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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggactagttccagtttacctgattgcttcatcaaattaactataatgtaatttggagcccaactctttgtgcattttatgtatagGATTTGGAAGTGGAAGATGCTGATCCATCAAAGCATTCCAAACCACAGAAAGGTCAAGGGAAGAGCAGTAAAGAGAAACTTTCGAGCCCCAAACATGCAG

Basic information

species Vitis vinifera
transcript Vv04s0008g05480.t01
intron # 2
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|110711956|gb|EE089029.1|EE089029
EST:     GAGAGGGATCACATATCCGTGCAAGAGTCAATGGATTGACCATTTCTGAG                         GATTTGGAAGTGGAAGATGCTGATCCATCAAAGCATTCCAAACCACAGAAA
genomic: GAGAGGGATCACATATCCGTGCAAGAGTCAATGGATTGACCATTTCTGAGgtaggactag ... ttatgtatagGATTTGGAAGTGGAAGATGCTGATCCATCAAAGCATTCCAAACCACAGAAA
EST: gi|37188322|gb|CF607671.1|CF607671
EST:     GAGAGGGATCACATATCCGTGCAAGAGTCAATGGATTGACCATTTCTGAG                         GATTTGGAAGTGGAAGATGCTGATCCATCAAAGCATTCCAAACCACAGAAA
genomic: GAGAGGGATCACATATCCGTGCAAGAGTCAATGGATTGACCATTTCTGAGgtaggactag ... ttatgtatagGATTTGGAAGTGGAAGATGCTGATCCATCAAAGCATTCCAAACCACAGAAA
EST: gi|110713754|gb|EE089952.1|EE089952
EST:     GAGAGGGATCACATATCCGTGCAAGAGTCAATGGATTGACCATTTCTGAG                         GATTTGGAAGTGGAAGATGCTGATCCATCAAAGCATTCCAAACCACAGAAA
genomic: GAGAGGGATCACATATCCGTGCAAGAGTCAATGGATTGACCATTTCTGAGgtaggactag ... ttatgtatagGATTTGGAAGTGGAAGATGCTGATCCATCAAAGCATTCCAAACCACAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaattaactataatgtaatttggagcccaactctttgtgcattttatgtatagGATTTGGAAGTGGAAGATGCTGATCCATCAAAGCATTCCAAACCACAGAAAGGTCAAGGGAAGAGCAGTAAAGAGAAACTTTCGAGCCCCAAACATGCAG
   aattaac  putative branch site (score: 2)
     ttaactataatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggactagttccagtttacctgattgcttcatcaaattaactataatgtaatttggagcccaactctttgtgcattttatgtatagGATTTGGAAGTGGAAGATGCTGATCCATCAAAGCATTCCAAACCACAGAAAGGTCAAGGGAAGAGCAGTAAAGAGAAACTTTCGAGCCCCAAACATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA