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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcacacaccatttttccttatagatactgtaaatggctttgaaagtactaattgggtccatgtgactttttctttgctgtatttatgttgtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAATGGTGCCTTTGCATGGGAAATAATTCCG

Basic information

species Vitis vinifera
transcript Vv00s0531g00050.t01
intron # 5
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|77584049|gb|DV221063.1|DV221063
EST:     TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAG                         GATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
genomic: TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAGgtagtagtct ... gtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
EST: gi|77586184|gb|DV222186.1|DV222186
EST:     TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAG                         GATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
genomic: TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAGgtagtagtct ... gtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
EST: gi|37190107|gb|CF609456.1|CF609456
EST:     TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACAAGAGAAGAACAG                         GATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
genomic: TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAGgtagtagtct ... gtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
EST: gi|71877133|gb|DT026188.1|DT026188
EST:     TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAG                         GATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
genomic: TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAGgtagtagtct ... gtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
EST: gi|110376548|gb|EC941608.1|EC941608
EST:     TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAG                         GATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
genomic: TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAGgtagtagtct ... gtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
EST: gi|37186247|gb|CF605600.1|CF605600
EST:     TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAG                         GATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAA
genomic: TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAGgtagtagtct ... gtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAA
EST: gi|110395476|gb|EC961142.1|EC961142
EST:     TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAG                         GATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
genomic: TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAGgtagtagtct ... gtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
EST: gi|110361851|gb|EC925352.1|EC925352
EST:     TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAG                         GATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT
genomic: TTTGTGCAGAAATATGTGCTGATCAGCATACGATAACGAGAGAAGAACAGgtagtagtct ... gtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactaattgggtccatgtgactttttctttgctgtatttatgttgtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAATGGTGCCTTTGCATGGGAAATAATTCCG
 tactaat  putative branch site (score: 1)
                                           ttgtctct  putative PPT
                                   tatttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcacacaccatttttccttatagatactgtaaatggctttgaaagtactaattgggtccatgtgactttttctttgctgtatttatgttgtctctgcagGATTCTTACTCTATCCAGAGTTTTGAGCGTGGTATTTCTGCACAAAATAATGGTGCCTTTGCATGGGAAATAATTCCG

-tcacaca
- - - - ccatttt
- - - - - - - - - - - - - - - - aatggct
- - - - - - - - - - - - - - - - - - - - -gaaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtga