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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCTACGGATAAATGCATAATGCTTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattctctcgcgtttatcatttatgaccttgaacttttgcaacgtgcttaactcacctgctttaattgaacttaaaggtgaaatgaaccccaaac...

Basic information

species Vitis vinifera
transcript Vv05s0020g00750.t01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g00750.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA17G04460.2 (Glycine max), 5'ss of exon 8
-------------------------GTGGCTACGGATAAATGCATAATGCTTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattctctcgcgtttatcatttatgaccttgaacttttgcaacgtgcttaactcacctgctttaattga-acttaaaggtgaaat----gaaccccaaac----
                         || ||||| || || ||||| |||||||| || || |||||||| ||||||||||| ||||||||  | |||||||||||   |   |  | |  || | || |||   |||| || |     |||  ||  |  ||| ||  ||| || | |||  | |  |||    |||    ||||    
CTGAATTGTCTTTCCATGTTATCAGGTAGCTACTGACAAGTGCATCATGCTTTTTCTGTTCCTTATTGTCTGTGGTGTAATTGCCATTATTGTCGTGAAGgtatggtgttcatttcatccattactt-tga---tgaatttgt----tgtggatatttttcct-ctcaaatagacaattactgttacaatttttgaaaattaaactaag

upper sequence: Vv05s0020g00750.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA17G04460.1 (Glycine max), 5'ss of exon 9
GTGGCTACGGATAAATGCATAATGCTTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattctctcgcgtttatcatttatgaccttgaacttttgcaacgtgcttaactcacctgctttaattga-acttaaaggtgaaat----gaaccccaaac----
|| ||||| || || ||||| |||||||| || || |||||||| ||||||||||| ||||||||  | |||||||||||   |   |  | |  || | || |||   |||| || |     |||  ||  |  ||| ||  ||| || | |||  | |  |||    |||    ||||    
GTAGCTACTGACAAGTGCATCATGCTTTTTCTGTTCCTTATTGTCTGTGGTGTAATTGCCATTATTGTCGTGAAGgtatggtgttcatttcatccattactt-tga---tgaatttgt----tgtggatatttttcct-ctcaaatagacaattactgttacaatttttgaaaattaaactaag

upper sequence: Vv05s0020g00750.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: GLYMA13G18030.1 (Glycine max), 5'ss of exon 9
GTGGCTACGGATAAATGCATAATGCTTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattctc-tcgcgtttatcattt--atgaccttgaacttttgcaacgtgcttaactcacctgctttaattgaacttaaaggtgaaatgaaccccaaac
|| ||||| || || ||||| |||||||| || || |||||||| ||||||||||| ||||||||  | |||||||||   ||  || |  | | | | | |   ||||  |||   || || |   |  |   ||||  | || | |   |  || ||  | |||  ||       |
GTAGCTACTGACAAGTGCATCATGCTTTTTCTGTTCCTTATTGTCTGTGGTGTAATTGCCATTATTGTGGTGAAGgtaatcatgttcatttcatctgttactctgatgaatttg---ttgtggatatttttcctctcaaatactgttacaaattttgaaatttaaactaagatgttcc

upper sequence: Vv05s0020g00750.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT1G48240.1 (Arabidopsis thaliana), 5'ss of exon 9
GTGGCTACGGATAAATGCATAATGCTTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgta-----tgtattctctcgcgtttatcatttatgaccttgaacttttgcaacgtgcttaactcacctgctttaattgaacttaaaggtgaaatgaaccccaaac
|| ||||| |||||||||||||||   ||||| ||||| ||||| |||||||| ||||| || |||||||||||||||     || | ||||   | ||| |||||   | ||    |    |   |  | |||||   |   | |||||     ||||||    ||   |         
GTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAGgtaaccattgcactctccaacttttctcattacggcccaaataaagctatgat-tccttaagcaa---gttttaacactgcttaaataaaaacacag--------

upper sequence: Vv05s0020g00750.t01 (Vitis vinifera), 5'ss of exon 9
lower sequence: AT3G17440.2 (Arabidopsis thaliana), 5'ss of exon 9
GTGGCTACGGATAAATGCATAATGCTTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgta---tgtattctctcgcgtttatcatttatgaccttgaacttttgcaacgtgcttaactcacctgctttaattgaacttaaaggtgaaatgaaccccaaac
|||||||| |||||||||||||||   ||||| ||||| ||||| || |||||| ||||||| ||||| |||||||||   | | ||||||| |  ||   | || |||  |||  | || ||||  ||  ||||||   |  ||  ||| |   |  ||                  
GTGGCTACCGATAAATGCATAATGGGGTTCCTGTTTCTCATTGTATGCGGTGTAGTAGCCATAATCATAGTGAAGgtactgtcttttctctctctgttgaaagttgtga--ttgctcattagcaagttg--taactctggtttttgtattaattcttcag------------------

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|351014847|gb|FQ438047.1|FQ438047
EST:     TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAG                         ATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
genomic: TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattc ... aaaattttagATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
EST: gi|110417235|gb|EC983274.1|EC983274
EST:     TTTTCCTATTTCTTATTGTCTGTGGTGTAATAGCCATTATCATTGTGAAG                         ATTGTGAACCCCAACAACAAGAGCATCAGGGACGTCCCTGGATTGGCACCT
genomic: TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattc ... aaaattttagATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
EST: gi|34362779|gb|CF404364.1|CF404364
EST:     TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAG                         ATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
genomic: TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattc ... aaaattttagATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
EST: gi|351044413|gb|FQ442944.1|FQ442944
EST:     TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAG                         ATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
genomic: TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattc ... aaaattttagATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
EST: gi|110400763|gb|EC967341.1|EC967341
EST:     TTTTCCTATTTCTTATTGTCTGTGGTGTAATAGCCATTATCATTGTGAAG                         ATTGTGAACCCCAACAACAAGAGCATCAGGGACGTCCCTGGATTGGCACCT
genomic: TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattc ... aaaattttagATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
EST: gi|110403990|gb|EC969898.1|EC969898
EST:     TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAG                         ATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
genomic: TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattc ... aaaattttagATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
EST: gi|46919418|gb|CN548747.1|CN548747
EST:     TTTTCCTATTTCTTATTGTGTGTGTTGTAATAGCCATTATCATTGTGAAG                         ATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
genomic: TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattc ... aaaattttagATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
EST: gi|351033770|gb|FQ447808.1|FQ447808
EST:     TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAG                         ATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT
genomic: TTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattc ... aaaattttagATTGTGAACCCCAACAACAAGAGCATCAAGGACGTCCCTGGATTGGCACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGCTACGGATAAATGCATAATGCTTTTCCTATTTCTTATTGTGTGTGGTGTAATAGCCATTATCATTGTGAAGgtatgtattctctcgcgtttatcatttatgaccttgaacttttgcaacgtgcttaactcacctgctttaattgaacttaaaggtgaaatgaaccccaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgaaa