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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaccttactatgataagatggaaactcccatattttcttgataggatgttgaatattgtgttttgtcgtgcactgataaaatgctttctatcttgcagGGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTCATACTGGCTTTTGCTTGCCATGGGCTTGCACTTCCTTCTTGCGTTAAGTGAGGGTGGTTG

Basic information

species Vitis vinifera
transcript Vv04s0008g05650.t01
intron # 3
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|351043453|gb|FQ444053.1|FQ444053
EST:     CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCAC                         GGTAGCACTGATAATAATCCTCCTCGTTATTGTATATGTTATACTGGCTTT
genomic: CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCACgtatgtgctc ... tatcttgcagGGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTCATACTGGCTTT
EST: gi|30252438|gb|CB969989.1|CB969989
EST:     CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCAC                         GGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTCATACTGGCTTT
genomic: CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCACgtatgtgctc ... tatcttgcagGGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTCATACTGGCTTT
EST: gi|351034506|gb|FQ448182.1|FQ448182
EST:     CA-GCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCAC                         GGTTGCACTGGATA-TAATCCTCTTCGTTATTGTATATGT
genomic: CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCACgtatgtgctc ... tatcttgcagGGTTGCACTG-ATAATAATCCTCCTCGTTATTGTATATGT
EST: gi|27586637|gb|CB009332.1|CB009332
EST:     CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCAC                         GGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTTATACTGGCTTT
genomic: CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCACgtatgtgctc ... tatcttgcagGGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTCATACTGGCTTT
EST: gi|27584778|gb|CB007473.1|CB007473
EST:     CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCAC                         GGTTGCACTGATAATA-TCCTCCTCGTTATTGTATATGTTATACTGGCTTT
genomic: CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCACgtatgtgctc ... tatcttgcagGGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTCATACTGGCTTT
EST: gi|351029819|gb|FQ427659.1|FQ427659
EST:     CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCAC                         GGTTGCACTGATAATAATCCTCTTCGGTATTGTATATGTTATACTGGCTTT
genomic: CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCACgtatgtgctc ... tatcttgcagGGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTCATACTGGCTTT
EST: gi|349808751|gb|FQ406601.1|FQ406601
EST:     CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAGATGTCAAACTCAC                         GGTTGCACTGATAATAATCCTCCT
genomic: CAAGCCCGTCGTTTTAGAAGCACTGTGTGGTGGAGAAATGTCAAACTCACgtatgtgctc ... tatcttgcagGGTTGCACTGATAATAATCCTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatgttgaatattgtgttttgtcgtgcactgataaaatgctttctatcttgcagGGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTCATACTGGCTTTTGCTTGCCATGGGCTTGCACTTCCTTCTTGCGTTAAGTGAGGGTGGTTG
                           cactgat  putative branch site (score: 3)
                                        ctttctatctt  putative PPT
     ttgaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaccttactatgataagatggaaactcccatattttcttgataggatgttgaatattgtgttttgtcgtgcactgataaaatgctttctatcttgcagGGTTGCACTGATAATAATCCTCCTCGTTATTGTATATGTCATACTGGCTTTTGCTTGCCATGGGCTTGCACTTCCTTCTTGCGTTAAGTGAGGGTGGTTG

- - - - - - -gataaga
- - - - - - - - - - - - -actccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttc