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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaatggcagataagacgtagagtgtaattaatgcatgtattttgtattatgtattaacggtttcttttatattgttgtatgttttcccttttttggcagATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCTAAATTCTGACCAACTTTACAATACAGGGAGGAATGGACAAACAAATATA

Basic information

species Vitis vinifera
transcript Vv11s0016g00440.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|110699790|gb|EE077097.1|EE077097
EST:     TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGT                         ATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCN
genomic: TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGTgtgagtcaga ... tttttggcagATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGC-
EST: gi|27579829|gb|CB002524.1|CB002524
EST:     TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGT                         ATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCT
genomic: TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGTgtgagtcaga ... tttttggcagATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCT
EST: gi|27580754|gb|CB003449.1|CB003449
EST:     TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGT                         ATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCT
genomic: TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGTgtgagtcaga ... tttttggcagATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCT
EST: gi|161715658|gb|FC067788.1|FC067788
EST:     TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGT                         ATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCT
genomic: TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGTgtgagtcaga ... tttttggcagATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCT
EST: gi|37189887|gb|CF609236.1|CF609236
EST:     TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGT                         ATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCT
genomic: TACTACAGCAATGCGTACATGGATGCAGAGAAACAAGCTGCAATTAATGTgtgagtcaga ... tttttggcagATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattatgtattaacggtttcttttatattgttgtatgttttcccttttttggcagATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCTAAATTCTGACCAACTTTACAATACAGGGAGGAATGGACAAACAAATATA
       tattaac  putative branch site (score: 1)
                                 tatgttttcccttttt  putative PPT
                    ttttatattgttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatggcagataagacgtagagtgtaattaatgcatgtattttgtattatgtattaacggtttcttttatattgttgtatgttttcccttttttggcagATTCCTGGGGCACTTCCAGCCACAACAGGGTAAACCTGCATTGTGGGAGCTAAATTCTGACCAACTTTACAATACAGGGAGGAATGGACAAACAAATATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
tgaatgg
- - - - -gataaga
- - - - - - - - - - - - - - - - -gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgt