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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtattccaagtttttgattagctttccatgtattgatggtgctgtgcttacaaccatgaaaatcttctttagAACCCAGAGAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTGGTATCTTTTGGTTTTGCCGGACAAGGTCGTGCAATAATGCGAGGTCCAA

Basic information

species Vitis vinifera
transcript Vv11s0016g04250.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g52170.1 (Oryza sativa), 3'ss of exon 6
gtagtattccaagtttttgatta-gctttccatgtattgatggtgctgtgcttacaaccatgaaaatctt---ctttagAACCCAGAGAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTGGTATCTTTTGGTTTTGCCGGACAAGGTCGTGCAATAATGCGAGGTCCAA
   |||  |  | |   | |||  | |  | |   |||  ||||  ||  || | ||   | || |  ||   |||||||||||||| |  ||||| ||  ||||||| ||||| ||||| |||||| |||| |||||||| ||||| ||||||||  | || |||||||| |||||||
---gtaagctgattgaataattgtgttaacaaaaaattagtggt--tgcactaataatggtaaacagatttacctttagAACCCAGAAAGCAGAAGTATTCTTCCAACCGAGTATTTGGGCGTCAAGATGGTGTCTTTTGGCTTTGCTGGACAAGGAAGAGCTATAATGCGTGGTCCAA

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G31980.1 (Glycine max), 3'ss of exon 6
--gtagtattccaag---tttttgattagctttccatgtattgatggtgctgtgcttacaaccatg-aaaatctt-ctttagAACCCAGAGAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTGGTATCTTTTGGTTTTGCCGGACAAGGTCGTGCAATAATGCGAGGTCCAA
   |  | |   ||    |||||  |||   ||   |  |||||  || ||||    | ||   |  | | |||| ||  |||| ||||||||||  | ||||||||||||||| ||||||||||| ||| || | |||||||| ||||| |||||||| |||||||||||||| || || |
gtatgatctgataaaccatttttttttaatatttagttgattga--gtactgtaaacataattgttcagagtcttgctgcagAATCCAGAGAAGAAGACCATAATTCCAACTGAATACTTGGGAGTGAAGTTGATCTCTTTTGGATTTGCTGGACAAGGACGTGCAATAATGCGTGGCCCCA

upper sequence: Vv11s0016g04250.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G09820.1 (Glycine max), 3'ss of exon 6
-------gtagtattccaagtttttgatt--agctttccatgtattgatggtgctgtgcttacaaccatgaaaatctt--ctttagAACCCAGAGAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTGGTATCTTTTGGTTTTGCCGGACAAGGTCGTGCAATAATGCGAGGTCCAA
        |  ||  |||| |||||  ||  |   ||   |  |||||  || |||     | ||   |  | ||  |  ||  |||| ||||||||||  | ||||||||| ||||| ||||||||||| ||| || | |||||||| ||||| |||||||| |||||||||||||| || || |
gtatgatctgataaaccaattttttctttttaatatttagttgattga--gtactgcaaacataattgttcagattcttgctgcagAATCCAGAGAAGAAGACCATAATTCCTACTGAATACTTGGGAGTAAAGTTGATCTCTTTTGGATTTGCTGGACAAGGACGTGCAATAATGCGTGGCCCCA

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|352773640|gb|FQ472422.1|FQ472422
EST:     GTCCAAGTTTACCAACAATGGTCTCCCCTGAAAATAGGCTGCTAGAAATG                         AACCCAGAAAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTG
genomic: GTCCAAGTTTACCAACAATGGTCTCCCCTGAAAATAGGCTGCTAGAAATGgtagtattcc ... tcttctttagAACCCAGAGAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTG
EST: gi|110718478|gb|EE095359.1|EE095359
EST:     GTCCAAGTTTACCAACAATGGTCTCCCCTGAAAATAGGCTGCTAGAAATG                         AACCCAGAGAAGAGAA-CATAATTCCAACTGAGTACTTGGGAGTCAAGCTG
genomic: GTCCAAGTTTACCAACAATGGTCTCCCCTGAAAATAGGCTGCTAGAAATGgtagtattcc ... tcttctttagAACCCAGAGAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTG
EST: gi|294966635|gb|GW839626.1|GW839626
EST:     GTCCAAGTTTACCAACAATGGTCTCCCCTGAAAATAGGCTGCTAGAAATG                         AACCCAGAGAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTG
genomic: GTCCAAGTTTACCAACAATGGTCTCCCCTGAAAATAGGCTGCTAGAAATGgtagtattcc ... tcttctttagAACCCAGAGAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagctttccatgtattgatggtgctgtgcttacaaccatgaaaatcttctttagAACCCAGAGAAGAGAAGCATAATTCCAACTGAGTACTTGGGAGTCAAGCTGGTATCTTTTGGTTTTGCCGGACAAGGTCGTGCAATAATGCGAGGTCCAA
                           tgcttac  putative branch site (score: 2)
                                             tcttcttt  putative PPT
                                      atgaaaat  TA-rich tract