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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttttttgacattataatctgaactttttctttcgaaaggttatagttatgctcatgtccttgttttctactaattttgtactgactctcatcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG

Basic information

species Vitis vinifera
transcript Vv05s0077g00690.t01
intron # 9
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|37184342|gb|CF603696.1|CF603696
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|110720147|gb|EE095816.1|EE095816
EST:     AAC-TCCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATT-CAG                         AGACCCTCCCCTGTATACTCTGAGGGCAAGCGTGT
genomic: AACCTC-TTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGT
EST: gi|110410868|gb|EC976562.1|EC976562
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|30299412|gb|CB976206.1|CB976206
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTTTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|27583346|gb|CB006041.1|CB006041
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|33406611|gb|CF212238.1|CF212238
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|33407058|gb|CF212685.1|CF212685
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|110392261|gb|EC957554.1|EC957554
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|30137246|gb|CB922584.1|CB922584
EST:     GCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: GCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|110392865|gb|EC957405.1|EC957405
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|27585689|gb|CB008384.1|CB008384
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|27585107|gb|CB007802.1|CB007802
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|32246094|gb|CD711913.1|CD711913
EST:     GGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: GGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|110719299|gb|EE097116.1|EE097116
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|30299334|gb|CB976128.1|CB976128
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|110406864|gb|EC972451.1|EC972451
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|33406531|gb|CF212158.1|CF212158
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|294964251|gb|GW838054.1|GW838054
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
EST: gi|110732746|gb|EE108300.1|EE108300
EST:     CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAG                         AGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC
genomic: CAACCTCTTTGGATGTGTTAAAAGCTGCCAAGCATTTTAAATTATTTCAGgtagctcatt ... catcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatgctcatgtccttgttttctactaattttgtactgactctcatcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG
                                   tactgac  putative branch site (score: 1)
 ctctcatcttcc  CT-rich tract
 ttttctactaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttttgacattataatctgaactttttctttcgaaaggttatagttatgctcatgtccttgttttctactaattttgtactgactctcatcttccagAGAGCCTCCCATGTATACTCTGAGGCCAGGCGTGTTCATGCTTTCAGGGACACTGTGTTGTCAGGGTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - tatgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgac