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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcccctatcttcatgttgttttattcttgataattatcttgacatttggggctaggaattctaatttttgctggatcacttgtattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g11700.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os11g17600.3 (Oryza sativa), 3'ss of exon 11
gtattcccctatcttcatgttgttttattcttgataattatcttgacatttggggctaggaattctaatttttgctggatcacttgtattaa--acagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG
                  ||   |||| ||| | |||||  |     ||||     ||        | ||||  |   || | |  | ||     ||| |||| ||  |  ||||||| |||||||||||| |  |||| ||||||||||| ||||| || ||||||||   | | |||
------------------gtaaatttagtctag-taattg-cagattatttaactttaaccggatcatttttctcaacataattccttttgctttcagAGAGGGCAACTCCAGAGGCCTGACCATGCTGATATGAGGTACAAATGCAGGACATATGCCCGACTTCTACAGTTCATCAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 11
gtattcccctatcttcatgttgttttattcttgataattatcttgacatttggggctaggaattctaatttttgctggatcacttgtattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG
|| |   | || |||||| ||   | |   |  ||| ||   ||  |||||| |   |   |    |   ||  ||   | |  || |   | ||||| ||||| |||||| |||| || ||||| || ||| |||||||||||||||| ||||| || ||||| || |||||||||
gtttcttcatagcttcatttt---tgaaagtaaatatttcctttcccatttgagatgaccgac---agagttcactt--ttaactgaa---agcagCGTGGACAATTGAAGCGGCCTGATCATGCAGACCTTAGGTATAAATGCAGGACATATGCCCGACTTCTGCAGCACTTAAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 11
gtattcccctatcttcatgttgttttattcttgataattatcttga-catttggggctaggaattctaatttttgctg-gatcacttgtattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG
           |||     |   |||||   | ||||   | |  |   || |    ||| |    | |||||  ||  | |  |||    ||||||||| ||||||||||| |||||||| ||||||||| |  |||| || |||||||| ||||| ||||||||  | || ||||||
-------gtattctctgcataaatttatgaattataaacttttaaagtgttagaaattagaatcattcattttcactttggttgcttactctaaacagCGGGGACAGTTGAAAAGGCCAGATCATGCTGATTTGAGGTACAAGTGCAGGACATATGCACGCCTTCTGAAGCATTTAAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 11
gtattcccctatcttcatgttgttttattcttgataattatcttgacatttggggctaggaattctaatttttgctggatcacttgtattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG
        |||  || ||    || |||||   |||       |||  | | | | |   |||||| | | ||  |  | | | | | |||||||| |||| ||| |||||||||| |||||||||||| | ||||| |||||||| || |||||||| ||| | ||||| ||||||
-----gtactaattttataaaattctattcc-aata-------tgaagtctagtgattataattctgaatatttatc-accgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTTTGCAACATTTAAAG

upper sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 11
gtattcccctatcttcatgttgttttattcttgataattatcttgacatttggggctaggaattctaatttttgctggatcacttgtattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG
        |||  || ||    ||  ||  |     |  |   |||  | | | |  |  |||||| | | ||  |  | | | | | |||||||| |||| ||| |||||||||| |||||||||||| | ||||| |||||||| || |||||||| ||| | ||||| ||||||
-----gtactacttttataaaattccatcgt-----accaatatgaagtctagtg--actaattctgaatatttatc-accgcatcttttaaacagAGAGGGCAGCTGAAGAGGCCTGACCATGCTGATTTGCGGTACAAATGCAGAACATATGCTCGTCTTATGCAACATTTAAAG

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|30130173|gb|CB915512.1|CB915512
EST:     TCGCCAGTTTGGTGGATTTTATGATAAGTGATAAGAGTTACTTCTCTCAG                         CGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGG
genomic: TCGCCAGTTTGGTGGATTTTATGATAAGTGATAAGAGTTACTTCTCTCAGgtattcccct ... tattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGG
EST: gi|30305614|gb|CB982408.1|CB982408
EST:     TCGCCAGTTTGGTGGATTTTATGATAAGTGATAAGAGTTACTTCTCTCAG                         CGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGG
genomic: TCGCCAGTTTGGTGGATTTTATGATAAGTGATAAGAGTTACTTCTCTCAGgtattcccct ... tattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgacatttggggctaggaattctaatttttgctggatcacttgtattaaacagCGAGGACAGTTGAAGAGGCCAGACCATGCTGATCTTCGGTATAAATGCAGGACTTATGCTCGCCTTCTACAACACTTAAAG
                     ttctaat  putative branch site (score: 2)
                   aattctaattttt  TA-rich tract