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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttttctaaaaaaatgataataataaaattgggcgtttgtgtgagtgtttggtttgatttgatttgattgtgaatttagggttttgatttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAATTCAGTAACGAAGCCGCCACCGACGCCGTCTCCTCTGCGAAATTCTAAG

Basic information

species Vitis vinifera
transcript Vv13s0019g00840.t01
intron # 1
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|110700937|gb|EE078028.1|EE078028
EST:     GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
EST: gi|71860037|gb|DT009092.1|DT009092
EST:     CAAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: C-AAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
EST: gi|110703601|gb|EE080591.1|EE080591
EST:     GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
EST: gi|71863746|gb|DT012801.1|DT012801
EST:     GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
EST: gi|110357315|gb|EC920771.1|EC920771
EST:     GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
EST: gi|110721290|gb|EE098120.1|EE098120
EST:     GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
EST: gi|110727671|gb|EE104694.1|EE104694
EST:     GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
EST: gi|110692310|gb|EE071412.1|EE071412
EST:     GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
EST: gi|110356627|gb|EC919593.1|EC919593
EST:     GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
EST: gi|30299440|gb|CB976234.1|CB976234
EST:     GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTC                         CGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA
genomic: GCAAGCTTCATCATTGCTATTTTCTTCGTTCATTTCTCGTCTTCTCTCTCcggttggtac ... ttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgtttggtttgatttgatttgattgtgaatttagggttttgatttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAATTCAGTAACGAAGCCGCCACCGACGCCGTCTCCTCTGCGAAATTCTAAG
                                      ttttgat  putative branch site (score: 4)
                                            tttgtttt  CT-rich tract
                                      ttttgatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttttctaaaaaaatgataataataaaattgggcgtttgtgtgagtgtttggtttgatttgatttgattgtgaatttagggttttgatttgttttgttCGGATTGAAATAGAGTTCAATGGCGAAGGAAGTTTCCAATGGGGATCACAATTCAGTAACGAAGCCGCCACCGACGCCGTCTCCTCTGCGAAATTCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - -aaaaaaa
- - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - -tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - -tgtttgg