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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttctcctcctttcattgattaaaattcttctttgttttgccatgttcctggtactatctaacatgtttgaaggatctatttctgggtagttacattcactgtcctgttcccaattttatttgaataaaatgctaacaaggttttgttgctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAAGGTGTGAAATTGAGCTGATGATCTATCATTAAACACAATTTTTATGTTG

Basic information

species Vitis vinifera
transcript Vv17s0000g00400.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|110419582|gb|EC985821.1|EC985821
EST:     ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCT                         GCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGAAAA
genomic: ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCTgtaagtttct ... ctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA
EST: gi|22015508|gb|BQ800542.1|BQ800542
EST:     ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCT                         GCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGAAAA
genomic: ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCTgtaagtttct ... ctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA
EST: gi|110394034|gb|EC958407.1|EC958407
EST:     ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCT                         GCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGAAAA
genomic: ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCTgtaagtttct ... ctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA
EST: gi|30305673|gb|CB982467.1|CB982467
EST:     ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCT                         GCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA
genomic: ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCTgtaagtttct ... ctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA
EST: gi|160482081|gb|EY255058.1|EY255058
EST:     ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCT                         GCCAACAACCGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA
genomic: ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCTgtaagtttct ... ctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA
EST: gi|110706767|gb|EE082591.1|EE082591
EST:     ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCT                         GCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA
genomic: ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCTgtaagtttct ... ctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA
EST: gi|110405066|gb|EC970596.1|EC970596
EST:     ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCT                         GCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGAAAA
genomic: ACAGGAGCCCAATGGGGTATCTACGATACTTTCAAAGTTTTTGTTGGGCTgtaagtttct ... ctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttcccaattttatttgaataaaatgctaacaaggttttgttgctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAAGGTGTGAAATTGAGCTGATGATCTATCATTAAACACAATTTTTATGTTG
                          tgctaac  putative branch site (score: 1)
        aattttatttgaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttctcctcctttcattgattaaaattcttctttgttttgccatgttcctggtactatctaacatgtttgaaggatctatttctgggtagttacattcactgtcctgttcccaattttatttgaataaaatgctaacaaggttttgttgctatccatagGCCAACAACTGGAGGTGTTACTCCTGCTCCTGCTGCCACTGTTCCTGCAAAGGTGTGAAATTGAGCTGATGATCTATCATTAAACACAATTTTTATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT