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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtaattttactttcaagaatttttatgctgtggtatgtttgataataagcttatgatggtcaaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGA

Basic information

species Vitis vinifera
transcript Vv01s0011g05630.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G04710.1 (Glycine max), 3'ss of exon 3
gtgggtaattttactttcaagaattt-ttatgctgtggtatgtttgataataagcttatga-tggtcaaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGA
|| |||||  ||      ||| |||  || | ||    | || ||||   | | ||||| | |    |||||||||||| || ||   | | || || |||||||||| |||||| || |||  ||||||||| ||||| ||||  |||||||||||||||||||||||||| || |
gtaggtaacattttcacaaaggattccttgtact----tgtgattgaatttgaacttataaatatctaaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACAATGGAAGACATTTTGATGCAATTGAAGAAAGAAATGATGTCTCCACAAA

upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G24950.4 (Glycine max), 3'ss of exon 3
gtgggtaattttactttcaagaatttttatgctgtggtatgtttgataataagcttat-gatggtcaaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGA
||  |      | ||| ||     ||   ||||||||| ||||||| | |   || ||  ||    |||||||||||| || ||   | | || || |||||||||| |||| |  | |||| ||||||||| ||||| |||| ||||||||||| |||||||||||||||||| |
gtaagaggcaattcttgcagaggcttcattgctgtggtgtgtttgaaattgtactcattaatcactaaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGAAACGTGAGCGTACAATGGAAGACATTTTGATTCAATTGAAGAGAGAAATGATGTCTCCCCAAA

upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G22600.1 (Glycine max), 3'ss of exon 3
gtgggtaattttactttcaagaatttttatgctgtggtatgtttgataataagcttat-gatggtcaaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGA
||  |  |   | ||| ||     |||  | |||||||  |||||  | | | || ||  ||    |||||||||||| || ||   | | || || |||||||||| |||| |  | |||||||||||||| ||| | |||| ||||||||||| ||||||||||||||| || |
gtaagagacaattcttgcataggctttattactgtggt--gtttggaattgaactcattaattactaaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGAAACGTGAGCATACAATGGAAGACGTTTTGATTCAATTGAAGAGAGAAATGATGTCTCCTCAAA

upper sequence: Vv01s0011g05630.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G35000.1 (Glycine max), 3'ss of exon 3
gtgggtaat-tttactttcaagaatttttatgctgtggtatgtttgataataagcttatga-tggtcaaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGA
|| |||||  ||| |  | | || |  || | ||    | || ||||   | | ||||| | |    |||||||||||| || ||   | | || || |||||||||| |||||| || |||  ||||||||| ||||| ||||  |||||||||||||||||||| ||||| || |
gtaggtaacattttcactaaggattccttgtact----tgtgattgaatttgaacttataaatatctaaattaccagGTTGAGCCACATTTGTTTCCTATGCTTGCTAATTGGCAAAGAGAGTGTACAATGGAAGACATTTTGATGCAATTGAAGAAAGAAATGATATCTCCACAAA

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|34550762|gb|CF518980.1|CF518980
EST:     AGTTTCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCAAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|32249291|gb|CD715110.1|CD715110
EST:     AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|110399220|gb|EC965717.1|EC965717
EST:     AGTTTCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCAAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|161717210|gb|FC067216.1|FC067216
EST:     AGTTTCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCAAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|26266147|gb|CA817210.1|CA817210
EST:     AGTTTCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCAAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|37190155|gb|CF609504.1|CF609504
EST:     AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|34548114|gb|CF516346.1|CF516346
EST:     AGTTTCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCAAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|30137020|gb|CB922358.1|CB922358
EST:     AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|30298336|gb|CB975130.1|CB975130
EST:     AGTTTCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCAAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|46918982|gb|CN548311.1|CN548311
EST:     AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|349830853|gb|FQ418161.1|FQ418161
EST:     AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|46918733|gb|CN548062.1|CN548062
EST:     GTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: GTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|34361563|gb|CF403148.1|CF403148
EST:     AGTTTCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCAAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
EST: gi|34549812|gb|CF518044.1|CF518044
EST:     AGTTTCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTG                         GTCGAACCAAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA
genomic: AGTTCCAGACTCGGATAAATATGACCTGTGTCAATCAGGAAACTGGAGTGgtgggtaatt ... aaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatttttatgctgtggtatgtttgataataagcttatgatggtcaaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGA
                    gtttgat  putative branch site (score: 5)
                 tatgtttgataataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtaattttactttcaagaatttttatgctgtggtatgtttgataataagcttatgatggtcaaattaccagGTCGAACCTAGTCTTTTCCCCATGCTTGCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA