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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttatgattatccccaagctccaatgatacaagtctaacatggatttcagatagtaaactgtacctgaaatttctctaaaatgtttctgaacttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g15050.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g15050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G38500.1 (Glycine max), 3'ss of exon 6
gttatgattatccccaagctccaatg-atacaagtct-aacatggatttcagatagtaaactgtacctga--aatttctctaaaatgtttctgaacttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG
| ||| || | || || || | | | | | || ||| | || || | | || || | | || | ||| | | |||||| ||| | ||||||||||||||||||||||| ||||||||||| | |||||||||||| | |||||||||||||| ||||||||||||
---gtaattttcttccagtatgggtgtatgccatttttggagttcatacttcataatgaattgataataaataaatttcttgcactgctgctgg-ttgatccagGAACATGGAGAGTTGGTGGTGTTCTTGCTGTTTCCCGTGCATTTGGAAACAAACTTCTTAAGCCCTATGTTGTTGCTGACCCAGAAATTCAG

upper sequence: Vv18s0001g15050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G43810.1 (Glycine max), 3'ss of exon 5
gttatgattatccccaagctccaatgatacaagtctaacatggatttcagatagtaaactgtacctga--aatttctctaaaatgtttctgaacttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG
| | | | | | | | | | | | | || ||| |||| || | | || || | | || | | | | | |||||| ||| | ||||||||||||||||||||||| ||||| ||||| || ||| |||||||| | |||||||||||||| ||||||||||||
-agcctctgggcaatgggatacgaagttttatacttcataataaattttcatattaaattgatgataaataaatttcttgcactgctgccgg-ttgatccagGAACATGGAGAGTTGGTGGTGTTCTTGCTGTTTCCCGTGCGTTTGGAGACAAATTTCTTAAGCCCTATGTTGTTGCTGACCCAGAAATTCAG

upper sequence: Vv18s0001g15050.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S17_286V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------gttatgattatcccc-aagctccaatgatacaag-tctaacatggatttcagatagtaaactgtacctgaaatttctctaaaatgtttctgaacttcact-----agGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG
| ||||| |||||| || || | | | | |||| | | | | ||| ||| | || ||| || ||| || ||||| || ||||||||||||||||| ||||| ||||||||||| ||||| || |||||| || ||||| ||||||||||||
gtgagtcacgtatctcgtctgtaccgaagattacttaagaagctcgaagtatttgggatttgaagcaaattttgtaaaatttgttccgtatgagtattcatcgcctcacct-tggtgttcgctgttgcagGCACTTGGCGTGTGGGTGGTGTTCTTGCTGTCTCTCGGGCATTTGGGGACCGCCTTCTGAAAAAATATGTAGTCGCTGAGCCAGAAATTCAG

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|110712077|gb|EE089286.1|EE089286
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGAT
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGG-TTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGAT
EST: gi|351030454|gb|FQ432392.1|FQ432392
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|45368324|gb|CK906683.1|CK906683
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351048563|gb|FQ448837.1|FQ448837
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGGCATTTGGGGAT
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTG-CATTTGGGGAT
EST: gi|349815543|gb|FQ400699.1|FQ400699
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|161716302|gb|FC064648.1|FC064648
EST:     GATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTTGGGCAG                         GA-CCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATT
genomic: GATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTT-GGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATT
EST: gi|32245933|gb|CD711752.1|CD711752
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|83274595|gb|DV938692.1|DV938692
EST:     GATGAACGCCAAAGGATTGAAGATGCGGGAGGTTTCGTTATTTGGGCAG                         GAACCGGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: GATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351023467|gb|FQ432850.1|FQ432850
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351029448|gb|FQ436842.1|FQ436842
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|349817905|gb|FQ407894.1|FQ407894
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|352791261|gb|FQ474951.1|FQ474951
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCCTGCTGTTTCTCGTGCATTTGG
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGG
EST: gi|351044250|gb|FQ447604.1|FQ447604
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|110371845|gb|EC935970.1|EC935970
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|349832452|gb|FQ421013.1|FQ421013
EST:     TGATGAACGCCAAAGGATTGAAGATGCCGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|27584677|gb|CB007372.1|CB007372
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|349815027|gb|FQ410250.1|FQ410250
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351025872|gb|FQ427884.1|FQ427884
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351025088|gb|FQ433505.1|FQ433505
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|32245467|gb|CD711286.1|CD711286
EST:     TTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351012826|gb|FQ430389.1|FQ430389
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGCGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351030991|gb|FQ439027.1|FQ439027
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|161717197|gb|FC066571.1|FC066571
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|349830246|gb|FQ420506.1|FQ420506
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351036088|gb|FQ463933.1|FQ463933
EST:     TGATGAACGCCACAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGACAG                         GAACCTGGCTGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|110711257|gb|EE087557.1|EE087557
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|161719283|gb|FC064823.1|FC064823
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGGTGGTGGTGTTTTCTGCTGTT
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCT-TGCTGTT
EST: gi|351033310|gb|FQ446542.1|FQ446542
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|110377520|gb|EC942589.1|EC942589
EST:     TGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351021784|gb|FQ437169.1|FQ437169
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|351046056|gb|FQ441439.1|FQ441439
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATA
EST: gi|161715035|gb|FC063620.1|FC063620
EST:     TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAG                         GAACCTGGCGGGGTGGTGGGTGT-CT-GCTGTT-CTCGTG
genomic: TGATGAACGCCAAAGGATTGAAGATGCTGGAGGTTTCGTTATTTGGGCAGgtaagtttca ... acttcactagGAACCTGGCGGGTTGGTGG-TGTTCTTGCTGTTTCTCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagatagtaaactgtacctgaaatttctctaaaatgtttctgaacttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG
                            ctctaaa  putative branch site (score: 3)
 cttcact  putative PPT
 aaatttctctaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatgattatccccaagctccaatgatacaagtctaacatggatttcagatagtaaactgtacctgaaatttctctaaaatgtttctgaacttcactagGAACCTGGCGGGTTGGTGGTGTTCTTGCTGTTTCTCGTGCATTTGGGGATAAACTTCTTAAGGCATATGTTGTTGCTGATCCAGAAATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - tccccaa
- - - - - - - - -gctccaa
- - - - - - - - - - - - -gatacaa
- - - - - - - - - - - - - - - - - - - catggat
- - - - - - - - - - - - - - - - - - - - - - - - - - agtaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatgt