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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatgttgctttttttcaattttatggtattttttttttctcttttagaatctttgatacattgctcttattaaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGATGGAAAAAGTTATAGCACAAACTTAGCCTTTACACCTCCTGAATATCTGA

Basic information

species Vitis vinifera
transcript Vv02s0025g03550.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G01730.2 (Glycine max), 3'ss of exon 5
--------------gtaagtatgttgctttttttcaattttatggtatttttt-ttttctcttttagaatctttgatacattgctcttattaaat-ctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGATGGAAAAAGTTATAGCACAAACTTAGCCTTTACACCTCCTGAATATCTGA
              | ||| |   |||| |   | | |  | |  ||   |   |  | | | | |   || ||  |   ||  || |  | | |  ||||||   | ||||||||||||||||||| ||| ||||||| |||||||||||||| |||||||| || ||||| || || || || || |||||||||||||
ggcactgatactgtggaagaa-actgctataaattagtgctttcttagcctaaatagtatgtgtgactgtcctttttctttttttcctccttattattcagGAATACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGATGGGAAAAGTTACAGTACAAATTTGGCATTCACTCCACCTGAATATCTGA

upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 6
-------------gtaagta--tgttgctttttttcaattttatggtattttttttttctcttttagaatctttgatacattgctcttattaaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGATGGAAAAAGTTATAGCACAAACTTAGCCTTTACACCTCCTGAATATCTGA
             | ||| |  || |     ||| |   ||  | |  |   |  |   | ||       ||||      || | |   ||      |||||   | ||||||||||||||||||| ||| ||||||| |||||||| ||||| | |||||| || ||||| || || ||||| || |||||||||||||
tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagcctaaatagtaagtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA

upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtatgttgctttttttcaattttatggtattttttttttctcttttagaatctttgatacattgctcttattaaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGATGGAAAAAGTTATAGCACAAACTTAGCCTTTACACCTCCTGAATATCTGA
|||||| || | |   ||||      | |||| | | |    | | | | |||||     ||    || | || ||   ||| ||||||   |||| |||||||||||||||||| ||||||| || |||||||||||||| ||||||||||| ||| | || || || ||||| || |||||||
gtaagtttgatacagatttttttacctttggtttctgtcaagtgtatatgagaat----aattttatgtttttgtt---tcttagGATGCAAATCCAAGACTTTCATGCTTTGGTTTGATGAAAAACAGTAGAGATGGAAAGAGTTATAGCACTAACCTGGCATTCACTCCTCCCGAGTATCTGA

upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G63500.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------------gtaagt-atgttgctttttttcaat-tttatggtattttttttttctcttttagaatctttgatacattgc----tcttattaaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGATGGAAAAAGTTATAGCACAAACTTAGCCTTTACACCTCCTGAATATCTGA
                                     ||||| | | |  | | ||| | | ||| |    ||| |   |  |  | |   |   | || ||||       | || |    | | ||||     |||| |||||||||||||| ||| ||||||| ||||||||||| ||||| ||||||||||| ||| | || || || ||||| || ||||| |
gtaagttaagcttatttttattttattttgggcaagataagttaagcttatatgtttgattatttttaacgtttgtcaatgttaatgtgtgaatatagaaacatcatcatatgttttgtgtttttagGACTCAAATCCAAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGACGGAAAGAGTTATAGCACCAACCTGGCGTTCACTCCTCCAGAGTATCTCA

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|349812356|gb|FQ406377.1|FQ406377
EST:     GACGTGCACTTTATCATGATCTTAATGCTTATAGAATTGTTTTTGATGAT                         GATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGAT
genomic: GACGTGCACTTTATCATGATCTTAATGCTTATAGAATTGTTTTTGATGATgtaagtatgt ... taaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGAT
EST: gi|349812229|gb|FQ411824.1|FQ411824
EST:     GACGTGCACTTTATCATGATCTTAATGCTTATAGAATTGTTTTTGATGAT                         GATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGAT
genomic: GACGTGCACTTTATCATGATCTTAATGCTTATAGAATTGTTTTTGATGATgtaagtatgt ... taaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGAT
EST: gi|349818651|gb|FQ403286.1|FQ403286
EST:     GACGTGCACTTTATCATGATCTTAATGCTTATAGAATTGTTTTTGATGAT                         GATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGAT
genomic: GACGTGCACTTTATCATGATCTTAATGCTTATAGAATTGTTTTTGATGATgtaagtatgt ... taaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGAT
EST: gi|351042322|gb|FQ442789.1|FQ442789
EST:     GACGTGCACTTTATCATGATCTTAATGCTTATAGAATTGTTTTTGATGAT                         GATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGAT
genomic: GACGTGCACTTTATCATGATCTTAATGCTTATAGAATTGTTTTTGATGATgtaagtatgt ... taaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattttttttttctcttttagaatctttgatacattgctcttattaaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGATGGAAAAAGTTATAGCACAAACTTAGCCTTTACACCTCCTGAATATCTGA
                         ctttgat  putative branch site (score: 5)
                                      ctcttatt  putative PPT
     ttttttttctctttta  TA-rich tract