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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAAATGAAGGCCAGTACTAATGTTAGGCATATTGTTCTTCCCTGTTCTAGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAGgtaagtttttctactattgactgcctctgagccatgcttttgtgatattctttataaattcattgcattttttttcctgtcttttctcttaattcag

Basic information

species Vitis vinifera
transcript Vv16s0022g02110.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g02110.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA10G38680.1 (Glycine max), 5'ss of exon 6
AAAAAATGAAGGCCAGTACTAATGTTAGGCATATTGTTCTTCCCTGTTCTAGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAGgtaagtttttctactattgactgcctctgagccatgcttttgtgatattctttataaattcattgcattttttttcctgtcttttctcttaattcag
 ||||||||||||||| || ||||||||||||||||||||||| ||| ||||||| |||||  ||||  | || || ||| ||||||||||||||||||||| |    || ||  ||| | ||  | |      | |   | | ||||   ||   | |  || | |||||  |     |  ||  |||   |||||
CAAAAATGAAGGCCAGCACCAATGTTAGGCATATTGTTCTTCCTTGTACTAGTTCTGCCAGGGCCCAACTTATCCCAGATATTATTCGCTGTTATAGCAGgtga----ttatatgattcaatgtgtttttttttttcacatatcatatctatttggagtatatggaattttaatcttcattgttgatct-ggttcag

upper sequence: Vv16s0022g02110.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA20G29060.1 (Glycine max), 5'ss of exon 6
AAAAAATGAAGGCCAGTACTAATGTTAGGCATATTGTTCTTCCCTGTTCTAGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAGgtaagtttttctactattgactgcctctgagccatgcttttgtgatattctttataaattcattgcatttt--ttttcctgtcttttctcttaattcag------
 ||||||||||||||| |  ||||||||||||||||||||||| ||| ||||||| |||||  ||||  | || || ||| ||||||||||||||||||||| |    || || |||| | ||  | |     || |   | ||||||   ||   | |  |||| |||||  | ||| |   |  | || |  ||| |      
CAAAAATGAAGGCCAGCATCAATGTTAGGCATATTGTTCTTCCTTGTACTAGTTCTGCCAGGGCCCAACTTATCCCAGATATTATTCGCTGTTATAGCAGgtga----ttttattattcaatgtgttttttttattcacatatgatatctgtttcgagtatattgaattttaatgttcattgttgatttcatggttctggttcag
















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|161707834|gb|FC055234.1|FC055234
EST:     AGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAG                         TGGAGGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT
genomic: AGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAGgtaagttttt ... cttaattcagTGGAGGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT
EST: gi|161720948|gb|FC070676.1|FC070676
EST:     AGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAG                         TGGAGGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT
genomic: AGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAGgtaagttttt ... cttaattcagTGGAGGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT
EST: gi|161721595|gb|FC070805.1|FC070805
EST:     AATTCAACCAGATCCCAGGTCATTCCTGATGTTATTCTCTGTTATAGCAG                         TGGATGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT
genomic: AGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAGgtaagttttt ... cttaattcagTGGAGGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT
EST: gi|294964618|gb|GW838421.1|GW838421
EST:     AGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAG                         TGGAGGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT
genomic: AGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAGgtaagttttt ... cttaattcagTGGAGGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT
EST: gi|30253071|gb|CB970622.1|CB970622
EST:     AGTTGANCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAG                         TGGAGGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT
genomic: AGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAGgtaagttttt ... cttaattcagTGGAGGTCGAACAATTATTTTTACTGAGACCAAGGATTCTGCTTCTGAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAAATGAAGGCCAGTACTAATGTTAGGCATATTGTTCTTCCCTGTTCTAGTTCAGCCAGATCCCAGGTCATTCCTGATGTTATTCGCTGTTATAGCAGgtaagtttttctactattgactgcctctgagccatgcttttgtgatattctttataaattcattgcattttttttcctgtcttttctcttaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT