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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcttaatttgcttattcattacaggtccagtcctactgttttctttctggttaggacttagagaaaagaaactgttattgtgctattgattgggcatgagagacaagactcaagaatggtttctgttttttgtcttccataatatttgcagGGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGATGCCATTCGTAAG

Basic information

species Vitis vinifera
transcript Vv11s0016g04620.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 16
-----------------gtattcttaattt---gcttattcattacag--gtccagtcctactgttttctttctggt--taggacttagagaaaagaaactgttattgtgctattgattgg-gcatgagagacaagactcaagaat---ggtttctgttttt-tgtcttcca-taatat--------------ttgcagGGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGATGCCATTCGTAAG
                  | ||  |||  |   | || |  | |||||  ||    |  |  ||   ||  | |  |  || |  |     | ||| |       | ||| | ||| | |     |||   |  | | |      |   || |||| ||| | | ||| | | || |||              ||  |||||||||||||||||||| || |||||||| ||||| || |||||  | ||||| || || |||
gtatgctactgcaaatactgtttataaactaacgtttgtagagtacagtagttagatatttgtggaatcaatttaatcctatgtatcttcaacaagtactgaacctagtgtttttgttcgctatttgaagtatgaaagttgctgttataggcttctatttgtatatctgctaatagtatcggtactgcttctcttctagGGATGGTGTCAGTGAAGGCCAATTCTACCAAGTTCTCCTCTATGAGTTGGATGCTATCCGCAAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 16
gtattcttaatttgcttattcattacaggtccagtcctactgttttctttct------ggttaggacttagagaaaagaaactgttattgtgctattg--attgggcatgagagacaagactcaagaatggtttctgttttttgtcttccataatatttgcagGGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGATGCCATTCGTAAG
|||    | || || |     |||     |    |  ||  ||| |  ||        | |||||  | |||  | ||  | || | | |   ||||    ||   ||     || ||      ||     ||  | ||| |  | ||    ||||||| ||||||||| || |||||||| ||||||||||||||| |  | ||||| ||||||||||| ||||||
gtaagagtgatctgttctgatatttttatttt--ttttaaagttgttcttgcaaaggagattagggatgagatgagaggcagtgatttggacatattacagttatccaaataggataatggaggagtgcctttattatttataatgttgtccaatatttacagGGATGGGGTAAGTGAAGGACAGTTCTACCAGGTTTTGTTGTATGAGCTTGATGCCATCCGTAAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA06G23920.1 (Glycine max), 3'ss of exon 16
gtattcttaatttgcttattcattacaggtccagtcctactgttttctttctggttaggacttagagaaaagaaactgttattgtgctattgattgggcatgagagacaagactcaagaatggtttctgttttt-tgtcttccataatatttgcagGGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGATGCCATTCGTAAG
                                                                     ||||      |||| || ||||| |   |  ||||  |||||| |   || |  | |   || |  |||  ||||  || ||| ||||||||| || ||||| || ||||||||||||||| | |||||||| ||||||||||| || |||
-------------------------------------------------------------------gtaagactgatctattctgatattgttcttg--tgaggaacaagaatgtggagttatattaattataatgttctccaatatgttttcagGGATGGGGTAAGTGAGGGACAGTTCTACCAGGTTTTGCTATATGAGCTTGATGCCATACGCAAG

upper sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA05G08170.1 (Glycine max), 3'ss of exon 14
gtattcttaatttgcttattcattacaggtccagtcctactgttttctttctggttaggacttagagaaaagaaactgttattgtgctattg--attgggcatgagagacaagactcaagaatggtttctgttttttgtcttccataatatttgcagGGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGATGCCATTCGTAAG
                                                         ||  | |||  | ||| | || | | |   ||||    ||   ||     || ||      ||  |  ||  | ||| |  | ||    ||||||| ||||||||| || |||||||| ||||||||||||||| |  |  |||| ||||||||||| ||||||
---------------------------------------------------------gggttgagatgagagacagtgatttgggcatattacagttatccaaataggataatggaggagtgtctttattatttataatgttgtccaatatttacagGGATGGGGTAAGTGAAGGACAGTTCTACCAGGTTTTGTTGCATGAGCTTGATGCCATCCGTAAG

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|33407837|gb|CF213464.1|CF213464
EST:     TCATTTAAGGCAGCCACTGGNNNNNNNCCATTGAGGATAATATTTTACAG                         GGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGA
genomic: TCATTTAAGGCAGCCACTGGAAAAAAACCATTGAGGATAATATTTTACAGgtattcttaa ... atatttgcagGGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGA
EST: gi|349828457|gb|FQ417199.1|FQ417199
EST:     TCATTTAAGGCAGCCACTGGNNNNNNNCCATTGAGGATAATATTTTACAG                         GGATGGTGTCAGTGAAGGGCAGTTCTACCAGGCTCTACTATATGAACTTGA
genomic: TCATTTAAGGCAGCCACTGGAAAAAAACCATTGAGGATAATATTTTACAGgtattcttaa ... atatttgcagGGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagagacaagactcaagaatggtttctgttttttgtcttccataatatttgcagGGATGGTGTCAGTGAAGGGCAGTTCTACCAGGTTCTACTATATGAACTTGATGCCATTCGTAAG
                                          ataatattt  TA-rich tract