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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacttctaagcttaattaatggacctacaagcattatcatgatcaaatttgatggacttgccttgctctgactgaattacatgtgttctctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGATAGTCTTCTATCCTGTTTATATTAATTCAAAAAAGACGATAGCTGAGGGG

Basic information

species Vitis vinifera
transcript Vv05s0020g00570.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|77580101|gb|DV218940.1|DV218940
EST:     CGCGATCTCTCTCCATATCTTGCCGGCGCCGATCTCTATTATCGCCTCAG                         GATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
genomic: CGCGATCTCTCTCCATATCTCGCCGGCGCCAATCTCTATTATCGCCTCAGgtcagtaatc ... ctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
EST: gi|71868537|gb|DT017592.1|DT017592
EST:     CGCGATCTCTCTCCATATCTTGCCGGCGCCGATCTCTATTATCGCCTCAG                         GATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
genomic: CGCGATCTCTCTCCATATCTCGCCGGCGCCAATCTCTATTATCGCCTCAGgtcagtaatc ... ctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
EST: gi|77586586|gb|DV222418.1|DV222418
EST:     CGCGATCTCTCTCCATATCTTGCCGGCGCCGATCTCTATTATCGCCTCAG                         GATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
genomic: CGCGATCTCTCTCCATATCTCGCCGGCGCCAATCTCTATTATCGCCTCAGgtcagtaatc ... ctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
EST: gi|22008948|gb|BQ793982.1|BQ793982
EST:     ATCTTGCCGGCGCCGATCTCTATTATCGCCTCAG                         GATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
genomic: ATCTCGCCGGCGCCAATCTCTATTATCGCCTCAGgtcagtaatc ... ctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
EST: gi|110375143|gb|EC940104.1|EC940104
EST:     ATCTCTATTATCGCCTCAG                         GATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
genomic: ATCTCTATTATCGCCTCAGgtcagtaatc ... ctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
EST: gi|110416251|gb|EC982219.1|EC982219
EST:     CGCGATCTCTCTCCATATCTTGCCGGCGCCGATCTCTATTATCGCCTCAG                         GATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
genomic: CGCGATCTCTCTCCATATCTCGCCGGCGCCAATCTCTATTATCGCCTCAGgtcagtaatc ... ctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
EST: gi|110407038|gb|EC972629.1|EC972629
EST:     GCGATCTCTCTCCATATCTTGCCGGCGCCGATCTCTATTATCGCCTCAG                         GATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
genomic: GCGATCTCTCTCCATATCTCGCCGGCGCCAATCTCTATTATCGCCTCAGgtcagtaatc ... ctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
EST: gi|110385463|gb|EC949995.1|EC949995
EST:     TCTCCATATCTTGCCGGCGCCGATCTCTATTATCGCCTCAG                         GATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT
genomic: TCTCCATATCTCGCCGGCGCCAATCTCTATTATCGCCTCAGgtcagtaatc ... ctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatttgatggacttgccttgctctgactgaattacatgtgttctctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGATAGTCTTCTATCCTGTTTATATTAATTCAAAAAAGACGATAGCTGAGGGG
                     ctctgac  putative branch site (score: 3)
                                       tgttctct  putative PPT
                              aattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atacttctaagcttaattaatggacctacaagcattatcatgatcaaatttgatggacttgccttgctctgactgaattacatgtgttctctatacatagGATACTGATTGGAGACATGGATGGAGAAGTCCCAAATATAAAGAAGTGGATAGTCTTCTATCCTGTTTATATTAATTCAAAAAAGACGATAGCTGAGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - -acaagca
- - - - - - - - - - - - - - - - - - - catgatc
- - - - - - - - - - - - - - - - - - - - - - - - - tgatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgt