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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAATGCTGCGGATGTTAAGGCAAAGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaacatagtgtttatggtgcatacttaaatgccatagaggaaagaagttggcattgatgatatattgtctctgcag

Basic information

species Vitis vinifera
transcript Vv16s0039g02750.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 7
AGAAAATGCTGCGGATGTTAAGGCAAAGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaac-atagtgtttatggtgcatacttaaatgccatagaggaaagaagttggcattgatgata-tattgtctctgcag----------------------
 ||||||||  | ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||||||||| |||||||| | ||     |   |   |||   ||     |    || | |  |  | | || ||  | | ||| |  | | |                      
GGAAAATGCACCTGATGTGAAGGCCAAATTTATAATTGAAGCTGCTAATCATCCAACTGATCCAGAAGCTGACGAGgtaaccacagaacaaaacat-tgtaccctaactttgtctttgagaaacatcagaaatgttgccaattttggcagttctgattgatgctgtatgcactacag

upper sequence: Vv16s0039g02750.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os02g43470.1 (Oryza sativa), 5'ss of exon 7
AGAAAATGCTGCGGATGTTAAGGCAAAGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaa---------catagtg-------tttatggtgcatacttaaatgccatagaggaaagaagtt--------ggcattgatgat-atattgtctctgcag----------------------------------
||||||||| || || || ||||| |  |||||||| || |  || |||||||| |||||| ||||||||||||||||||         || | ||       | | |    |   ||      || |  |||||      |        | |||  |  || ||| | | | |  |                                   
AGAAAATGCAGCTGAAGTGAAGGCCAGATTCATAATTGAGGGGGCTAATCATCCCACTGATACAGAAGCTGATGAGgtaagctcaaaaccacaatgagctctctctctctctctctctctctctccttcaaggaacatgaatatcctcaagacatcaagaatgataatttatttataattctaatcttttgagcttactctctgccttgaag
















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|110383828|gb|EC948229.1|EC948229
EST:     AGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAG                         ATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCT
genomic: AGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaacatagt ... gtctctgcagATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCT
EST: gi|30133193|gb|CB918532.1|CB918532
EST:     AGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAG                         ATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCT
genomic: AGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaacatagt ... gtctctgcagATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCT
EST: gi|37190544|gb|CF609893.1|CF609893
EST:     AGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAG                         ATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCT
genomic: AGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaacatagt ... gtctctgcagATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCT
EST: gi|30251187|gb|CB968920.1|CB968920
EST:     AGTTCACAATAGAAGCAGCAAACCATCCTACTGATCCAGGAGCTGATGAG                         ATTTTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATTTATGCTAATGCT
genomic: AGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaacatagt ... gtctctgcagATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCT
EST: gi|156737272|gb|EV241386.1|EV241386
EST:     AGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAG                         ATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCT
genomic: AGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaacatagt ... gtctctgcagATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAATGCTGCGGATGTTAAGGCAAAGTTCATAATAGAAGCAGCAAATCATCCTACTGATCCAGAAGCTGATGAGgtaacatagtgtttatggtgcatacttaaatgccatagaggaaagaagttggcattgatgatatattgtctctgcag

- - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT