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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatgatgagaaattagtctaatccaaaagaatctgctaagtaagaactgataaacttagaacttcatggggtggctgaatggttcatgttcactttcagGCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATAGACAGCCGAAAACTCTCGCCGGAGGCCTCTTTCCATGCAGCTCACAATG

Basic information

species Vitis vinifera
transcript Vv09s0002g05700.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|110427425|gb|EC993862.1|EC993862
EST:     CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAA                         GCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA
genomic: CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAAgtaagtaaaa ... tcactttcagGCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA
EST: gi|351026080|gb|FQ428092.1|FQ428092
EST:     CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCATA                         GCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA
genomic: CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAAgtaagtaaaa ... tcactttcagGCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA
EST: gi|351035414|gb|FQ459681.1|FQ459681
EST:     CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAA                         GCACATCCCGGGGTGTCCAACCAAGATAGAAA
genomic: CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAAgtaagtaaaa ... tcactttcagGCACATCCCGGGGTGTCCAAGCAAGATAGAAA
EST: gi|110374886|gb|EC939827.1|EC939827
EST:     CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAA                         GCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA
genomic: CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAAgtaagtaaaa ... tcactttcagGCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA
EST: gi|351049227|gb|FQ449949.1|FQ449949
EST:     CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCANA                         GCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA
genomic: CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAAgtaagtaaaa ... tcactttcagGCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA
EST: gi|351054379|gb|FQ450462.1|FQ450462
EST:     CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAA                         GCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA
genomic: CCCGATCAACAGACGATGGGCTATACCGGGCCATCGATACTTATCTCAAAgtaagtaaaa ... tcactttcagGCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgataaacttagaacttcatggggtggctgaatggttcatgttcactttcagGCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATAGACAGCCGAAAACTCTCGCCGGAGGCCTCTTTCCATGCAGCTCACAATG
 aactgat  putative branch site (score: 3)
                                            ttcactttc  putative PPT
     ataaactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatgatgagaaattagtctaatccaaaagaatctgctaagtaagaactgataaacttagaacttcatggggtggctgaatggttcatgttcactttcagGCACATCCCGGGGTGTCCAAGCAAGATAGAAAGGTACTTTGCAGGATAATAGACAGCCGAAAACTCTCGCCGGAGGCCTCTTTCCATGCAGCTCACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
ccatgat
- - - - agaaatt
- - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - -ctgctaa
- - - - - - - - - - - - - - - - - - - - - - - - -gataaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatgg