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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGTTAGAGCTTGGCATCTTCGGCCATCTCTCATCTGGAAGGATGGGGAATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatctagatgtgcttatgcttgaattccttttgatgctagattgaaacttcttagttgtttattaacttcaatatctggtgcccag

Basic information

species Vitis vinifera
transcript Vv00s0229g00110.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0229g00110.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA01G41730.1 (Glycine max), 5'ss of exon 8
AGTTGTTAGAGCTTGGCATCTTCGGCCATCTCTCATCTGGAAGGATGGGGAATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatctagatgtgcttatgcttgaattccttttgatgctagattgaaacttcttagttgtttattaacttcaatatctggtgcccag
 |||||||||||||||||||| || ||||| || ||||||||||||||| ||||||||||||  || |      | | |||||||    ||  |||||||||  | | | |||  || ||| ||      ||||                 |||||| |    || |  ||||||  | || | |    |||
GGTTGTTAGAGCTTGGCATCTCCGTCCATCCCTTATCTGGAAGGATGGGAAATGGATTGAATCTTCCAAAGTGGGGGCAAATGACAGTTCTACCCATGAGgtactttgtttag--gttcttctg-----gttcccc---------------aacttcatgtgagtctgctaacttttacattttgcatgcag

upper sequence: Vv00s0229g00110.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA11G03650.1 (Glycine max), 5'ss of exon 12
AGTTGTTAGAGCTTGGCATCTTCGGCCATCTCTCATCTGGAAGGATGGGGAATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatct--agatgtgcttatgcttgaattccttttgatgctagattgaaacttcttagttgtttattaacttcaatatctggtgcccag
 |||||||||||||||||||| || ||||| || ||||||||||||||  ||||||||||||  |  |      |   |||||||    ||  ||||||||| || | | |   | | | ||  |||   || | | |  |   ||    |  ||||| |   || |  ||  |                    
GGTTGTTAGAGCTTGGCATCTCCGTCCATCCCTTATCTGGAAGGATGGAAAATGGATTGAATCTTACAAAGTGGGGACAAATGACAGTTCTACCCATGAGgtattttgttttaggttcttctactgccccaacttcatgcgggtctgtgct--aacttttacattttgcatgcag-------------------
















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|71872839|gb|DT021894.1|DT021894
EST:     AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAG                         GGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
genomic: AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatc ... tggtgcccagGGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
EST: gi|294966464|gb|GW839571.1|GW839571
EST:     AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAG                         GGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
genomic: AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatc ... tggtgcccagGGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
EST: gi|34542799|gb|CF511031.1|CF511031
EST:     AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAG                         GGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
genomic: AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatc ... tggtgcccagGGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
EST: gi|110691518|gb|EE069708.1|EE069708
EST:     AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAG                         GGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
genomic: AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatc ... tggtgcccagGGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
EST: gi|34542883|gb|CF511115.1|CF511115
EST:     AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAG                         GGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
genomic: AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatc ... tggtgcccagGGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
EST: gi|110713658|gb|EE089772.1|EE089772
EST:     AATGGATTGNATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAG                         GGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG
genomic: AATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatc ... tggtgcccagGGTGATACACCACAGGAAAAGCGATTGAAGTTGGGCAGTCCAGCAGTAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGTTAGAGCTTGGCATCTTCGGCCATCTCTCATCTGGAAGGATGGGGAATGGATTGAATGGTCAAGTTCAAGAGAAAATGACCACACTGTCCATGAGgtgttatatctagatgtgcttatgcttgaattccttttgatgctagattgaaacttcttagttgtttattaacttcaatatctggtgcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA