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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcatgctagttttgctattagtctaaatggttttatcacaaatgaggtatttatcgaacattttgaccgtagattaagaaatctatatctggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAATTCTTTGAGTTACCAGGTTTTGAGGAGCTAGTTCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g03070.t01
intron # 8
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|30125453|gb|CB910792.1|CB910792
EST:     GCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGGTCGG                         GTTGGAGAGTTGGAGGAGGCTGTATCATATGGAAGGACTAAATTGGCTAAA
genomic: GCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGGgtatatggtt ... tggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAA
EST: gi|30320437|gb|CD003699.1|CD003699
EST:     TTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGG                         GTTGGAGAGTTGGAGGAGGCTGTATCATATGGAAGGACTAAATTGGCTAAA
genomic: TTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGGgtatatggtt ... tggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAA
EST: gi|110428231|gb|EC994696.1|EC994696
EST:     CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGG                         GTTGGAGAGTTGGAGGAGGCTGTATCATATGGAAGGACTAAATTGGCTAAA
genomic: CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGGgtatatggtt ... tggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAA
EST: gi|110361320|gb|EC924786.1|EC924786
EST:     CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGG                         GTTGGAGAGTTGGAGGAGGCTGTATCATATGGAAGGACTAAATTGGCTAAA
genomic: CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGGgtatatggtt ... tggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAA
EST: gi|32270615|gb|CD719774.1|CD719774
EST:     CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGG                         GTTGGAGAGTTGGAGGAGGCTGTATCATATGGAAGGACTAAATTGGCTAAA
genomic: CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGGgtatatggtt ... tggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAA
EST: gi|110730262|gb|EE107138.1|EE107138
EST:     CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGG                         GTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAA
genomic: CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGGgtatatggtt ... tggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAA
EST: gi|77577816|gb|DV217661.1|DV217661
EST:     CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGG                         GCTGGAGAGTTGGAAGAGGCTGTATCATATGGAAGGACTAAATTGGCTAAA
genomic: CAGCTACTTGCTTTCTGCTTTACTGCCAAAAATTTATAGAACTAGTTCGGgtatatggtt ... tggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtatttatcgaacattttgaccgtagattaagaaatctatatctggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAATTCTTTGAGTTACCAGGTTTTGAGGAGCTAGTTCAG
                ttttgac  putative branch site (score: 3)
                            attaagaaatctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatgctagttttgctattagtctaaatggttttatcacaaatgaggtatttatcgaacattttgaccgtagattaagaaatctatatctggtgtgcagGTTGGAGAGTTGGAGGAGGCAGTATCATATGGAAGGACTAAATTGGCTAAATTCTTTGAGTTACCAGGTTTTGAGGAGCTAGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
-tcatgct
- - - - - - - - - - - - - - - - - - -cacaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaat