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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagtttacaagggcttgtgcatgttcattatgcattttttctgtttcaattcttgcttgttcttctctgcttaccattatatattcatacataacgttagatttcttggttgtgccccatcttgactgagttgcaaattacatgttctctaaccag

Basic information

species Vitis vinifera
transcript Vv08s0007g00530.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA18G39930.1 (Glycine max), 5'ss of exon 6
AGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagtttacaagggcttgtgcatgttcattatgcattttttctgtttcaattcttgcttgttcttctctgcttaccattatatattcatacataacgttagatttcttggttgtgccccatcttgactgagttgcaaattacatgttctctaaccag
 || ||  | |||||| ||||||| || |||||||||||||||||  |||| ||||| || ||||| |||||   ||||||||||||||| ||||||||||||     ||   |    |  |  ||       ||| |  |          ||  | | |  |  | | ||  |  || |  | | | ||  ||||    || |    |  ||||  |                                          
TGGAGGTCTTCGGGAACTACTTGTAGGGAAGGATGATGAGCTTCTCCAGACTGAAACCAGAACCATAACTAGATCTGATGTTGCAGAAGTCTGCATTCAGgtatcttatttttattattgataaataactcagatggacat----------aacacctccccgcacgtttc--cccacta--aaaaaatccaacattgttttgg----cccggtttag------------------------------------------

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA07G15960.1 (Glycine max), 5'ss of exon 6
AGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagtttacaagggcttgtgcatgttcattatgcattttttctgtttcaattcttgcttgttcttctctgcttaccattatatattcatacataacgttagatttcttggttgtgccccatcttgactgagttgcaaattacatgttctctaaccag
 || ||  | |||||| ||||||| || |||||||||||||||||  |||| ||||| || ||||| | |||   ||||||||||||||| ||||||||||||     ||   |  | |  |  |   |   |   |||     ||    || || ||    | || | | ||  ||  || | | |   | | |  |   || |                                                       
TGGAGGTCTTCGGGAACTACTTGTAGGGAAGGATGATGAGCTTCTCCAGACTGAAACCAGAACCATAAGTAGATCTGATGTTGCAGAAGTCTGCATTCAGgtatcttatttttattgttaataaac--ttgatggacataacacctcccccatttttta---ggtcatgtttggatattataagagaagaaaataagaaagtaaa-------------------------------------------------------

upper sequence: Vv08s0007g00530.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT2G37660.1 (Arabidopsis thaliana), 5'ss of exon 6
AGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagtttacaagggcttgtgcatgttcattatgcattttttctgtttcaattcttgcttgttcttctctgcttaccat-tatatattcatacataacgttagatttcttggttgtgccccatcttgactgagttgcaaattacatgttctctaaccag
 |||||||| || ||||||||||| || || ||||| ||||| ||| ||||||||||||| || ||  | ||   ||||||||||||||| ||  |||||||    ||| |  | | |         ||| | |      |  ||  |  |||   || |    |||| |   |      |   | |  | || |||   |||   | | |  |  |                                            
CGGTGGCATTCGAGAATTACTTGTGGGAAAAGATGACGAGCTACTTGAGACAGAAACAAGAACAATCGCAAGAGCTGATGTTGCAGAAGTCTGTGTTCAGgtgtgtgttcattatgaccaaaagggcttcgtaaactgcataatccat--caacagttaccatatcttttaaaccagttttgcttctcctaatccatggtgtttattatttgagcag--------------------------------------------

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|349810529|gb|FQ402772.1|FQ402772
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAT                         GCACTCCAGTTTGAGGAAAGCCAA-TTCA
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAA-GCCAAATTCA
EST: gi|28959045|gb|CB339524.1|CB339524
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|351016336|gb|FQ446196.1|FQ446196
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|349821239|gb|FQ404371.1|FQ404371
EST:     CAGAAACAAGAACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACACCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|28959215|gb|CB339608.1|CB339608
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|22008555|gb|BQ793589.1|BQ793589
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|110700744|gb|EE077667.1|EE077667
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAA-TTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|110385557|gb|EC950093.1|EC950093
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|110731770|gb|EE106470.1|EE106470
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|45771772|gb|CN007624.1|CN007624
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|351023663|gb|FQ448214.1|FQ448214
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|352790186|gb|FQ481385.1|FQ481385
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|110419625|gb|EC985868.1|EC985868
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|351051751|gb|FQ449565.1|FQ449565
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAC                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|351054211|gb|FQ450293.1|FQ450293
EST:     CAGAAACAAGGACCATTACCAGGAATGATGTTGCAGAGGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
EST: gi|351028714|gb|FQ433144.1|FQ433144
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCATTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGG
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGG
EST: gi|351055225|gb|FQ440564.1|FQ440564
EST:     CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAG                         GCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT
genomic: CAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagttt ... ctctaaccagGCACTCCAGTTTGAGGAAGCCAAATTCAAGGCATTTGATCTGGCCTCAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTGGCATCCGGGAATTACTTGTTGGCAAGGATGATGAGCTTCTTAAGACAGAAACAAGGACCATTACTAGGAATGATGTTGCAGAAGTTTGCATTCAGgtaatagtttacaagggcttgtgcatgttcattatgcattttttctgtttcaattcttgcttgttcttctctgcttaccattatatattcatacataacgttagatttcttggttgtgccccatcttgactgagttgcaaattacatgttctctaaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT