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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagagagaggatgaaatgtcgtataagaacaaatattcaacctcttgtatatggagctgagattttcgcttgactctaatccattgtttacctggtctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTTTCCATATGGGTGTCGGTGGTGCAGCCATTGCCCATGTTATATCTCA

Basic information

species Vitis vinifera
transcript Vv06s0004g02140.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os10g13940.1 (Oryza sativa), 3'ss of exon 5
gtaagtagagagaggatgaaatgtcgtataagaacaaatattcaacctcttgtata-tggagctgagattttcgcttgactctaatccattgtttacctggtctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTTTCCATATGGGTGTCGGTGGTGCAGCCATTGCCCATGTTATATCTCA
           |  ||||  || |   |    |  | || ||     |  || ||| |    || ||  |    | |    |||||    |||| ||    | ||   ||||||| ||||| | ||| |||||| |||| || || |||||||||||||| |||||    |||||| |||||||||| ||||| ||||||||||| ||
---------ttgtagatggtatatttaaatgcatgagatgttacgattagtgaataatttgcctcaggataatacatatacctaat--ggtgttaactctttttataccagTGGCTGGAGATGCAACCAACATAGTTTTGGATCCAATATTTATGTTTGTCTTCCAGTATGGTGTCAGTGGTGCAGCAATTGCTCATGTTATATCACA

upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G41460.1 (Glycine max), 3'ss of exon 5
gtaagtagagagaggatgaaatgtcgtataagaacaaatatt-caacctcttgtatatggagctgagattttcgcttgactctaatccattgtttacctggtctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTTTCCATATGGGTGTCGGTGGTGCAGCCATTGCCCATGTTATATCTCA
||| |    || |   | ||||   || |  || ||||| |  |||  || ||                | |    ||| ||||| | | | |||   || | || |  |||||||||||| ||||| ||||||    |||| ||  |||| |||||||| ||||   |||||||| ||||||||||||| |||||||||||||||||
gtatgccttgacaaacttaaat--tgtctttgatcaaatgtcacaatatcctgc---------------tattatctgattctaa-ctactctttctttgatgta-tctagTGGCAGGAGATGTAACCAACATAGCACTAGATCCTTTATTCATGTTTGTATTCCGCTTGGGTGTCAGTGGTGCAGCCATCGCCCATGTTATATCTCA

upper sequence: Vv06s0004g02140.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G03930.1 (Glycine max), 3'ss of exon 5
gtaagtagagagaggatgaaatgtcgt-ataagaacaaatattcaacc-tcttgtatatggagctgagattttcgcttgactctaatccattgtttacctggtctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTTTCCATATGGGTGTCGGTGGTGCAGCCATTGCCCATGTTATATCTCA
                    ||| | | | ||    |||| ||||    |||  | |    |  |     | |   |||| ||||    | | |||   || | || |  |||||||||||| ||||| ||||||    |||| ||  |||| |||||||| ||||   |||||||| ||||||||||||| |||||||||||||||||
------------------gtatgccttgacaaacttaaattttcattgatctaatgtcacaatatcctgctattatttgattctaggt-actctttctttgatgta-tctagTGGCAGGAGATGTAACCAACATAGCACTAGATCCTTTATTCATGTTTGTATTCCGCTTGGGTGTCAGTGGTGCAGCCATCGCCCATGTTATATCTCA

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|110699707|gb|EE076951.1|EE076951
EST:     AGGGGTCTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTG                         TGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT
genomic: AGGGGTCTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTGgtaagtagag ... tctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT
EST: gi|110698510|gb|EE076088.1|EE076088
EST:     CTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTG                         TGGTAGGACACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT
genomic: CTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTGgtaagtagag ... tctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT
EST: gi|294965646|gb|GW837245.1|GW837245
EST:     GGATACAAAAACTCCTCTATATGCCACTG                         TGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT
genomic: GGATACAAAAACTCCTCTATATGCCACTGgtaagtagag ... tctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT
EST: gi|30300493|gb|CB977287.1|CB977287
EST:     AGGGGTCTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTG                         TGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT
genomic: AGGGGTCTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTGgtaagtagag ... tctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT
EST: gi|161707688|gb|FC056917.1|FC056917
EST:     AGGGGTCTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTG                         TGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTAT
genomic: AGGGGTCTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTGgtaagtagag ... tctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTAT
EST: gi|30301245|gb|CB978039.1|CB978039
EST:     AGGGGTCTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTG                         TGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT
genomic: AGGGGTCTTTCGCGGATTTAAGGATACAAAAACTCCTCTATATGCCACTGgtaagtagag ... tctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggagctgagattttcgcttgactctaatccattgtttacctggtctaattcagTGGCAGGAGACGTAACAAACATAATTTTAGACCCGATATTTATGTTTGTTTTCCATATGGGTGTCGGTGGTGCAGCCATTGCCCATGTTATATCTCA
                                            gtctaat  putative branch site (score: 3)
                                attgttta  TA-rich tract