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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatttctttaaggcactgtaagtttagcttttttaaagtactcaagtagtaaggaaaaaaaaaattgattgattgatttatttatggctttttaaaactgatttatctctaaatggttcctttttatatattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCTGGGTGTTATAATTGTAG

Basic information

species Vitis vinifera
transcript Vv06s0004g01860.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G336783_T01 (Zea mays), 3'ss of exon 8
gtaagaatttctttaaggcactgtaagtttagcttttttaaagtactcaagtagtaaggaaaaaaaaaattgattgattgatttatttatggctttttaaaactgatttatctctaaatggttcctttttatatattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCTGGGTGTTATAATTGTAG
                         |    ||  |  ||   | | | |  ||||||  |||| |||                ||| | ||   |||||  | |  ||| ||        ||   | ||  |        |||||||||||| ||||||||| | |||||||| ||||| ||||| ||||| |||||||| || ||||| |
---------------------aaataacaaagaatgattgcggcatttatttagtaaacaaaataaa---------------ctatatttgaacttttagtaatactttgtcgtcgccatgtctttgttggtg-------cagCAAATGGCAAGCCTTCAAATTAGCAACTCTATCTGGTTTTGCAGAGCCACTGGGTGTGATTATTGTGG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G41580.5 (Glycine max), 3'ss of exon 8
gtaagaatttctttaaggcactgtaagtttagcttttttaaagtactcaagtagtaaggaaaaaaaaaattgattgattgatttatttatggctttttaaaactgatttatctctaaatggttcctttttatatattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCTGGGTGTTATAATTGTAG
                                         | | ||  | |  |   |  |    ||||  | |  |  |  || |||||      ||||| ||| | ||     ||   ||   || |  || |  |  || ||||||||||| |||||| | ||| | ||||||||||||||||| |||||||| |||||||||||||
-----------------------------------------aat-cttgatttttgttgctatgttaaatgaagttgtgcaagtaattatg------taaaattgaataat-----aacctttttattctggatgtgtcctagtaaatggcagGCATTCAAATTAGCATCACTTTCTGGCTTTGCTGAACCCCTGGGAGTTATAATTGTAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G41580.1 (Glycine max), 3'ss of exon 8
gtaagaatttctttaaggcactgtaagtttagcttttttaaagtactcaagtagtaaggaaaaaaaaaattgattgattgatttatttatggctttttaaaactgatttatctctaaatggttcctttttatatattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCTGGGTGTTATAATTGTAG
            ||||   ||  ||| | | | |||||            || |  | |  |||  || |||    | | |||     |||      ||||| ||| | ||     ||   ||   || |  || |  |  || ||||||||||| |||||| | ||| | ||||||||||||||||| |||||||| |||||||||||||
------------ttaa---accttaaatcttgattttt------------gttgctatgttaaatgaagttgtgcaagtaatt-----atg------taaaattgaataat-----aacctttttattctggatgtgtcctagTAAATGGCAGGCATTCAAATTAGCATCACTTTCTGGCTTTGCTGAACCCCTGGGAGTTATAATTGTAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G14090.1 (Glycine max), 3'ss of exon 6
gtaagaatttctttaaggcactgtaagtttagcttttt--------taaagtactcaagtagtaaggaaaaaaaaaattgattgattgatttatttatggc-tttttaaaac-tgatttatctctaaatgg----------------------------ttcctttttatatattcct----------cagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCTGGGTGTTATAATTGTAG
|||||||  |   | ||   ||||   |||||| ||||        ||| ||  |    | || |  |  |     |   ||| |||||| | ||| |    ||| || |||  || ||||  | | | ||                            ||  ||||| |  ||| ||          |||||||||| |||| |||||| ||||| | |||||||||||||||||||| ||||| ||| |||||||||
gtaagaaccttagtgagctcctgttgttttagccttttgtttgacataatgtgattctcttgttaatagcatctggaactatttattgatctgtttgttatgtttatataacacgagttataccaataaggcaataactacaaatttgaattataactattttttttttttaatttctgaatgtgttgcagCAAATGGGAGGCATTCAAATTGGCATCACTTTCTGGCTTTGCTGAGCCACTGGGCGTTGTAATTGTAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G06060.1 (Glycine max), 3'ss of exon 7
gtaagaatttctttaaggcactgtaagtttagcttttttaaagtactcaagtagtaaggaaaaaaaaaattgattgattgatttatttatggctttttaaaactgat-ttatctctaaatggttcctttttatatattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCTGGGTGTTATAATTGTAG
                                          ||  |    | || | |   | | ||  ||| | ||     ||  ||    |||  ||||    | || | | ||     || ||   |  || |     ||||||||| |||| |||||| ||||| | |||||||||||||||||||| ||||| ||| |||||||||
------------------------------------------gtgtt--gtttgttatgtttatataacatgagttataccaataactacaaatttgaaaaataactattttttttattccatttctgaatgcatgtgttgtagCAAATGGGAGGCATTCAAATTGGCATCACTTTCTGGCTTTGCTGAGCCACTGGGCGTTGTAATTGTAG

upper sequence: Vv06s0004g01860.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G03820.2 (Glycine max), 3'ss of exon 8
gtaagaatttctttaaggcactgtaagtttagcttttttaaagtactcaagtagtaaggaaaaaaaaaattgattgattgatttatttatggctttttaaaactgatttatctctaaatggttcctttttatatattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCTGGGTGTTATAATTGTAG
                          ||| | |||   |   ||  |   || |  | |  |||  || |||    | | |||     |||      ||||| ||| | ||     ||   ||   || |  || |  |  || ||||||||||| |||||| | ||| | ||||||||||||||||| |||||||| |||||||| ||||
--------------------------gttaaccttaaatcttgtttttt-gttgctatgttaaatgaagttgtgcaagtaatt-----atg------taaaattgaataat-----aacctttttattctggatgtgtcctagTAAATGGCAGGCATTCAAATTAGCATCACTTTCTGGCTTTGCTGAACCCCTGGGAGTTATAATCGTAG

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|30251805|gb|CB969538.1|CB969538
EST:     GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG                         CAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGTTTTGCTGAGCCCCT
genomic: GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAGgtaagaattt ... tattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCT
EST: gi|30251808|gb|CB969541.1|CB969541
EST:     GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG                         CAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGTTTTGCTGAGCCCCT
genomic: GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAGgtaagaattt ... tattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCT
EST: gi|110693804|gb|EE070356.1|EE070356
EST:     GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG                         CAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCT
genomic: GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAGgtaagaattt ... tattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCT
EST: gi|110689440|gb|EE065664.1|EE065664
EST:     GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG                         CAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAACCCCT
genomic: GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAGgtaagaattt ... tattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCT
EST: gi|110698572|gb|EE076222.1|EE076222
EST:     GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAG                         CAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCT
genomic: GGTGTTGCTGTTGCACTTCCTGTTTATTTTGCAACACAGAGgtaagaattt ... tattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggctttttaaaactgatttatctctaaatggttcctttttatatattcctcagCAAATGGCAGGCCTTCAAACTGGCAACTCTTTCTGGCTTTGCTGAGCCCCTGGGTGTTATAATTGTAG
                       ctctaaa  putative branch site (score: 3)
                                             tattcctc  putative PPT
     tttttaaaactgattt  TA-rich tract