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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaattaacaaggataaaatgttttctttccattaaaaagattttgatttctagttagtcttgtttttttgagcattgagaccaactattcctttttcagGAATCTGTGAAGGGAACATGGCATGTGCCCGTAGCAAGCGAAAGCAGTGACGAGTCTTTGAGAACGTGGCACTGCATTACTAGGCCCAGCTCACATGAAC

Basic information

species Vitis vinifera
transcript Vv12s0035g01850.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|34545501|gb|CF513733.1|CF513733
EST:     AGGGTAATGTGAAACTTCTGATGCCGCCTTCATATTCTTTATTCATCCAG                         GAATCTGTGAAGGGAACATGGCATGTGTCCGTAGCAAGCGAAAGCAGTGAC
genomic: AGGGTAATGTGAAACTTCTGATGCCGCCTTCATATTCTTTATTCATCCAGgtattgttcc ... cctttttcagGAATCTGTGAAGGGAACATGGCATGTGCCCGTAGCAAGCGAAAGCAGTGAC
EST: gi|34319726|gb|CF372480.1|CF372480
EST:     AGGGTAATGTGAAACTTCTGATGCCGCCTTCATATTCTTTATTCATCCAG                         GAATCTGTGAAGCGAACATGGCATGTGCCCGTAGCAAGCGAAAGCAGTGAC
genomic: AGGGTAATGTGAAACTTCTGATGCCGCCTTCATATTCTTTATTCATCCAGgtattgttcc ... cctttttcagGAATCTGTGAAGGGAACATGGCATGTGCCCGTAGCAAGCGAAAGCAGTGAC
EST: gi|34545414|gb|CF513646.1|CF513646
EST:     AGGGTAATGTGAAACTTCTGATGCCGCCTTCATATTCTTTATTCATCCAG                         GAATCTGTGAAGGGAACATGGCATGTGTCCGTAGCAAGCGAAAGCAGTGAC
genomic: AGGGTAATGTGAAACTTCTGATGCCGCCTTCATATTCTTTATTCATCCAGgtattgttcc ... cctttttcagGAATCTGTGAAGGGAACATGGCATGTGCCCGTAGCAAGCGAAAGCAGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttctagttagtcttgtttttttgagcattgagaccaactattcctttttcagGAATCTGTGAAGGGAACATGGCATGTGCCCGTAGCAAGCGAAAGCAGTGACGAGTCTTTGAGAACGTGGCACTGCATTACTAGGCCCAGCTCACATGAAC
 ttttgat  putative branch site (score: 4)
                                        ctattcctttttc  putative PPT
               ttgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaattaacaaggataaaatgttttctttccattaaaaagattttgatttctagttagtcttgtttttttgagcattgagaccaactattcctttttcagGAATCTGTGAAGGGAACATGGCATGTGCCCGTAGCAAGCGAAAGCAGTGACGAGTCTTTGAGAACGTGGCACTGCATTACTAGGCCCAGCTCACATGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - -ggataaa
- - - - - - - - - - - - tctttcc
- - - - - - - - - - - - - - - - - aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaacta