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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaattcgagctttatattttttaacagtaattaatagtcatggtttctagtggttagctttggctgtggaaacctcgaattaatagtaactggggtttgactctaaatgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATTGCAGGATTAGCAGAATCAAAGAAGGAAAATGGAGTAGAATTGCTTGGCA

Basic information

species Vitis vinifera
transcript Vv14s0066g01410.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g01410.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 2
gtaagaaattcgagctttatattttttaacagtaattaatagtcatggtttctagtggttagctttggctgtggaaacctcgaattaatagtaactggggtttgactctaaatgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATTGCAGGATTAGCAGAATCAAAGAAGGAAAATGGAGTAGAATTGCTTGGCA
|||||| ||   || || |   || ||  |  |      |   |||||  | |  || ||   ||    |  |||             ||  || ||    || ||| || ||| | |||||||||||||||| |||||||||||||| ||||| || |||| ||||||| |  | || ||||| ||||||||||| ||| ||||||| ||| |||||  ||
gtaagacat--aagattaaagattcttgtctatgcggcttgtgcatgggattttatgtttcatttcccttaggga-------------taaaaattga---tttactttacatggaatgtagAATGTGAGGCAGGCGTCTCGAGCTCTGAAGCAAGGGAAGACTTTAATTGTATCTGGTTTAGCTGAATCAAAGAAAGAACATGGAGTTGAACTGCTTAACA

upper sequence: Vv14s0066g01410.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G01260.1 (Glycine max), 3'ss of exon 2
-----gtaagaaattcgagctttatattttttaacagta---attaatagtcatggtttctagtggttagctttggctgtggaaacctcgaattaatagtaactggggtttgactctaaatgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATTGCAGGATTAGCAGAATCAAAGAAGGAAAATGGAGTAGAATTGCTTGGCA
       |  | |||  || ||  | ||||||| | |||    |  || |||   ||  || |||  | |  ||   |||   |    |   |||    |||     | || ||| ||  || | |||||||||||||||| ||||||||| |||||||||| || |||| ||||||| |  | || ||||| ||||||||||| ||| |||| || ||| ||||| | |
gtaagacataagattaaagattcttgttttttatctgtagaagtgtattgtctatgtggcttgtgcatgggattttatgtttcatttccc--ttagggataaaaattgatttactttacgtggaatgtagAATGTGAGGCAGGCGTCTCGAACTCTCAAGCAAGGAAAGACTTTAATTGTATCCGGTTTAGCTGAATCAAAGAAAGAACATGGCGTTGAACTGCTTAGTA
















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|351015151|gb|FQ444440.1|FQ444440
EST:     GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGG                         AATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT
genomic: GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGGgtaagaaatt ... tgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT
EST: gi|110372810|gb|EC937002.1|EC937002
EST:     GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGG                         AATGTGAGGCAAGCG
genomic: GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGGgtaagaaatt ... tgaattgtagAATGTGAGGCAAGCG
EST: gi|351034441|gb|FQ463254.1|FQ463254
EST:     GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGG                         AATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT
genomic: GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGGgtaagaaatt ... tgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT
EST: gi|351013037|gb|FQ433764.1|FQ433764
EST:     GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGG                         AATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT
genomic: GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGGgtaagaaatt ... tgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT
EST: gi|349826215|gb|FQ416020.1|FQ416020
EST:     GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGG                         AATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT
genomic: GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGGgtaagaaatt ... tgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT
EST: gi|110395323|gb|EC960981.1|EC960981
EST:     GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGG                         AATGTGAGGCAAGCG
genomic: GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGGgtaagaaatt ... tgaattgtagAATGTGAGGCAAGCG
EST: gi|77580476|gb|DV219125.1|DV219125
EST:     GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGG                         AATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT
genomic: GTGAGAGTCTGAAGTTAGCTGGAGTCAAGGCACTCGACTCTGTTGAGAGGgtaagaaatt ... tgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgtggaaacctcgaattaatagtaactggggtttgactctaaatgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATTGCAGGATTAGCAGAATCAAAGAAGGAAAATGGAGTAGAATTGCTTGGCA
               aattaatagtaact  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaattcgagctttatattttttaacagtaattaatagtcatggtttctagtggttagctttggctgtggaaacctcgaattaatagtaactggggtttgactctaaatgaattgtagAATGTGAGGCAAGCGTCTCGAGCTCTCAAGCAGGGTAAGAGTTTAATTATTGCAGGATTAGCAGAATCAAAGAAGGAAAATGGAGTAGAATTGCTTGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA