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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtgacttgtcaacttttatttctgacttaaaagtttgattagttggtttttttaataaacctttcttcctgacagaaaagtctcaatagttggtttttaattaatggttttatgcccttgtcttattacagATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACTTGGCCTGCCAAAGTATAATAAACAGTTGATCAGCAAACTTCTTAACAAT

Basic information

species Vitis vinifera
transcript Vv06s0004g01360.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os06g21600.1 (Oryza sativa), 3'ss of exon 6
gtatttgtgacttgtcaacttttatttctgacttaaaagtttgattagttggtttttttaataaacctttcttcctgacagaaaagtctcaatagttggtttttaattaatggtt--ttatgcccttgtcttattacagATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACTTGGCCTGCCAAAGTATAATAAACAGTTGATCAGCAAACTTCTTAACAAT
                                               ||   || ||||    ||  |||       || ||  | |  | ||  ||   |    ||  ||  |   || ||   |     || | ||| || || || || |||||||||||||||||| | ||||||||||| |||||||| || || ||||||||||| ||| | ||  |||| || |||||||| 
-----------------------------------------------gtgcattgttttgtccaatattt-------actgattattacccatgattatgtccagatgtatcatacattttgatttctgtgtactgcagGTACGGGACAAAGTTTATGGATGAGTATCAATCCATAATGACCAGGAAACTTGGTCTACCCAAGTATAATAAGCAGCTAATAGGCAAGCTGCTTAACAAC

upper sequence: Vv06s0004g01360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G44280.1 (Glycine max), 3'ss of exon 3
gtatttgtgacttgtcaacttttatttctgacttaaaagtttgattagttggtttttttaataa-acctttcttcctgacagaaaagtctcaat---agttggtttttaattaatggttttatgcccttgtcttattacagATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACTTGGCCTGCCAAAGTATAATAAACAGTTGATCAGCAAACTTCTTAACAAT
                                           | ||||     ||| | |||  |  |||   ||| | || | |   |   |   | |||  ||| |||   | |  | |||   |||  || || |||||||||||| | |||||||||||| ||||| | ||||||||||| ||| |||||||| || ||||||||||| ||| |||| |  |||||||||| ||||
-----------------------------------------gtagtagtaacactttctgataccattttttaacctcagaggagaaaataggtgtgaattgcctttaaatgtttcgcctcatgg--ttgctttgtttcagATATGGAACGAGATTTATGGATGATTATCAGGTTATAATGACCAAAAAGCTTGGCCTCCCTAAGTATAATAAGCAGATGATTAATAAACTTCTTAGCAAT

upper sequence: Vv06s0004g01360.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G39090.2 (Glycine max), 3'ss of exon 3
gtatttgtgacttgtcaacttttatttctgacttaaaagtttgattagttggtttttttaataaacctttcttcctgacagaaaagtctcaatagttggtttttaattaatggttttatgcccttgtcttattacagATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACTTGGCCTGCCAAAGTATAATAAACAGTTGATCAGCAAACTTCTTAACAAT
                                 ||  |||     |   || |    ||  | ||||| |         | | | || | |||   ||  ||| |||   |    | |||   |||  || || |||||||||||| | |||||||||||| ||||| | || |||||||| ||| |||||||| || ||||||||||| ||| |||| |  |||||||||| ||||
--------------------------------gtagtagtaacgctttctgataccattttttaacctcttagaggagaaaataggtgtgaat---tgcctttaaatgtttcacctcatgg--ttggtttgtttcagATATGGAACGAGATTTATGGATGATTATCAGGTTACAATGACCAAAAAGCTTGGCCTCCCTAAGTATAATAAGCAGATGATTAATAAACTTCTTAGCAAT

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|110360788|gb|EC924163.1|EC924163
EST:     ATGTCTGCTGAGTTGATAAATGATAAGGAGGCAAACTATGCCATGGAAAG                         ATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACT
genomic: ATGTCTGCTGAGTTGATAAATGATAAGGAGGCAAACTATGCCATGGAAAGgtatttgtga ... cttattacagATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACT
EST: gi|110369077|gb|EC933222.1|EC933222
EST:     ATGTCTGCTGAGTTGATAAATGATAAGGAGGCAAACTATGCCATGGAAAG                         ATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACT
genomic: ATGTCTGCTGAGTTGATAAATGATAAGGAGGCAAACTATGCCATGGAAAGgtatttgtga ... cttattacagATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACT
EST: gi|110390115|gb|EC955006.1|EC955006
EST:     GTTGATAAATGATAAGGAGGCAAACTATGCCATGGAAAG                         ATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACT
genomic: GTTGATAAATGATAAGGAGGCAAACTATGCCATGGAAAGgtatttgtga ... cttattacagATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagtctcaatagttggtttttaattaatggttttatgcccttgtcttattacagATATGGAACCAAATTTATGGATGAGTATCAAGCTATAATGACCAGAAAACTTGGCCTGCCAAAGTATAATAAACAGTTGATCAGCAAACTTCTTAACAAT
                      aattaat  putative branch site (score: 3)
                                      cccttgtctt  putative PPT
                 tttttaattaatggtt  TA-rich tract