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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTCCCTCCAAACTCATGTCAAGGATTTGGCTCAAAAGTGCGCCGATGCCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgctgagctcacgtttctaattgtttttcattttttatccaaaaggtcggcgtttatcctgtcggacgtttgaactggttttcttgtagatgg...

Basic information

species Vitis vinifera
transcript Vv18s0001g11710.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g11710.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g31690.1 (Oryza sativa), 5'ss of exon 1
TTGCTCCCTCCAAACTCATGTCAAGGATTTGGCTCAAAAGTGCGCCGATGCCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgctgagctcacgtttctaattgtttttcatt-ttttatccaaaaggtcggcgtttatcctgtcggacgtttgaactggttttcttgtagatgg------------------
 |||||||| ||  |  |  ||  |||  | ||  | ||||||||||||||||||||| | ||||||||||| ||||||||||| ||  | || ||||||||| | |  || |  |    |||   | | | || |||      ||    |||| |   ||  |  |  ||| |    |  |   ||      ||  |||                   
GTGCTCCCTGCAGTCCGACATCCGGGAGGTCGCCAACAAGTGCGCCGATGCCGCCAAGCTCGCCGGCTTCGCCCTCGCCACCTCAGCTCTGCTCGTCTCGgtaagac--cttaattaggatttaggagtatgttgcatggcgccatggccaaggccaaggtggaaacgatcgaattactatatatgtaacgccgtgcatgtggtggccggccggtgtag

upper sequence: Vv18s0001g11710.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G113349_T01 (Zea mays), 5'ss of exon 1
TTGCTCCCTCCAAACTCATGTCAAGGATTTGGCTCAAAAGTGCGCCGATGCCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggct--gctgagctcacgtttctaattgtttttcattttttatccaaaaggtcggcgtttat-cctgtcggacgtttgaactggttttcttgtagatgg
 |||||||||||  |  | |||| |||  | ||    ||||||| ||| ||||||||| | ||||||||||| ||||||||||| ||  |||| ||||||||| |  |  | | |||   | ||   |      || |  ||    |      | ||  |    |   |  ||| |  |    ||  || |    | ||    
GTGCTCCCTCCAGTCCGACGTCAGGGACGTCGCCAGCAAGTGCGTCGACGCCGCCAAGCTCGCCGGCTTCGCGCTCGCCACCTCGGCGCTCCTCGTCTCGgtaagtataagataagcgtgcattatcagcaagcttacgcttacc-tgtgcctgctcctcaacaacgtcgatcgaagctgatgacacgtgtgtgcgcag----
















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|351038476|gb|FQ464342.1|FQ464342
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|32268321|gb|CD717480.1|CD717480
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|110690649|gb|EE067991.1|EE067991
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|110719792|gb|EE095231.1|EE095231
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71869812|gb|DT018867.1|DT018867
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|77586296|gb|DV222249.1|DV222249
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|110381024|gb|EC946332.1|EC946332
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|37190055|gb|CF609404.1|CF609404
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71871735|gb|DT020790.1|DT020790
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71876526|gb|DT025581.1|DT025581
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71876361|gb|DT025416.1|DT025416
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71877076|gb|DT026131.1|DT026131
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71867758|gb|DT016813.1|DT016813
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71866799|gb|DT015854.1|DT015854
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71868365|gb|DT017420.1|DT017420
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71875395|gb|DT024450.1|DT024450
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|110694000|gb|EE070721.1|EE070721
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|351043209|gb|FQ443930.1|FQ443930
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|110685685|gb|EE062619.1|EE062619
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|110685305|gb|EE063572.1|EE063572
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACACATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|77585002|gb|DV221585.1|DV221585
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|71877266|gb|DT026321.1|DT026321
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|110686534|gb|EE064278.1|EE064278
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|110711588|gb|EE088237.1|EE088237
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|77580600|gb|DV219202.1|DV219202
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|351025160|gb|FQ433577.1|FQ433577
EST:     CGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
genomic: CGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA
EST: gi|351034150|gb|FQ463084.1|FQ463084
EST:     CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCG                         GGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAGCATATGACGAAATCCAA
genomic: CCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgc ... taattaacagGGAGCAGGTGCTGAGGGAGTTCCGAAGCGGCTAACATATGACGAAATCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTCCCTCCAAACTCATGTCAAGGATTTGGCTCAAAAGTGCGCCGATGCCGCCAAGATTGCCGGCTTCGCTCTCGCCACCTCCGCCTTCCTTGTCTCGgtatggctgctgagctcacgtttctaattgtttttcattttttatccaaaaggtcggcgtttatcctgtcggacgtttgaactggttttcttgtagatgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaggt