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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAATTATTCTGGGCAGTTCAAGAATTTGGATAAGCTCGTGAAGACTCTGGATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaacttagttggtactggatcttgctcttgcaacttctttatactagggaaactaggaacatacttgggaagcactttatacatgatatggtgtg...

Basic information

species Vitis vinifera
transcript Vv08s0007g01340.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01340.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA15G17840.1 (Glycine max), 5'ss of exon 3
CCAATTATTCTGGGCAGTTCAAGAATTTGGATAAGCTCGTGAAGACTCTGGATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATA--AACCCACCAGgtaataaacttagttggtact---ggatcttgctcttgcaacttctttatactagggaaactaggaacata---cttgggaagcactttatacatgatatggtgtg----
         ||  |||||||||||||||||||||||| |||||||   | |||  ||| |||||||| |||||  |||||||  || |    | | || || |||  |     | ||||   |   | |  |||   |||   | | ||| || |  |  ||   ||||   |   |||    | | ||||     ||| ||| |       
---------CTCAGCAGTTCAAGAATTTGGATAAGCTTGTGAAGAGAATAGATGGGGATATTTTGTCCAAATTAGATGGTTCTGCTAAAGCCAGCTCATCAAGTAGAAGgtgaatttgggttttgggaactttgtgtttgtgccctttttttaat--gttaatcgggaatgcaaatcttatataactctttgacagtga-atgcttcaagtt

upper sequence: Vv08s0007g01340.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G06650.1 (Glycine max), 5'ss of exon 3
CCAATTATTCTGGGCAGTTCAAGAATTTGGATAAGCTCGTGAAGACTCTGGATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATA--AACCCACCAGgtaataaacttagttggtact---ggatcttgctcttgcaacttctttatactagggaaactaggaacata---cttgggaagcactttatacatgatatggtgtg----
         ||  |||||||||||||||||||||||| |||||||   | |||  ||| || ||||| |||||  |||||||  || |    | | || || |||  |     | ||||   |   | |  |||    ||   | | ||| || ||    |||| | ||   |   |||    | | ||||     ||| ||| |       
---------CTCAGCAGTTCAAGAATTTGGATAAGCTTGTGAAGAAAATAGATGGGGATATCTTGTCTAAATTAGATGGTTCTGCTAAAGCCAGCTCATCAAGTAGAAGgtgaatttggatttcgggaactttgtgtctgtgtcctttttttaatatt--aactggaaatgcaaatcttatataactctttgacagtga-atgcttcaagtt
















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|349824491|gb|FQ413158.1|FQ413158
EST:     GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGGACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|110372149|gb|EC936298.1|EC936298
EST:     GATAAGGAGATTTTGTCGAAATTGGATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|110718881|gb|EE096218.1|EE096218
EST:     GATAAGGAGATTTTGTCGAAATTGGATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|110723305|gb|EE100463.1|EE100463
EST:     GATAAAGAGATTTTGTCGAAATTGGATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACTAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|110356854|gb|EC919981.1|EC919981
EST:     GATAAGGAGATTTTGTCGAAATTGGATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|351023717|gb|FQ448268.1|FQ448268
EST:     GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|110688830|gb|EE067830.1|EE067830
EST:     GATAAGGAGATTTTGTCGAAATTGGATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|352785766|gb|FQ475769.1|FQ475769
EST:     GATAAGGAGATTTTGTCGAAATTGGATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|110718248|gb|EE094865.1|EE094865
EST:     GATAAGGAGATTTTGTCGAAATTGGATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|110731453|gb|EE105880.1|EE105880
EST:     GATAAGGAGATTTTGTCGAAATTGGATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|37187578|gb|CF606931.1|CF606931
EST:     GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|351025561|gb|FQ437049.1|FQ437049
EST:     GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
EST: gi|349830477|gb|FQ416775.1|FQ416775
EST:     GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAG                         TTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG
genomic: GATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaact ... gtgtttgcagTTCAGAAACAAGACCAGGACAGAGACAGAACCTAAACGAGCCTGGCATGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAATTATTCTGGGCAGTTCAAGAATTTGGATAAGCTCGTGAAGACTCTGGATAAGGAGATTTTGTCGAAATTGAATGGTTCATCTGATAAACCCACCAGgtaataaacttagttggtactggatcttgctcttgcaacttctttatactagggaaactaggaacatacttgggaagcactttatacatgatatggtgtg

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aggaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggaagc