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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAAAGGCCCGGGATGTTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattctccatccagtttcctttttgaattccataaaatgatataatggtgtcatcattgtcatgtaattgtttcttgcacactag

Basic information

species Vitis vinifera
transcript Vv18s0001g02550.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os06g49110.2 (Oryza sativa), 5'ss of exon 4
GTTGCAAAGGCCCGGGATGTTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattctccatccagtttcctttttgaattccataaaatgatataatggtgtcatcattgtcatgtaattgtttcttgcacactag
||    ||| | || ||||||||||| |||||| ||||||| ||||| |||||||| ||||| ||||||||  ||   |   ||  | ||   ||| ||  |    |  | | ||||  ||  ||   | |  |  | |  ||||| |||         
GTCTACAAGTCTCGTGATGTTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaacga-atataattcattttctgtttcatgtgtattaatatcttga-gttgacttaatactct--ttgttccttcag------

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G12110.1 (Glycine max), 5'ss of exon 4
GTTGCAAAGGCCCGGGATGTTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattctccatccagtttcctttttgaattccataaaatgatataatggtgtcatcattgtcatgtaattgtttcttgcacactag
|||||||| || |||||||||||||| || ||||| |||||||| |||||| |||||||||| ||||||||||| ||||||  ||| |  | || |  |  |||  ||  || |     | |||| |||    |  | |||  | ||    | |  |||
GTTGCAAAAGCACGGGATGTTGGTGTTAATAGTGTCGTGCTCTTCCCTAAAATTCCAGATGCTTTGAAGgttct-attctctctcctgcatactataggctttcagtaggataact--gtagtgtaatc----tagtataacagatttcccc-ctttag

upper sequence: Vv18s0001g02550.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G42670.1 (Glycine max), 5'ss of exon 5
GTTGCAAAGGCCCGGGATGTTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattctccatccagtttcctttttgaattccataaaatgatataatggtgtcatcattgtcatgtaattgtttcttgcacactag
   ||||| || |||||||||||||| || |||||||||||||| || ||| |||||||||| ||||||||||| ||||||  ||| |  | || |  |  |||  ||| || |       |||  |||    |  | |||  | ||    | |  |||
---GCAAAAGCACGGGATGTTGGTGTTAATAGTGTTGTGCTCTTCCCCAAAATTCCAGATGC-TTGAAGGTTCT-ATTCTCTCTCCTGCATACTATAGGCTTTCAgtaagataact--gcagtgcaatc----tagtataacagatttcccc-ctttag

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|352789677|gb|FQ476275.1|FQ476275
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351023176|gb|FQ432559.1|FQ432559
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351039238|gb|FQ457913.1|FQ457913
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|349830570|gb|FQ416868.1|FQ416868
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351044281|gb|FQ447635.1|FQ447635
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351036615|gb|FQ457328.1|FQ457328
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|349828957|gb|FQ419290.1|FQ419290
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351052784|gb|FQ456511.1|FQ456511
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|110386828|gb|EC951456.1|EC951456
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351044566|gb|FQ443097.1|FQ443097
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|110373793|gb|EC938150.1|EC938150
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|110732090|gb|EE107070.1|EE107070
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGT-CCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTANTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351055179|gb|FQ440518.1|FQ440518
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351012975|gb|FQ433702.1|FQ433702
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351020103|gb|FQ445710.1|FQ445710
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|161718611|gb|FC068206.1|FC068206
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAA
EST: gi|351054528|gb|FQ452004.1|FQ452004
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|349830492|gb|FQ416790.1|FQ416790
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|351015476|gb|FQ447305.1|FQ447305
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
EST: gi|349826066|gb|FQ415871.1|FQ415871
EST:     TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAG                         TCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA
genomic: TTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattc ... tgcacactagTCTCCCACAGGAGATGAAGCATTCAATGACAATGGTTTAGTGCCCCGGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCAAAGGCCCGGGATGTTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattctccatccagtttcctttttgaattccataaaatgatataatggtgtcatcattgtcatgtaattgtttcttgcacactag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG