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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAGGTGAAACTACTGCTGCAATCTGCACTTGATGTAGCACTCTCTGTTGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaattactgctttcttattttttaaattatgtttcagtgcatctatatggtactataattctttcaaggatttatctaggactatttaattggat...

Basic information

species Vitis vinifera
transcript Vv06s0004g06120.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA14G37090.1 (Glycine max), 5'ss of exon 13
AGAGAGGTGAAACTACTGCTGCAATCTGCACTTGATGTAGCACTCTCTGTTGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgta-ctaaat-tactgctttcttattttttaaattatgtttcagtgcatctatatggtactataattctttcaaggatttatctaggactatttaattggat
||||||||||||  | ||||||| ||||| || || ||| |||| ||| ||||||| ||||| ||||||||||||||||| ||||| |||||||| ||||||| ||  |  | |||  || |||| |||     | || |  | ||  | | |    | | | ||  ||   |  || |  |       | ||||| |  ||
AGAGAGGTGAAAGCATTGCTGCAGTCTGCGCTGGAAGTATCACTTTCTATTGTGCGGGCTAATCCTACTGTTTTGGAGGGTCTTGGTGCTCATTTAGAAGgtaactgtacgtgctgtatt-ttatatttggtgat-tggtggaatgtttgtgttgattgccaaaaaactaatagtgaatacttacaatttttttaacttaat

upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA02G39040.1 (Glycine max), 5'ss of exon 14
AGAGAGGTGAAACTACTGCTGCAATCTGCACTTGATGTAGCACTCTCTGTTGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgta-ctaaat-tactgctttcttattttttaaattatgtttcagtgcatctatatggtactataattctttcaaggatttatctaggactatttaattggat
||||||||||||  | ||||||| |||||||| || ||| |||| ||| ||||||| || || ||||||||||||||||| ||||| |||||||| ||||||| ||  |  | |||  || |||| |||     | || |  | ||  |   |    | | | ||   |   || || | |  ||    | ||| |     |
AGAGAGGTGAAAGCATTGCTGCAGTCTGCACTGGAAGTATCACTTTCTATTGTGCGGGCAAATCCTACTGTTTTGGAGGGTCTTGGTGCTCATTTAGAAGgtaactgtacgtgctgtatttttatatttggtgat-tggtggaatgtttgcgttgattgccaaaaaattaataatgaat-acttaaattttttttaaaactt

upper sequence: Vv06s0004g06120.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA18G07280.1 (Glycine max), 5'ss of exon 12
AGAGAGGTGAAACTACTGCTGCAATCTGCACTTGATGTAGCACTCTCTGTTGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaattactgctttcttattttttaaattatgtttcagtgcatctat-atggtactataattctttcaaggatttatctaggactatttaattggat--
| ||||||| ||  | | ||||| |||||||| | ||||||||| ||  || | || || || ||||||||||||||||| ||||| ||| |||||||||||| | |     |   || ||| | |||   | || |   | ||  |   | || ||   |||||      | | ||  ||  |  |   |||||     |  
AAAGAGGTGCAAACATTACTGCAGTCTGCACTGGCTGTAGCACTTTCCATTATCCGAGCCAATCCTACTGTTTTGGAGGGCCTTGGTGCTGATTTGGAAGgtaattatactttctgtttttaatgtttgg-taatttggaattgtgttggtgattgtcaaataatagca--atgaatacatgcaatatcttttaaaacactta

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|30324341|gb|CD007603.1|CD007603
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
EST: gi|351041361|gb|FQ447488.1|FQ447488
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
EST: gi|32248981|gb|CD714800.1|CD714800
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
EST: gi|32272115|gb|CD721274.1|CD721274
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
EST: gi|22012057|gb|BQ797091.1|BQ797091
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
EST: gi|32249018|gb|CD714837.1|CD714837
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
EST: gi|30327216|gb|CD010478.1|CD010478
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGA
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGA
EST: gi|32270752|gb|CD719911.1|CD719911
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
EST: gi|30135654|gb|CB920992.1|CB920992
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
EST: gi|30131038|gb|CB916377.1|CB916377
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
EST: gi|32267532|gb|CD716495.1|CD716495
EST:     TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAG                         AAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG
genomic: TGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaatt ... tttgattcagAAAATGAGAAAGTGGAAGGTGAGGAGCTACAAGAATGGTTGAAGATGGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAGGTGAAACTACTGCTGCAATCTGCACTTGATGTAGCACTCTCTGTTGTGCGTGCTAACCCTACTGTTTTGGAGGGGCTTGGAGCTCATTTGGAAGgtactaaattactgctttcttattttttaaattatgtttcagtgcatctatatggtactataattctttcaaggatttatctaggactatttaattggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG