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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcaaatattctttttcttcgtattttcggtttcatctagtttctaatgtatgaaactgcatcaaaatttgatggatgattaattttgtttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGTTTATCTGAAGCTAGTGTAGACACAATAAGGAGAGCCCATGCAGTTCATC

Basic information

species Vitis vinifera
transcript Vv05s0020g04130.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|33408926|gb|CF214553.1|CF214553
EST:     ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATTCA                         ATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
genomic: ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATACAgtgagtatca ... tttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
EST: gi|32458980|gb|CD800154.1|CD800154
EST:     CTGTACTATCAGCATCGCGTGTGGACATGTCAGTCCCAATAGAGGATACA                         ATGGAGGAACTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
genomic: CTTTACTATCAGCAT--CGTGTGGACATGTCAGTCCCAATAGAGGATACAgtgagtatca ... tttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
EST: gi|30254501|gb|CB971246.1|CB971246
EST:     ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATTCA                         ATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
genomic: ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATACAgtgagtatca ... tttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
EST: gi|110712082|gb|EE089299.1|EE089299
EST:     ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATACA                         ATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
genomic: ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATACAgtgagtatca ... tttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
EST: gi|33407206|gb|CF212833.1|CF212833
EST:     ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATTCA                         ATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
genomic: ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATACAgtgagtatca ... tttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
EST: gi|33406944|gb|CF212571.1|CF212571
EST:     ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATTCA                         ATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
genomic: ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATACAgtgagtatca ... tttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
EST: gi|110373812|gb|EC938182.1|EC938182
EST:     ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATTCA                         ATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
genomic: ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATACAgtgagtatca ... tttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
EST: gi|30254500|gb|CB971245.1|CB971245
EST:     ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATTCA                         ATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT
genomic: ACCTTTACTATCAGCATCGTGTGGACATGTCAGTCCCAATAGAGGATACAgtgagtatca ... tttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatgtatgaaactgcatcaaaatttgatggatgattaattttgtttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGTTTATCTGAAGCTAGTGTAGACACAATAAGGAGAGCCCATGCAGTTCATC
                                        ttttgttt  CT-rich tract
                                atgattaattttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatcaaatattctttttcttcgtattttcggtttcatctagtttctaatgtatgaaactgcatcaaaatttgatggatgattaattttgtttgatttagATGGAGGAGCTTAAGAAGTTGGTGGAGGAGGGAAAGATAAAATACATCGGTTTATCTGAAGCTAGTGTAGACACAATAAGGAGAGCCCATGCAGTTCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA