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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGATGAGGGGAAGAATCCTGATGAATTCACGAGGGATGTTTTGAATAGCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttctaactctatttccagttgatgtcatgagaattctgagcttccagatttcatcaatgaggataattctatttacctttcccctttatatttta...

Basic information

species Vitis vinifera
transcript Vv02s0025g02580.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02580.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G110500_T02 (Zea mays), 5'ss of exon 3
AATTGATGAGGGGAAGAATCCTGATGAATTCACGAGGGATGTTTTGAATAGCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttctaactctatttccagttgatgtcatgagaattctgagcttccagatttcatcaa--tgaggataattctatttacctttcccctttatatttta-
 || || || |||||||| || || || || || ||||||||  | || ||||||||||| ||||| ||||||||||| ||||| || ||| | |||||||||   |  |||| |   | || | |||    | |    |   |||     | |  |||  |  ||  |   | |     |||   |   | |   || |   
GATCGACGATGGGAAGAACCCCGACGAGTTTACTAGGGATGTGCTCAACAGCTGCATTGCCAAGAACCAGATCACCAAGGGCAAGACTGACGCTTTCAAGgta---tggaactatggatgcattggattctctcaatcattgcagcgattggttgacatggagctgctgggtacttaggatacacattttcatacgatgtaga

upper sequence: Vv02s0025g02580.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G16280.1 (Glycine max), 5'ss of exon 5
AATTGATGAGGGGAAGAATCCTGATGAATTCACGAGGGATGTTTTGAATAGCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttctaactct--atttccagttgatgtca----------tgagaattctgagcttcc---agatttcatcaatgaggataattctatttacctttcccctttatatttta
||||||||| || |||||||| || ||||| || |  |||||| | || ||||| |||||||||||||||||||||||||| ||||| ||  | || |||||    ||| | |||  |||| || | ||| | |          |   | || ||   ||||   | |||| || |       || | | | ||| | || |  |||        
AATTGATGATGGAAAGAATCCAGACGAATTTACCAAAGATGTTATAAACAGCTGTATTGCAAAGAATCAGATCACCAAAGGAAAAACTGATGCTTTAAAGgtctaatcttattcttgattttcattagatatgaatttctttgtttccagttttgtctttcccatatatttaataagaagctttagtccaacttagcatttctgtttgggcag--

upper sequence: Vv02s0025g02580.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA08G40780.1 (Glycine max), 5'ss of exon 6
AATTGATGAGGGGAAGAATCCTGATGAATTCACGAGGGATGTTTTGAATAGCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttctaactct--atttccagttgatgtcatgagaattctgagcttccagatttcatcaatgaggataattctatttacctttcccctttatatttta
||||||||| || |||||||| || || || || |  |||||| | |||||||| |||| ||||||||||||||||||||| ||||| ||  | || ||||||  |||| | |||  |||| |  |  || | |    | ||||  | |||||| |||   |       ||| ||  | |||   || |  | |        
AATTGATGATGGAAAGAATCCAGACGAGTTTACCAAAGATGTTATAAATAGCTGTATTGTAAAGAATCAGATCACCAAAGGAAAAACTGATGCTTTAAAGgtatattcttattcttgattttcgttacatatga----atttctttgtttccag-ttttgccttcccttata-tttaacttagtgtttctgtgtgggcag--

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|349827410|gb|FQ421683.1|FQ421683
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|351016885|gb|FQ424312.1|FQ424312
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|110733138|gb|EE109065.1|EE109065
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAAGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|349828426|gb|FQ417168.1|FQ417168
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|30256282|gb|CB972125.1|CB972125
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|351041206|gb|FQ444183.1|FQ444183
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|30256348|gb|CB972191.1|CB972191
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|71890691|gb|DT039746.1|DT039746
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|110390771|gb|EC955698.1|EC955698
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|110407439|gb|EC973039.1|EC973039
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|351043055|gb|FQ443897.1|FQ443897
EST:     GCTGCATTGCAAAGAATCAGACCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|110403992|gb|EC969905.1|EC969905
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|110397387|gb|EC963122.1|EC963122
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|30134136|gb|CB919474.1|CB919474
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|30298115|gb|CB974909.1|CB974909
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|30130763|gb|CB916102.1|CB916102
EST:     CTGCATTGCAAAGAATCAGATCACCAAAGGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGA-CTTGAGCAAGCATTTCCTGA
genomic: CTGCATTGCAAAGAATCAGATCACCAAAGG-CAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGA
EST: gi|110394418|gb|EC959344.1|EC959344
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|26264389|gb|CA815452.1|CA815452
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
EST: gi|110381900|gb|EC937958.1|EC937958
EST:     GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAG                         GGTTTACGCAGACATTTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA
genomic: GCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttcta ... ttctgtgcagGGTTTACGCAGACATCTCTTGGAGGAACTTGAGCAAGCATTTCCTGATGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTGATGAGGGGAAGAATCCTGATGAATTCACGAGGGATGTTTTGAATAGCTGCATTGCAAAGAATCAGATCACCAAAGGCAAAACGGACTCCTTCAAGgtagtttctaactctatttccagttgatgtcatgagaattctgagcttccagatttcatcaatgaggataattctatttacctttcccctttatatttta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttccc