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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attacaattctctcgaccctttcattatgtgatagctttaattccttaagcatcaataatatggctatgcatttgataaaacatgttttgcaaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAGGCTAAACAAGAACCCCTGAAGACATTCACACCAGGTGAAATGCCAAATG

Basic information

species Vitis vinifera
transcript Vv01s0150g00590.t01
intron # 4
splice site 3'
intron type U2

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|110712685|gb|EE087945.1|EE087945
EST:     ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAG                         GAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
genomic: ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAGgtgaggttgt ... caaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
EST: gi|110710820|gb|EE087309.1|EE087309
EST:     ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAG                         GAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
genomic: ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAGgtgaggttgt ... caaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
EST: gi|110707870|gb|EE084759.1|EE084759
EST:     ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAG                         GAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
genomic: ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAGgtgaggttgt ... caaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
EST: gi|32269037|gb|CD718196.1|CD718196
EST:     ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAG                         GAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
genomic: ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAGgtgaggttgt ... caaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
EST: gi|110701540|gb|EE079224.1|EE079224
EST:     ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAG                         GAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
genomic: ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAGgtgaggttgt ... caaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
EST: gi|161714413|gb|FC064424.1|FC064424
EST:     ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAG                         GAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
genomic: ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAGgtgaggttgt ... caaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
EST: gi|110702872|gb|EE079225.1|EE079225
EST:     ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAG                         GAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG
genomic: ACAGACTAAAGTCACTTCGGTTGCTAGATTTCAAGAAAGTAAAAAATAAGgtgaggttgt ... caaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagcatcaataatatggctatgcatttgataaaacatgttttgcaaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAGGCTAAACAAGAACCCCTGAAGACATTCACACCAGGTGAAATGCCAAATG
                         atttgat  putative branch site (score: 5)
                         atttgataaaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attacaattctctcgaccctttcattatgtgatagctttaattccttaagcatcaataatatggctatgcatttgataaaacatgttttgcaaattatagGAGAGACTGGAAGCAGAGAATTTGTTTGCATCTAAAGAAGTTGAAGAAGAGGCTAAACAAGAACCCCTGAAGACATTCACACCAGGTGAAATGCCAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - ccctttc
- - - - - - - - - - - - - - - - - - - - - - - - -gcatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttt