||||||||| |||||| |||| ||||  || |||||||| |  |||||||||||| |  | || | ||||    ||| | || |             |||   ||| | | | || | |   | | |  |||| ||   |    | | | ||   |     ||| | |  ||    || | | | ||| ||||||                                       
TGCATGGTTCCGTCTTAAGTTTCCCCATTTAACATGTGGAAGTCTGGCTAGTTCTGCAGTTGTTCTTGCTGTTTATAACTACACAGAATTTGATCAGCAGgtgaagatagttcttttttctttc---catggtcatca-----------tttgtttctttag-gctaaatgctataaagtttccaaaattccctcctatttaatttccatcaaattttaagttctc----agttttatttttcatgtgcag-------------------------------------

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA16G24270.1 (Glycine max), 5'ss of exon 5
TGCATGGTTTCGTCTAAAGTTCCCACATTTAACATGTGGAAGTCTTGCCAGTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataatcatattatttttcatgtatgctgattaaaacgatatatcctgtcaatttggagttgaacgttcatgctagcaaacttttattgcctctcagttatgtgttgcttttactcatcttacaggtgtttcttttatgtgctatttgagaagtcctatcaatttagtttttttagtgcag
||||||||| ||||| ||||| || |||||||||||||||||||| || |||||||||||||| |||||| |||| ||||| || |||| ||| |  |||||||| ||| | || || | |||||  ||      ||       | | | || |   | | ||    ||  |   |   ||    ||||||||   | ||||| |  | |||  |||| |    | |  | | | ||||| |  |||                                       
TGCATGGTTCCGTCTCAAGTTTCCCCATTTAACATGTGGAAGTCTGGCAAGTTCTGCAGTTGTTCTTGCTGTTTATAACTTCACAGAATATGATCAACAGgtgaacatagttatttt-tgtttcacatacatcttttg------ttttttctat---tctagatgctaaaataagtcaaagttcccttttattcaatttcagtcaaattttgaatttagttgagtga--gttctatctttcacatgcag-------------------------------------

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G18080.1 (Arabidopsis thaliana), 5'ss of exon 4
TGCATGGTTTCGTCTAAAGTTCCCACATTTAACATGTGGAAGTCTTGCCAGTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataatcatattatt-tttcatgtatgctgattaaaacgatatatcctgtcaatttggagttgaacgttcatgctagcaaacttt-----tattgcctctcagttatgtgttgcttttactcatc-ttacaggtgtt-tcttttatgtgctatttgagaagtcctatcaatttagtttttttagtgcag
||| |||||||| || |||||||| ||||| || |||||||| ||||| ||||||||||| || | ||| || ||  | ||  |||||||||| |  |||||  | ||| |  ||  ||  |||  | |||  | || |    |  ||        |||  ||| || |||  || |  | ||||  |||     ||     | | ||| ||| |    ||| | | |   | |||  | |  |||||| | | |  |  ||||||                            
TGCGTGGTTTCGGCTTAAGTTCCCGCATTTGACGTGTGGAAGCCTTGCTAGTTCTGCAGTCGTTCGTGCAATCTATGAATTCTCTGAATTTGATCAGCAGgtatatatattagtagcatagttttctttattgtcatcattctggcatg-------aat--ggaattaaacaatcttctttgcaagatttaaggttaaaaagtataagtaatgagggtttttaagttacggtgacaaatttgatcttttgtatacactacgagaag----------------------------

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G36195.3 (Arabidopsis thaliana), 5'ss of exon 5
TGCATGGTTTCGTCTAAAGTTCCCACATTTAACATGTGGAAGTCTTGCCAGTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataatcatattatttttcatgtatgctgattaaaacgatatatcctgtcaatttggagttgaacgttcatgctagcaaacttttattgcctctcagttatgtgttgcttttactcatcttacaggtgtttcttttatgtgctatttgagaagtcctatcaatttagtttttttagtgcag
||| ||||| || || |||||||| ||||| || |||||||| ||||| |||||||||||||| | |||  | ||| | ||  |||||||||| |  |||||     |    | ||||   || |  |          | | | | | |    |||  | |   ||    | | |    | | || ||||  |||||     ||  ||                                                                              
TGCTTGGTTCCGGCTTAAGTTCCCTCATTTGACCTGTGGAAGCCTTGCTAGTTCTGCAGTTGTTCGTGCAGTCTACGAATTCCCTGAATTTGATCAACAGgtatttgtttcaagattaaactttaaatgaa------gacatggtgtgtttcttcatatagagtttagttgctgacagaatcgaaatttttgtgcctt---attgagtag----------------------------------------------------------------------------

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|161710212|gb|FC058942.1|FC058942
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
EST: gi|71888773|gb|DT037828.1|DT037828
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
EST: gi|161714295|gb|FC063541.1|FC063541
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTG-AGAGTCAGCTGGTGCTGAATGTAA-GCTGTATTA
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTA
EST: gi|110703482|gb|EE080367.1|EE080367
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
EST: gi|71885650|gb|DT034705.1|DT034705
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTAC
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTAC
EST: gi|110710992|gb|EE087681.1|EE087681
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
EST: gi|33402941|gb|CF208568.1|CF208568
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
EST: gi|71882638|gb|DT031693.1|DT031693
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
EST: gi|71886539|gb|DT035594.1|DT035594
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
EST: gi|71887889|gb|DT036944.1|DT036944
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
EST: gi|110367557|gb|EC931495.1|EC931495
EST:     GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAG                         ATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT
genomic: GTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataa ... tttagtgcagATTGGAGAGTCAGCTGGTGCTGAATGTAAAGCTGTATTACAAGAAGTTAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCATGGTTTCGTCTAAAGTTCCCACATTTAACATGTGGAAGTCTTGCCAGTTCTGCAGTTGTCCTTGCTATTTACAACTTTACTGAATTTGACCGTCAGgtgaagataatcatattatttttcatgtatgctgattaaaacgatatatcctgtcaatttggagttgaacgttcatgctagcaaacttttattgcctctcagttatgtgttgcttttactcatcttacaggtgtttcttttatgtgctatttgagaagtcctatcaatttagtttttttagtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG