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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagttcatgagatgttatgtttaggctcttatgtgatacttctgaaattggaaattttgattggaagaaattgttatatattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG

Basic information

species Vitis vinifera
transcript Vv12s0142g00360.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|110728991|gb|EE105103.1|EE105103
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
EST: gi|110726323|gb|EE102002.1|EE102002
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
EST: gi|110715529|gb|EE093682.1|EE093682
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
EST: gi|110730325|gb|EE107273.1|EE107273
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
EST: gi|30298144|gb|CB974938.1|CB974938
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
EST: gi|30135782|gb|CB921120.1|CB921120
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
EST: gi|110710338|gb|EE086596.1|EE086596
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
EST: gi|30133145|gb|CB918484.1|CB918484
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
EST: gi|30298778|gb|CB975572.1|CB975572
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCCCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
EST: gi|110726263|gb|EE101892.1|EE101892
EST:     GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAG                         GCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA
genomic: GAAGCCTCCAAATTGCGCCGTCAAATCAGGGATATACAGAATTTGAACAGgtaaagttca ... atattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatacttctgaaattggaaattttgattggaagaaattgttatatattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG
                      ttttgat  putative branch site (score: 4)
                                              tattttc  putative PPT
                                aagaaattgttatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagttcatgagatgttatgtttaggctcttatgtgatacttctgaaattggaaattttgattggaagaaattgttatatattttcagGCATATTCTGGGTGAGGCTCTTAGCTCTCTGAACTTTAAGGAACTCAAGAATCTGGAGACCAGGTTGGAGAAAGGTATCAGCAGAATCAGATCCAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA