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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttattaaatttgatatctgccatgtactcaaattgttatgaactaacttgcaacaaaaaagttgtgactatgtcaacaattaactcttttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTTCAGACAACAG

Basic information

species Vitis vinifera
transcript Vv13s0064g01270.t01
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

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|351022623|gb|FQ447145.1|FQ447145
EST:     TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC                         ATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
genomic: TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCCgtatcctagc ... tttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
EST: gi|26257252|gb|CA808315.1|CA808315
EST:     TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC                         ATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
genomic: TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCCgtatcctagc ... tttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
EST: gi|351015543|gb|FQ447372.1|FQ447372
EST:     TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC                         ATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
genomic: TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCCgtatcctagc ... tttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
EST: gi|349825487|gb|FQ419404.1|FQ419404
EST:     TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC                         ATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
genomic: TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCCgtatcctagc ... tttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
EST: gi|349831115|gb|FQ420785.1|FQ420785
EST:     TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC                         ATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
genomic: TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCCgtatcctagc ... tttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
EST: gi|26257522|gb|CA808585.1|CA808585
EST:     TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC                         ATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
genomic: TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCCgtatcctagc ... tttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
EST: gi|349825184|gb|FQ415731.1|FQ415731
EST:     TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCC                         ATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT
genomic: TTTCAGGTGGATGATGCAAAACTGAAGCGTGCTGGGTTGGATTATTGGCCgtatcctagc ... tttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaacttgcaacaaaaaagttgtgactatgtcaacaattaactcttttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTTCAGACAACAG
                                 acaattaac  putative branch site 
                                         ctcttttgt  CT-rich tract
         aacaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttattaaatttgatatctgccatgtactcaaattgttatgaactaacttgcaacaaaaaagttgtgactatgtcaacaattaactcttttgtactagATATGTGGTTGTTAAAGTTCATGACTCGTGGGCAGAATTTCGGGAATATTTCAGACAACAG

- - - - - - - - - tctgcca
- - - - - - - - - - - - - - - - - - - -tatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - ttgcaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaacaa