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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCTCGTGATGGAGGTCAGCAGATAATTGATTCTGTAGATGTCACATGCGGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatgtaatttagtagcatgacaataatgctttcagtatatgcttttcttaccgtttaaatgaaagcaacatcatgcttttcttaatagtgaatg...

Basic information

species Vitis vinifera
transcript Vv06s0004g07380.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g07380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g18590.1 (Oryza sativa), 5'ss of exon 4
GTGCTCGTGATGGAGGTCAGCAGATAATTGATTCTGTAGATGTCACATGCGGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatgtaatttagtagcatgacaataatgctttcagtatatgcttttcttaccgtttaaatgaaagcaacatcatgcttttctta-atagtgaatg--
|  | ||||||||||| ||  |  ||||||| ||||||||||||||||||||||| ||||| || |||||||||||  | ||||||||||| || || |||| |  | | || | |  ||  |    ||| |||| | || ||| |       | | |   |  ||         || ||   ||    | | |||  | |  
GCTCACGTGATGGAGGCCAAAATGTAATTGACTCTGTAGATGTCACATGCGGTCTCAGCTTAGGGGAATACACTGCACTTGCATTTGCTGGTGCCTTTAGgtatttcctttattctgttaataa---aatcatgcatgcattattttgaaaaataagcacatggattcgtttcctattataggttgaacatacagtataggtt

upper sequence: Vv06s0004g07380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA18G06500.1 (Glycine max), 5'ss of exon 4
GTGCTCGTGATGGAGGTCAGCAGATAATTGATTCTGTAGATGTCACATGCGGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatgtaatttagtagca--tgacaataatgctttcagtatatgcttttcttaccgtttaaatgaaagcaacatcatgcttttcttaatagtgaatg
|||| ||||| |||||||||||||| ||||| || || ||||| ||||| ||| ||||| |||||||||| |||||| | ||||||||||| ||||||||||| |  |   |   ||    |   | |  | |||| |||   ||| || ||| |||  | |||   | |        ||||  |||||   | |    | |
GTGCACGTGAAGGAGGTCAGCAGATTATTGACTCAGTTGATGTTACATGTGGTTTAAGCCTGGGAGAATATACTGCTCTGGCATTTGCTGGGGCTTTCAGgtgagttaccaagagtaactactatttatcacaatggtttttctat-tgttttccttttcatttct-tcattttcttttcatatttttccccacatatcaag

upper sequence: Vv06s0004g07380.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G29520.1 (Glycine max), 5'ss of exon 1
GTGCTCGTGATGGAGGTCAGCAGATAATTGATTCTGTAGATGTCACATGCGGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatgtaatttag-tagcatg-acaataatgctttcagtatatgcttttcttaccgtttaaatgaaagcaacatcatgcttttcttaatagtgaatg
|||| |||||||||||||||||||| ||||| || || ||||| ||||| ||| ||||| |||||||||| |||||| | ||||||||||| ||||| ||||| |  |   |   ||  || |||  |  | ||||  ||   ||| || ||| | |  | |||   | |        ||||  ||||   ||      | |
GTGCGCGTGATGGAGGTCAGCAGATTATTGACTCAGTTGATGTTACATGTGGTTTAAGCCTGGGAGAATATACTGCTCTGGCATTTGCTGGGGCTTTTAGgtgagttaccaagagtaactaccatttattacaatggcttttctat-tgttttccctttcatttct-tcattttcttttcatattttttccaacgtatcaag

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|161714260|gb|FC063524.1|FC063524
EST:     GGTCTAAGCTTGAGAGAA-ACACTGCTTTAGCATTTGCTGGAG-TTTCAG                         CTTTGAAGATG-ACTCA-GCTGGTCAA
genomic: GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatg ... tgttttaaagCTTTGAGGATGGACTCAAGCTGGTCAA
EST: gi|110361598|gb|EC925084.1|EC925084
EST:     GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAG                         CTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAAGCAATGCAG
genomic: GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatg ... tgttttaaagCTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAAGCAATGCAG
EST: gi|110687429|gb|EE064834.1|EE064834
EST:     CGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAG                         CTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAAGCAATGCAG
genomic: GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatg ... tgttttaaagCTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAAGCAATGCAG
EST: gi|30128526|gb|CB913865.1|CB913865
EST:     GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAG                         CTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAAGCAATGCAG
genomic: GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatg ... tgttttaaagCTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAAGCAATGCAG
EST: gi|161713818|gb|FC063453.1|FC063453
EST:     GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAG                         CTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAAAGCA-TGCAG
genomic: GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatg ... tgttttaaagCTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAA-GCAATGCAG
EST: gi|71872032|gb|DT021087.1|DT021087
EST:     GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAG                         CTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAAGCAATGCAG
genomic: GGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatg ... tgttttaaagCTTTGAGGATGGACTCAAGCTGGTCAAATTAAGGGGTGAAGCAATGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCTCGTGATGGAGGTCAGCAGATAATTGATTCTGTAGATGTCACATGCGGTCTAAGCTTGGGAGAATACACTGCTTTAGCATTTGCTGGAGCTTTCAGgtgtgccatgtaatttagtagcatgacaataatgctttcagtatatgcttttcttaccgtttaaatgaaagcaacatcatgcttttcttaatagtgaatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gacaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaaa