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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagagcgcaaaaatctcatatgttggtctattgttttggttctttctctcatattgtttttcattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTGGATGAAGAGGAAGCTAACAACAAGCTTGGCCTCCTAAAG

Basic information

species Vitis vinifera
transcript Vv04s0008g01770.t01
intron # 2
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|351013093|gb|FQ433820.1|FQ433820
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|349823575|gb|FQ414985.1|FQ414985
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351025083|gb|FQ433500.1|FQ433500
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351043372|gb|FQ451424.1|FQ451424
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACATTTGCATATGAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351017918|gb|FQ439084.1|FQ439084
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACATTTGCATATGAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351027426|gb|FQ444675.1|FQ444675
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACATTTGCATATGAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351022289|gb|FQ445064.1|FQ445064
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACATTTGCATATGAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|349829060|gb|FQ419592.1|FQ419592
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACATTTGCATATGAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351024208|gb|FQ423631.1|FQ423631
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351031099|gb|FQ444926.1|FQ444926
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|349823831|gb|FQ415242.1|FQ415242
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351029729|gb|FQ427569.1|FQ427569
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|32270228|gb|CD719387.1|CD719387
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|349832423|gb|FQ420984.1|FQ420984
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351041469|gb|FQ431495.1|FQ431495
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351049033|gb|FQ431577.1|FQ431577
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|32269003|gb|CD718162.1|CD718162
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351014460|gb|FQ437462.1|FQ437462
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351014516|gb|FQ437518.1|FQ437518
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351024758|gb|FQ430583.1|FQ430583
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351027302|gb|FQ444551.1|FQ444551
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351021803|gb|FQ437188.1|FQ437188
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351016245|gb|FQ446105.1|FQ446105
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTTAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|32268551|gb|CD717710.1|CD717710
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351027563|gb|FQ446726.1|FQ446726
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGGATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTTAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|351019064|gb|FQ426563.1|FQ426563
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACATTTGCATATGAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|349826520|gb|FQ418611.1|FQ418611
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
EST: gi|349829990|gb|FQ420250.1|FQ420250
EST:     CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAA                         GTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG
genomic: CAGATCACTACGGCAGACTTGGACTTCAGAGAGAATGCTCATACGATCAAgtcagagcgc ... cattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgttggtctattgttttggttctttctctcatattgtttttcattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTGGATGAAGAGGAAGCTAACAACAAGCTTGGCCTCCTAAAG
                       ttctttctctcatatt  CT-rich tract
                                  atattgtttttcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagagcgcaaaaatctcatatgttggtctattgttttggttctttctctcatattgtttttcattactcagGTTACAGTTGCATATAAGAGAAAGGTTGAAGAACTGAAGAGTCAGGAATTGGATGAAGAGGAAGCTAACAACAAGCTTGGCCTCCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT