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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAAGCAATGGTGATGTTCAAGGTTTCTCGAGTCACAACTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatccttctattgatttctctaaattagggttatgatttctctgtgttttgacgtttgatcttcgatattagtagatctgtgttcatgaaaaca...

Basic information

species Vitis vinifera
transcript Vv01s0011g05370.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 1
-----------GGGAAGCAATGGTGATGTTCAAGGTTTCTCGAGTCACAACTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatccttctattgatttctctaaattagggttatgatttc-tctgtgttttgacgtttgatcttcgatattagt---agatctgtgttcatgaaaaca
           |    | |||||||  ||||||||| ||||  ||| | ||||||||  |||||||||||||||| || |||||||| ||| | |||||||||      | |||  ||   |||||    |||     ||     | |   | ||| ||  || |||    ||| | | |   | ||     |    | ||   
GATTTTCTTCAGATTTGAAATGGTGTCGTTCAAGGTCTCTCTCGTCTCTACTTCGCCTATTGATGGCCAGAAACCTGGGACTTCTGGACTCCGTAAGAAGgttcgttcgctttcgctt--cttctccttgttatatcaatccccgcgttcttatttcgaaattggattagagatttgaattctaaattcagatcttcgcaac--

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G70730.2 (Arabidopsis thaliana), 5'ss of exon 2
GGGAAGCAATGGTGATGTTCAAGGTTTCTCGAGTCACAACTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatccttctattgatttctctaaattagggttatgatttc-tctgtgttttgacgtttgatcttcgatattagt---agatctgtgttcatgaaaaca
                       || ||||  ||| | ||||||||  |||||||||||||||| || |||||||| ||| | |||||||||      | |||  ||   |||||    |||     ||     | |   | ||| ||  || |||    ||| | | |   | ||     |    | ||   
-----------------------GTCTCTCTCGTCTCTACTTCGCCTATTGATGGCCAGAAACCTGGGACTTCTGGACTCCGTAAGAAGgttcgttcgctttcgctt--cttctccttgttatatcaatccccgcgttcttatttcgaaattggattagagatttgaattctaaattcagatcttcgcaac--
















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|30133485|gb|CB918824.1|CB918824
EST:     CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAG                         GTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
genomic: CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatc ... aacttttcagGTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
EST: gi|71862440|gb|DT011495.1|DT011495
EST:     CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAG                         GTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
genomic: CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatc ... aacttttcagGTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
EST: gi|32270931|gb|CD720090.1|CD720090
EST:     CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAG                         GTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
genomic: CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatc ... aacttttcagGTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
EST: gi|32268210|gb|CD717369.1|CD717369
EST:     CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAG                         GTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
genomic: CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatc ... aacttttcagGTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
EST: gi|77583444|gb|DV220763.1|DV220763
EST:     CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAG                         GTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
genomic: CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatc ... aacttttcagGTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
EST: gi|161715336|gb|FC066459.1|FC066459
EST:     CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAG                         GTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA
genomic: CTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatc ... aacttttcagGTGAAAGTATTCAAGCAACAAAATTACTTGCACAATTTTGTTCAGTCAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAAGCAATGGTGATGTTCAAGGTTTCTCGAGTCACAACTTCGCCGTTTGATGGCCAGAAACCGGGAACTTCTGGCCTCAGGAAGAAGgttttagatccttctattgatttctctaaattagggttatgatttctctgtgttttgacgtttgatcttcgatattagtagatctgtgttcatgaaaaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaaa