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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttggataaattcatacctattcagactacagacgagaaaacaaacccaagctaattaagtttctgcaggatcatgaactgacttccaaatatttgcagGCGTAGACTTCACGAATGCGGTTCTGGACCGGGTGAATTTTGGGAAGGCCAATCTCCAAGGAGCTGTGTTCAAGAACACTGTATTATCAGGCTCCACCTT

Basic information

species Vitis vinifera
transcript Vv16s0098g01540.t01
intron # 3
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|110694090|gb|EE070894.1|EE070894
EST:     GTCCGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAG                         GTGTAGACTTCACGAATGCAGTTCTGGACCGGGTGAATTTTGGGAAGGCCA
genomic: GTCCGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAGgtaagtaggt ... atatttgcagGCGTAGACTTCACGAATGCGGTTCTGGACCGGGTGAATTTTGGGAAGGCCA
EST: gi|349828381|gb|FQ416334.1|FQ416334
EST:     GTCGGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAG                         GTGTAGACTTCACGAATGCAGTTCTGGACCGGGTGAATTTTGGGAAGGCCA
genomic: GTCCGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAGgtaagtaggt ... atatttgcagGCGTAGACTTCACGAATGCGGTTCTGGACCGGGTGAATTTTGGGAAGGCCA
EST: gi|351044239|gb|FQ447593.1|FQ447593
EST:     GTCCGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAG                         GCGTAGACTTCACGAATGCGGTTCTGGACCGGGTGAATTTTGGGAAGGCCA
genomic: GTCCGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAGgtaagtaggt ... atatttgcagGCGTAGACTTCACGAATGCGGTTCTGGACCGGGTGAATTTTGGGAAGGCCA
EST: gi|349821222|gb|FQ408809.1|FQ408809
EST:     GTCGGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAG                         GTGTAGACTTCACGAATGCAGTTCTGGACCGGGTGAATTTTGGGAAGGCCA
genomic: GTCCGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAGgtaagtaggt ... atatttgcagGCGTAGACTTCACGAATGCGGTTCTGGACCGGGTGAATTTTGGGAAGGCCA
EST: gi|18458877|gb|BM437155.1|BM437155
EST:     GTCGGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAG                         GTGTAGACTTCACGAATGCAGTTCTGGACCGGGTGAATTTTGGGAAGGCCA
genomic: GTCCGAGGTAGTGATGTCAAAGGCTTATGCCGTTGGAGCCAGCTTCAAAGgtaagtaggt ... atatttgcagGCGTAGACTTCACGAATGCGGTTCTGGACCGGGTGAATTTTGGGAAGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccaagctaattaagtttctgcaggatcatgaactgacttccaaatatttgcagGCGTAGACTTCACGAATGCGGTTCTGGACCGGGTGAATTTTGGGAAGGCCAATCTCCAAGGAGCTGTGTTCAAGAACACTGTATTATCAGGCTCCACCTT
                                aactgac  putative branch site (score: 2)
        taattaagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttggataaattcatacctattcagactacagacgagaaaacaaacccaagctaattaagtttctgcaggatcatgaactgacttccaaatatttgcagGCGTAGACTTCACGAATGCGGTTCTGGACCGGGTGAATTTTGGGAAGGCCAATCTCCAAGGAGCTGTGTTCAAGAACACTGTATTATCAGGCTCCACCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - ggataaa
- - - - - - -catacct
- - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - cccaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttccaa