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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagctattgaaagaaatgaaaatgtggttcctttggtatatttttctgttctgttttaattttgagagattctgatttggtgataacacggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCCCTCCTTTCTCTGAGAGCCTTGATTCAGACAACTAAGTGCACATCTGTTT

Basic information

species Vitis vinifera
transcript Vv11s0016g04480.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|110713247|gb|EE089011.1|EE089011
EST:     CCTCATTCACACTTAGCTCATTTCTTTCGTTTTGCTATCTCTCGTTGGAG                         GAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
genomic: CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAGgtacggacct ... cggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
EST: gi|30126101|gb|CB911440.1|CB911440
EST:     CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAG                         GAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
genomic: CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAGgtacggacct ... cggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
EST: gi|352764715|gb|FQ471775.1|FQ471775
EST:     CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAG                         GAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
genomic: CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAGgtacggacct ... cggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
EST: gi|30133927|gb|CB919266.1|CB919266
EST:     CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAG                         GAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
genomic: CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAGgtacggacct ... cggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
EST: gi|71887738|gb|DT036793.1|DT036793
EST:     CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAG                         GAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
genomic: CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAGgtacggacct ... cggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
EST: gi|71885539|gb|DT034594.1|DT034594
EST:     CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAG                         GAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
genomic: CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAGgtacggacct ... cggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
EST: gi|161714649|gb|FC062654.1|FC062654
EST:     CCTCATTCACACTTAGCTCATTTCTTTCGTTTTGCTATCTCTCGTTGGAG                         GAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
genomic: CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAGgtacggacct ... cggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
EST: gi|30253113|gb|CB970664.1|CB970664
EST:     CCTCATTCACACTTAGCTCATTTCTTTCGTTTTGCTATCTCTCGTTGGAG                         GAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC
genomic: CCTCATTCACACTTAGCTCTTTTCTTTCGTTTTGCTATCTCTCGTTGGAGgtacggacct ... cggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttctgttttaattttgagagattctgatttggtgataacacggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCCCTCCTTTCTCTGAGAGCCTTGATTCAGACAACTAAGTGCACATCTGTTT
                                     tgataac  putative branch site (score: 2)
     ttctgttttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaagctattgaaagaaatgaaaatgtggttcctttggtatatttttctgttctgttttaattttgagagattctgatttggtgataacacggcatgcagGAACATGTCACAGCCAACCTCATTCTGGTGAAGACCAACAATTTTCTGTCCCTCCTTTCTCTGAGAGCCTTGATTCAGACAACTAAGTGCACATCTGTTT

tgaagct
- - - - - -aaagaaa
- - - - - - - - - -gaaaatg
- - - - - - - - - - - - - tggttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaca