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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtttatttgacatcggtggtgttttttactctactgaattatatattgttattgatgcttgatctcactctaccagcttgttaatgttggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCATCATTCCAGGAAACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCT

Basic information

species Vitis vinifera
transcript Vv18s0001g02550.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|351023176|gb|FQ432559.1|FQ432559
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351039238|gb|FQ457913.1|FQ457913
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|349830570|gb|FQ416868.1|FQ416868
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351044281|gb|FQ447635.1|FQ447635
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351036615|gb|FQ457328.1|FQ457328
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTCAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|349828957|gb|FQ419290.1|FQ419290
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351052784|gb|FQ456511.1|FQ456511
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|37187408|gb|CF606761.1|CF606761
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|110386828|gb|EC951456.1|EC951456
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351044566|gb|FQ443097.1|FQ443097
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|110373793|gb|EC938150.1|EC938150
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|110732090|gb|EE107070.1|EE107070
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351055179|gb|FQ440518.1|FQ440518
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351012975|gb|FQ433702.1|FQ433702
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351020103|gb|FQ445710.1|FQ445710
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|161718611|gb|FC068206.1|FC068206
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351054528|gb|FQ452004.1|FQ452004
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|161714115|gb|FC064398.1|FC064398
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGG-AGTCCGTCGATTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCCGTATTGAGGGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|349830492|gb|FQ416790.1|FQ416790
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|351015476|gb|FQ447305.1|FQ447305
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA
EST: gi|349826066|gb|FQ415871.1|FQ415871
EST:     TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTT                         CCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGAGCA
genomic: TGCCTCCCAAGCCGGCGGCCCCAGCTGGAACTCCGTCGGTTCCTTTTCTTgtgagtattt ... ggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgttattgatgcttgatctcactctaccagcttgttaatgttggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCATCATTCCAGGAAACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCT
                                   tgttaat  putative branch site (score: 3)
     ttattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtttatttgacatcggtggtgttttttactctactgaattatatattgttattgatgcttgatctcactctaccagcttgttaatgttggtttgtcagCCACTTAATCGACGCCCTCGTCGTAATCGAAGGTCGCCTGTATTGAGGGCATCATTCCAGGAAACAAATTTATCTCCTGCAAATTTTGTCTATCCACTCT

- - - - - - - - ggtggtg
- - - - - - - - - - - - - - - - ctactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cagcttg