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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGCCTTTATGAGGGCTTGGACTGGTTAGCCGGAACTCTCAAGGAATTAAGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactcctccaacttcagttgggaaagcaaccattttttcagtttcttctgttcttaatgattttcctcctgcag

Basic information

species Vitis vinifera
transcript Vv16s0039g02240.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G02110.1 (Glycine max), 5'ss of exon 6
ATGGCCTTTATGAGGGCTTGGACTGGTTAGCCGGAACTCTCAAGGAATTAAGAGCCGCTGGATACTCCTCAGTGGG------CACTTCATCCTTCTAACCAACCAGgtcaaaact--cctccaacttcagttgggaaagcaaccattttttcagtttcttctgttcttaatgattttcctc--ctgcag
      ||||||||||||||||||||||  ||  |||||| |||||   |||||| ||||||||||| ||| | ||      ||||||||||||||||    | ||||   ||||  | ||  | |||| |   ||  || ||| |  | |   |     |  | | | ||   ||| |||  ||||||
------TTTATGAGGGCTTGGACTGGTTGTCCACAACTCTGAAGGAGAGAAGAGCTGCTGGATACTCTTCAATAGGACTAGGCACTTCATCCTTCTAATTTTCAAGgtttgaactatcatcttatttcaatcacga--gctaccttcatgtttatcatcccattacattataggttttctccgctgcag
















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|26264563|gb|CA815626.1|CA815626
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|30296696|gb|CB973490.1|CB973490
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|71879757|gb|DT028812.1|DT028812
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|71880432|gb|DT029487.1|DT029487
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|71878380|gb|DT027435.1|DT027435
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|71880637|gb|DT029692.1|DT029692
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|110430069|gb|EC996597.1|EC996597
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|30133341|gb|CB918680.1|CB918680
EST:     CTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: CTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|110716367|gb|EE091287.1|EE091287
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|71880723|gb|DT029778.1|DT029778
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGC
EST: gi|33409512|gb|CF215139.1|CF215139
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|110729888|gb|EE106340.1|EE106340
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCANAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|71879383|gb|DT028438.1|DT028438
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCA
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCA
EST: gi|351036486|gb|FQ457199.1|FQ457199
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
EST: gi|110375930|gb|EC940960.1|EC940960
EST:     AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAG                         GACTTTCGAGGCTCTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC
genomic: AGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactc ... cctcctgcagGACTTTCGAGGCTTTAAGTTGGCTGATGGATGAAGCTGCAGAATTGGGCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGCCTTTATGAGGGCTTGGACTGGTTAGCCGGAACTCTCAAGGAATTAAGAGCCGCTGGATACTCCTCAGTGGGCACTTCATCCTTCTAACCAACCAGgtcaaaactcctccaacttcagttgggaaagcaaccattttttcagtttcttctgttcttaatgattttcctcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC