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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag

Basic information

species Vitis vinifera
transcript Vv09s0002g04680.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g08560.2 (Oryza sativa), 5'ss of exon 6
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag
 ||||| |||| |||||||||| | || ||  | || |||||||| |||||||| |||||||||||||||||| | ||||||||||||||| ||||||||||  |    || || | | |   |    |   | | || | || || |    ||   |||||||     | ||| |  | ||| |      
GGAAAAAGAGTATGAAATGGCTCTTCAGGACAGGGTGATGGAAGAGACAAAAGATAAGAAGAATGCCGTGGAGTCTTATGTTTATGACATGCGAAACAAGgtttga---tcgattccactcttt----cctgacttcatctttagttagaggcagaaactgata-----atatgttatttttcag------

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os05g08840.1 (Oryza sativa), 5'ss of exon 5
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag
 || || |||| |||||||||| | || ||  |||| ||||||||||| || || || |||||||| || ||||| ||||||||||||||| | ||||||||| |        |   |||   |  ||    ||   | |||||| |  |   ||||  |||  |     | |  | |             
TGAGAATGAGTATGAAATGGCTCTTCAGGACAGAGTAATGGAAGAAACCAAGGAGAAAAAGAATGCTGTCGAGGCTTATGTTTATGACATGCGTAACAAGgtatgc---cgagtttaatt--ttgtgatgatatatgaacatttgaa--cagtacctgatgagtttcttgcgt--tcag------------

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G023232_T01 (Zea mays), 5'ss of exon 6
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag
||| || |||| ||| |||||| | |||||  |||| |||||||||||||| || ||||||||||| || || || ||||| ||||||||| | |||||||||  |   |   ||       ||||    |  |||     ||   | |||     |  |    ||||   |                   
AGAGAAAGAGTATGAGATGGCTCTTCAAGACAGAGTAATGGAAGAAACAAAGGAGAAGAAGAATGCTGTTGAAGCTTATGTGTATGACATGCGTAACAAGgtatat---tgagtcacgcatactaatgttgtcttatgaagttgtgagcctgattttgttctcttctatttag------------------

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G063676_T01 (Zea mays), 5'ss of exon 6
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag
||| || |||| ||| |||||| | || ||  |||| ||||||||||| ||||| ||||| ||||| ||||| || ||||| ||||||||| | ||||||||| |||    |         ||   ||  |  || |      | ||| |   | ||| ||   | |     | ||| | ||  |      
AGAGAAAGAGTATGAGATGGCTCTTCAGGACAGAGTAATGGAAGAAACCAAAGAGAAGAAAAATGCTGTGGAAGCTTATGTCTATGACATGCGTAACAAGgtatgtggagatgcat-----gccttgatggttttccttgtgatataaacagtatctaatgtcctttt----ttattgtatttag------

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G22100.1 (Glycine max), 5'ss of exon 5
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtt---tctatcctattggctaagacagaatt--acagcatttgtaac--cttcacctactgatatctacacatgattatcttctgcc---ccag
||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||||||||||||  |||||   | | || | ||  || |  |||  |   ||| ||  |  ||   | |  | ||    | |  |    |  || ||   |  |    |||
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAATGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggtgttatctttttcttcttctcttactcagggtctaacatcaactacaaatgcctgtcatataattgttgatttttttttttccgttatcatttcag

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA07G00820.1 (Glycine max), 5'ss of exon 5
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtt-tctatcctattggctaagacagaatt--acagcatttgtaaccttcacctac-tgatatctacacatgattatcttctgccccag------
||| ||||||||||||||||||||||||||||| || ||||||||||||||||||||||| || || || ||||| ||||||||||||||||||||||||||  | | | ||| || | ||  || |  |||  |   ||| ||  |  ||    |    |  | |||  |    ||  || | | |||            
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATCGTGTGATGGAAGAAACAAAAGACAAGAAAAACGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgggcgctatctttcttgttctcttacccagggtctaacatcacatacaaatgcctgtcatataataattgttgattttt-tttcctgttatcatttcag

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA13G43630.2 (Glycine max), 5'ss of exon 6
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctat------cctattggctaagacagaattacagcatttgtaaccttcacct--actgatatctacacatgattatcttctgccccag
||| ||||||||||||||||||||||||||| |||||||||| ||||| ||||| ||||| ||||| || ||||| |||||||||||||||||||||||||| ||  || | ||      | | ||   | ||    ||||     |||| |||   | ||    ||| || |||  | || ||| |            
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATAGAGTCATGGAGGAAACGAAAGATAAGAAAAATGCAGTTGAGGCTTATGTTTATGACATGAGAAACAAGgtgaggattgccatggttttcttgttatttgaggtc-aatttttttatttttaattattactaaaactaatttcttgatatcattttag----------

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA15G01750.1 (Glycine max), 5'ss of exon 6
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag
||| ||||||||||||||||||||||||||| |||| ||||| |||||||| || ||||| ||||| || ||||| ||||||||||||| |||||||||||| ||  || | ||  | ||   |   |   ||  |     ||||||   ||   |||    ||  | | ||| || || ||| |      
AGAGAAGGAGTTTGAAATGGCTTTGCAAGATAGAGTGATGGAGGAAACAAAGGATAAGAAAAATGCAGTAGAGGCTTATGTTTATGACACGAGAAACAAGgtgaggattgccatggttttc-ttgttatttaaggatgaattttgtattatta--ctaaaactaatttctcattatcat-ttcag------

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G79920.2 (Arabidopsis thaliana), 5'ss of exon 6
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtg-tttctatcctattggctaagacagaattacagcatttgtaac-cttcacctactga-tatctacacatgattatcttctgccccag
 || ||||| ||||| |||||| |||||||  |||| |||||||| || || |||  ||||||||| || ||| | ||||||||||| ||| ||||||| || ||   | | |||    |    | |    | | ||  |||| |||||   ||    || ||| ||   ||   |  || | ||| |      
GGAGAAGGAATTTGAGATGGCTCTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGAAACAAAgtgagaaatctttatttcgtcttttcat-tggcagtat-gcatatgtaaagttttgagtattgagtactgacgtgtc-ttgttttcag------

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G79930.1 (Arabidopsis thaliana), 5'ss of exon 6
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaacctt-cacctactgatatctacacatga-ttatcttctgccccag
 || ||||| ||||| ||||||||||||||  |||| |||||||| || || |||  ||||||||| || ||| | ||||||||||| ||| | ||||| || ||  | | |||    |    | |    | | ||  |||| |||||  ||     || ||    ||| || ||  || | ||| |      
GGAGAAGGAATTTGAGATGGCTTTGCAAGACAGAGTTATGGAAGAGACCAAGGACCGGAAGAATGCTGTTGAGTCTTATGTTTATGATATGCGGAACAAAgtgagaatctttatttcgtcttttcat-tggcagtat-gcatatgtaaagttgtgagtattgggtacta-acgtgtcttgttttcag------

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ12319 (Selaginella moellendorffii), 5'ss of exon 5
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttc-tatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag
 || |||||||  ||    ||  | || ||| |||||||||||||||| |||||||  |||||||| ||||| || || || ||||||||| | ||||||||  |  | || |||    || |         ||||  |     ||   | |      |                                 
GGAGAAGGAGTACGAGTATGCCCTTCAGGATAGAGTCATGGAAGAAACCAAAGACAGAAAGAATGCAGTGGAAGCCTACGTCTATGACATGCGGAACAAGgtttgcatctcgtatgtggtttgt--------aattttaatggctgctgcttcttttcag--------------------------------

upper sequence: Vv09s0002g04680.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ19903 (Selaginella moellendorffii), 5'ss of exon 5
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag
 || |||||||  ||    ||  | || ||| |||| ||||||||||| |||||||  |||||||| ||||| || || || ||||||||| | ||||||||     ||   |||   |  | | |     ||||  |     ||   | |      |                                 
GGAGAAGGAGTACGAGTATGCCCTTCAGGATAGAGTTATGGAAGAAACCAAAGACAGAAAGAATGCAGTGGAAGCCTACGTCTATGACATGCGGAACAAGgt-----ttgtcatctcgtatg-tgatttgtaattttaatggctgctgcttcttttcag--------------------------------

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|351035450|gb|FQ463295.1|FQ463295
EST:     AAGACAAGAAGAATGCCCTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAA
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAA
EST: gi|349825219|gb|FQ417940.1|FQ417940
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCANGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|71856570|gb|DT005625.1|DT005625
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|351056576|gb|FQ442404.1|FQ442404
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCA
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCA
EST: gi|71857129|gb|DT006184.1|DT006184
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|32245466|gb|CD711285.1|CD711285
EST:     GTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: GTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|349830554|gb|FQ416852.1|FQ416852
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAAGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|351022620|gb|FQ447142.1|FQ447142
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGA
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGA
EST: gi|351045993|gb|FQ441376.1|FQ441376
EST:     A-GACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGATTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|110721835|gb|EE097540.1|EE097540
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|351031000|gb|FQ439036.1|FQ439036
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|110364620|gb|EC928007.1|EC928007
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|110699605|gb|EE076751.1|EE076751
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|351026310|gb|FQ428322.1|FQ428322
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCANGACTTTGTCACTTCATCAGAG
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAG
EST: gi|351044463|gb|FQ442994.1|FQ442994
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATG
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATG
EST: gi|351016635|gb|FQ424062.1|FQ424062
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
EST: gi|71856214|gb|DT005269.1|DT005269
EST:     AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAG                         CTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT
genomic: AAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgttt ... tctgccccagCTTCATGACAAGTATCAGGACTTTGTCACTTCATCAGAGAGGGATGAGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAAGGAGTTTGAAATGGCTTTGCAAGATCGAGTCATGGAAGAAACAAAAGACAAGAAGAATGCCGTGGAGGCATATGTTTATGACATGAGAAACAAGgtaagtgtttctatcctattggctaagacagaattacagcatttgtaaccttcacctactgatatctacacatgattatcttctgccccag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG