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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcctaatttttcagatttacttttatgggaaatatcttattggtagtgtgatgtgcaactagtttgttttcatgaatgttgaatgaaagcattggagcatttttggttgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTGAAGTGTGATTTGACTGAAAATCTCACTCTGAAGGCTAATGCTCAG

Basic information

species Vitis vinifera
transcript Vv03s0097g00590.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G05280.1 (Glycine max), 3'ss of exon 3
gtaggcctaatttttcagatttacttttatgggaaatatcttattggtagtgtgatgtgcaactagtttgttttcatgaatgttgaatgaaagcattggagcat-ttttggttgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTGAAGTGTGATTTGACTGAAAATCTCACTCTGAAGGCTAATGCTCAG
                |  ||    || ||   ||    |||   | | ||||| ||||    |  ||| |||  ||  || |  |  |   |  ||  |  ||  |   | ||||   |||||| |||| |  |||||||| ||||| || |||||||| ||||| ||||| |||||||||||| | |||||||||||| | || || |||||||||
--------------gtaacttggacttcatttaaatgccctttcagtttgtgtg-tgtgtgttttttttctttatatatatatatagcgtgcgttttcaatgatgctgctgctgctctgcagTTGTTGCTCTGGGGGAGAATTTTGACTGATGGGAGGCTCAATGCCAGAGTCAAGTGTGATTTGTCCGAAAATCTCACTTTTAAAGCCAATGCTCAG

upper sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G34360.3 (Glycine max), 3'ss of exon 3
gtaggcctaatttttcagatttacttttatgggaaatatcttattggtagtgtgatgtgcaactagtttgttttcatgaatgttgaatgaaagcattggagcatttttggttgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTGAAGTGTGATTTGACTGAAAATCTCACTCTGAAGGCTAATGCTCAG
                                              |||   ||   | ||   |  | |  ||  | | | |||  |      ||||  | ||  |  | |  |   |||||| |||| |  || ||||| ||||| || |||||||| ||||| ||||| |||||||||||| | |||||||||||| | || || |||||||||
----------------------------------------------gtaacttggacttcattcaaatggcctt--tcagt-ttgtgtttttttattgatg-atgat--gcttttctgcagttgttgctctggggcagAATTTTGACTGATGGGAGGCTCAATGCCAGAGTCAAGTGTGATTTGTCCGAAAATCTCACTTTTAAAGCCAATGCTCAG
















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|56409330|gb|CX017582.1|CX017582
EST:     AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAG                         TTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
genomic: AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAGgtaggcctaa ... tgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
EST: gi|110687534|gb|EE065054.1|EE065054
EST:     AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAG                         TTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
genomic: AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAGgtaggcctaa ... tgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
EST: gi|110730004|gb|EE106584.1|EE106584
EST:     AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAG                         TTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
genomic: AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAGgtaggcctaa ... tgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
EST: gi|352765106|gb|FQ465803.1|FQ465803
EST:     AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAG                         TTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
genomic: AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAGgtaggcctaa ... tgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
EST: gi|110698670|gb|EE076432.1|EE076432
EST:     AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAG                         TTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
genomic: AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAGgtaggcctaa ... tgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
EST: gi|110686396|gb|EE063988.1|EE063988
EST:     AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAG                         TTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
genomic: AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAGgtaggcctaa ... tgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
EST: gi|351046106|gb|FQ442484.1|FQ442484
EST:     AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAG                         TTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG
genomic: AAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAGgtaggcctaa ... tgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttttcatgaatgttgaatgaaagcattggagcatttttggttgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTGAAGTGTGATTTGACTGAAAATCTCACTCTGAAGGCTAATGCTCAG
                                    attttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcctaatttttcagatttacttttatgggaaatatcttattggtagtgtgatgtgcaactagtttgttttcatgaatgttgaatgaaagcattggagcatttttggttgcttaacagTTGATGCTTTTTGGGAGAATATTGACCGACGGGAGGCTGAATGCAAGAGTGAAGTGTGATTTGACTGAAAATCTCACTCTGAAGGCTAATGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG