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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctgtctcttttacatgtttgcaatgtgaatatcttatccttttactaaataatcaatcacacatatatatagtagttgtaaccatttctatggtaattctgtttgaacag

Basic information

species Vitis vinifera
transcript Vv08s0105g00590.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00590.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: LOC_Os05g28200.1 (Oryza sativa), 5'ss of exon 11
CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctgtctcttttacatgtttgcaatgtgaatatcttatccttttactaaataatcaatcacacatatatatagtagttgtaaccatttctatggtaattctgtttgaacag
|| || || || ||||||||||||||||| |||||||| |||||||||||  |||| ||||||||| ||| | | ||| |    |    |   | | |    | | | || |   |  | |   || ||  |||  ||||        | ||| ||| |  |                  
CTAGGGATTGCTATTGTAAATGACTTTAAGAGTGTTGAGGGAGATAGAGCTCTGGGGCTTCAGgttcttcttctgtctgtagtgta---gagttatcacagcccttttctgtagttccaaagaaaagcaatcatccatatcac-----ttaccttttttcag------------------
















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|30252103|gb|CB968742.1|CB968742
EST:     TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG                         TCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
genomic: TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctg ... gtttgaacagTCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
EST: gi|161705814|gb|FC057091.1|FC057091
EST:     TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG                         TCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
genomic: TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctg ... gtttgaacagTCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
EST: gi|351034199|gb|FQ463133.1|FQ463133
EST:     TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCGG                         TCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
genomic: TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctg ... gtttgaacagTCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
EST: gi|351025946|gb|FQ427958.1|FQ427958
EST:     TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG                         TCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
genomic: TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctg ... gtttgaacagTCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
EST: gi|351031189|gb|FQ445016.1|FQ445016
EST:     TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAA                         TCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGT
genomic: TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctg ... gtttgaacagTCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGT
EST: gi|351018561|gb|FQ424668.1|FQ424668
EST:     TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG                         TCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
genomic: TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctg ... gtttgaacagTCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
EST: gi|349829107|gb|FQ419639.1|FQ419639
EST:     TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAG                         TCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT
genomic: TTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctg ... gtttgaacagTCCCTACCGGTGGCATTTGGTGCTGAAACTGCTAAATGGATTTGTGTGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGGCATCGCCATTGTAAATGACTTTAAAAGTGTTGAAGGAGATAGAGCATTGGGACTTCAGgtttttcctgtctcttttacatgtttgcaatgtgaatatcttatccttttactaaataatcaatcacacatatatatagtagttgtaaccatttctatggtaattctgtttgaacag

- - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - -  AGAGCA