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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgacattttttgttgttatagttgagcaatgttgcatttttatctgctaccaaattaaattggtggtgcttattgactcctgtttattgtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATGACCAAGAAGAAGAATCCATTGGTCTATCTAGATGTGTCTATTGATGGAG

Basic information

species Vitis vinifera
transcript Vv04s0008g05090.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|110687168|gb|EE064342.1|EE064342
EST:     CAGCTTCACAGCGTCTCTGAG                         GTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
genomic: CAGCTTCACAGCGTCTCTGAGgtataaccct ... gtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
EST: gi|30295674|gb|CB972468.1|CB972468
EST:     CAGCTTCACAGCGTCTCTGAG                         GTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
genomic: CAGCTTCACAGCGTCTCTGAGgtataaccct ... gtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
EST: gi|352777331|gb|FQ473965.1|FQ473965
EST:     CAGCTTCACAGCGTCTCTGAG                         GTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
genomic: CAGCTTCACAGCGTCTCTGAGgtataaccct ... gtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
EST: gi|34550009|gb|CF518241.1|CF518241
EST:     CAGCTTCACAGCGTCTCTGAG                         GTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
genomic: CAGCTTCACAGCGTCTCTGAGgtataaccct ... gtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
EST: gi|34550884|gb|CF519098.1|CF519098
EST:     CAGCTTCACAGCGTCTCTGAG                         GTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
genomic: CAGCTTCACAGCGTCTCTGAGgtataaccct ... gtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
EST: gi|352765311|gb|FQ466008.1|FQ466008
EST:     CAGCTTCACAGCGTCTCTGAG                         GTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
genomic: CAGCTTCACAGCGTCTCTGAGgtataaccct ... gtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
EST: gi|26262030|gb|CA813093.1|CA813093
EST:     CAGCTTC-CAGCGTCTCTGAG                         GTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
genomic: CAGCTTCACAGCGTCTCTGAGgtataaccct ... gtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
EST: gi|352772302|gb|FQ469827.1|FQ469827
EST:     CAGCTTCACAGCGTCTCTGAG                         GTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
genomic: CAGCTTCACAGCGTCTCTGAGgtataaccct ... gtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
EST: gi|110723917|gb|EE099287.1|EE099287
EST:     CAGCTTCACAGCGTCTCTGAG                         GTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG
genomic: CAGCTTCACAGCGTCTCTGAGgtataaccct ... gtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctaccaaattaaattggtggtgcttattgactcctgtttattgtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATGACCAAGAAGAAGAATCCATTGGTCTATCTAGATGTGTCTATTGATGGAG
                           tattgac  putative branch site (score: 2)
        aaattaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgacattttttgttgttatagttgagcaatgttgcatttttatctgctaccaaattaaattggtggtgcttattgactcctgtttattgtgtggtcagGTCATTAGTAGTGGTGTCTTGACTCTGTGATATTGGAAAACTAAGAAAATGACCAAGAAGAAGAATCCATTGGTCTATCTAGATGTGTCTATTGATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - caatgtt
- - - - - - - - - - - - - - - - - - - - - - -ctgctac
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtg