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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacattatgcctctatttcggtttgctttccgaaatactcatttttagcacttacccgcctttcattagctctctgacaattatatgcaatatccatatatctatgcttgataagcag

Basic information

species Vitis vinifera
transcript Vv07s0031g02130.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G21430.1 (Glycine max), 5'ss of exon 3
GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacattatgcctctatttcggtttgctttccgaaatactcatttttagcacttacccgcctttcattagctctctgacaattatatgcaatatccatatatctatgcttgataagcag
||||||||||| ||||||||||||||||||||||| || || |||||||| || | |||||  ||  || |   |    |  |    || |  | | | | |    |   | |                                                          
GATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAGgt-agaaaattatctctgcatattattcaaatagctattatgcaaaatctaatcttgcatgtggcag--------------------------------------------------------

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G33020.1 (Glycine max), 5'ss of exon 3
GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacattatgcctctatttcggtttgctttccgaaatactcatttttagcactta--cccgcctttcattagctctctgacaattatatgcaatatccatatatctatgcttgataagcag
||||||||||| ||||||||||||||||||||||| || || |||||||| || | ||| |  ||||      |  |  | | | ||   ||  | |  |  |  ||  |  || | |                                                       
GATCACCTTGCCCTGATGATGGAACTCCTTGGAAAGATGCCCCGGAAGgt-agaaaattctctctct------gcatattattcaaatagctattatgcaaaatctaatcttgcatgttgcag--------------------------------------------------

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA01G36260.1 (Glycine max), 5'ss of exon 3
GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtga--gcacattatgcctctatttcggtttgctttccgaaatactcatttttagcacttacccgcctttcattagctctctgacaattatatgcaatatccatatatctatgcttgataagcag
||||||||||| || |||||||||||||||||||| || || ||||||||||  | ||| |    || ||| |   | |  ||||   || |   |||| ||     || |    | | |||       || || ||  |                                 
GATCACCTTGCCCTAATGATGGAACTCCTTGGAAAGATGCCCCGGAAGgtgagagtacactcccactgtatgtttatattatttcttgaagagctatttctatt--ctagcgatatctaatt-----cttgtcagttgcag--------------------------------

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G09180.1 (Glycine max), 5'ss of exon 3
GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtga--gcacattatgcctctatttcggtttgctttccgaaatactcatttttagcacttacccgcctttcattagctctctgacaattatatgcaatatccatatatctatgcttgataagcag
||||||||||| || |||||||||||||||||||| || || ||||||||||  | ||| |    || |||     | |  ||||   || |   |||  ||     ||  |   | | |||       || |  ||  |                                 
GATCACCTTGCCCTAATGATGGAACTCCTTGGAAAGATGCCGCGGAAGgtgagagtacactcccactgtatgcttatattatttcttgaagatctattcctatt--ctagacatatctaatt-----cttgtcggttgcag--------------------------------

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G35500.1 (Arabidopsis thaliana), 5'ss of exon 3
GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacattatgcctctatttcggtttgctttccgaa---atactcatttttagcacttacccgcctttcattagctctctgacaattatatgcaatatccatatatctatgcttgataagcag
|||||||||||||| |||||||||||||| ||||| || ||||| |||||  |    || |    || |  |  | || ||||       ||| ||   |||   |  | |  |  ||| |  ||                                                 
GATCACCTTGCTCTTATGATGGAACTCCTAGGAAAGATGCCTCGAAAGgtatgtgtttttttttgctttcccactgtgttttcttggtttatagtctgctttttgatatgcttg--tttgagcag-------------------------------------------------

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G17530.1 (Arabidopsis thaliana), 5'ss of exon 3
GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacattatgcctctatttcggtttgctttccgaaatactcatttttagcacttacccgcctttcattagctctctgacaattatatgcaatatccatatatctatgcttgataagcag
|| ||||||||||| |||||||||||| | |||||||| ||||| |||||   |  |  |   ||   |||| || |   |   ||  |  ||  || |||    |    |    |  | |  |  ||                                           
GACCACCTTGCTCTTATGATGGAACTCTTAGGAAAAATGCCTCGAAAGgtacccggaaaaatacttggtttctgtctatctcttgat-tgatcggttatagt--ctcgttgatacttgtgatttaactag-----------------------------------------

upper sequence: Vv07s0031g02130.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G17530.2 (Arabidopsis thaliana), 5'ss of exon 3
GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacattatgcctctatttcggtttgctttccgaaatactcatttttagcacttacccgcctttcatt-agctctctgacaattatatgcaatatccatatatctatgcttgataagcag
|| ||||||||||| |||||||||||| | |||||||| ||||| |||||   |  |  |   ||   |||| || |   |   ||   |    || |   | | |     | | | ||| | ||   |  | |||  |                                 
GACCACCTTGCTCTTATGATGGAACTCTTAGGAAAAATGCCTCGAAAGgtacccggaaaaatacttggtttctgtctatctcttgattgatcggttatagtctcgttgatacttgtgatttaactagattgccattggag--------------------------------

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|110699121|gb|EE075840.1|EE075840
EST:     GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
EST: gi|110358839|gb|EC923345.1|EC923345
EST:     GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
EST: gi|30136408|gb|CB921746.1|CB921746
EST:     GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
EST: gi|110394338|gb|EC959136.1|EC959136
EST:     GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
EST: gi|110363309|gb|EC926886.1|EC926886
EST:     GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
EST: gi|71870433|gb|DT019488.1|DT019488
EST:     GGATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GGATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
EST: gi|27586674|gb|CB009369.1|CB009369
EST:     GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
EST: gi|32461051|gb|CD802225.1|CD802225
EST:     GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
EST: gi|30330441|gb|CD013703.1|CD013703
EST:     GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
EST: gi|161712169|gb|FC061541.1|FC061541
EST:     GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAG                         GTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT
genomic: GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacat ... tgataagcagGTAGCCATTGGGGGAGCTCGATCAAAAGACCTCTTTGACAGACATGGGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCACCTTGCTCTGATGATGGAACTCCTTGGAAAAATACCTCGGAAGgtgagcacattatgcctctatttcggtttgctttccgaaatactcatttttagcacttacccgcctttcattagctctctgacaattatatgcaatatccatatatctatgcttgataagcag

- - - - - - - -  GATGGA