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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtcatgatttttatacttcgtaatccaatgccagtacgcaggtttcaatttcttgcttgcttgcttgcttcacctgcaattaatctaatggaggtttttttttttttttttgggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGATGTCCACTTCTGTAGTTTATCATGCTCCTCTCTTCCCCCTATATCTTTGT

Basic information

species Vitis vinifera
transcript Vv18s0001g12960.t01
intron # 11
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|32245576|gb|CD711395.1|CD711395
EST:     GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAG                         TTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAG
genomic: GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAGgcatgtcatg ... ggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAT
EST: gi|45770383|gb|CN006235.1|CN006235
EST:     GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAG                         TTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAG
genomic: GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAGgcatgtcatg ... ggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAT
EST: gi|22007151|gb|BQ792185.1|BQ792185
EST:     GGCGGGACAAACTCACCCAATTTCGTTTTAAGAGGAACTGGACATAACAG                         TTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAG
genomic: GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAGgcatgtcatg ... ggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAT
EST: gi|26261297|gb|CA812360.1|CA812360
EST:     GGCGGGACAAACTCACCCAATTTCGTTTTAAGAGGAACTGGACATAACAG                         TTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAG
genomic: GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAGgcatgtcatg ... ggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAT
EST: gi|254915447|gb|GR904878.1|GR904878
EST:     GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAG                         TTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAG
genomic: GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAGgcatgtcatg ... ggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAT
EST: gi|46919387|gb|CN548716.1|CN548716
EST:     GGCGGGACAAACTCACCCAATTTCGTTTTAAGAGGAACTGGACATAACAG                         ATCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAG
genomic: GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAGgcatgtcatg ... ggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAT
EST: gi|32246108|gb|CD711927.1|CD711927
EST:     GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAG                         TTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAG
genomic: GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAGgcatgtcatg ... ggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGAT
EST: gi|26260812|gb|CA811875.1|CA811875
EST:     GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAG                         TTCCAAGACTTTACTTTGTAAATACATAAAACATTGTTCAAGGCTGATG
genomic: GGCGGGACAAACTCACCCAATTTCGTTCTAAGAGGAACTGGACATAACAGgcatgtcatg ... ggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcacctgcaattaatctaatggaggtttttttttttttttttgggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGATGTCCACTTCTGTAGTTTATCATGCTCCTCTCTTCCCCCTATATCTTTGT
               atctaat  putative branch site (score: 3)
                           tttttttttttttttt  putative PPT
          aattaatctaatggag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtcatgatttttatacttcgtaatccaatgccagtacgcaggtttcaatttcttgcttgcttgcttgcttcacctgcaattaatctaatggaggtttttttttttttttttgggtgtttcagTTCCAAGACTTTAGTTTGTAAATAGATAAAACATTGTTCAAGGCTGATGATGTCCACTTCTGTAGTTTATCATGCTCCTCTCTTCCCCCTATATCTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC