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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagctgtcatttttattttacatgtcatgtgagtgtgtgttcctatttgtctctgaggttacttttattattgcag

Basic information

species Vitis vinifera
transcript Vv19s0014g05210.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os08g04270.1 (Oryza sativa), 5'ss of exon 8
AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgag-tagctgtcattt--ttattttaca-----tgtcatgtgagtgtgtgttcctatttgtctctgaggttacttttattattgcag--------
|||||||| | ||||| ||| |||| || |||||||| || |||||||| |||||||| ||||||||||| || ||||| ||  | ||  | || |||  | || ||  |     | |  ||  ||  | ||||  |   |   | ||   | |     ||  ||            
AATTCTGGCCATATGTTGAGCAATCCTTTACATGGACTGACCTTCCATCAAAATTTCCAACAAAATATGTGCAATTTCCGgtatgctaaatatcttttgatcatctttgaactattattttgcaagattttgttatttcatccatgtggcatcataccaatctttctctgcttccag

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G148924_T06 (Zea mays), 5'ss of exon 7
AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagt------agctgtcattt-----ttattttacat-gtcatgtgagtgtgtgttcctatttgtctctga---ggttacttttattattgcag
|||| |||   ||||| || ||||| |   ||||||| || |||||||| || ||||| ||||||||||| |||||||| ||  ||      |  |||| | |     |||| || ||  ||| |||  |||| |  ||||  |    || ||      |  || | || || |||
AATTTTGGCTATATGTTGACAAATCATATTCATGGACTGACCTTCCATCAAAGTTTCCAACAAAATATGTCCAGTTTCCAgtatgttttcacaattgtcttatatccattatcttgcaaagtcctgttggtgtctaatcctcatgccatcagactgacctgtttcttttgtttcag

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA02G17110.1 (Glycine max), 5'ss of exon 7
AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagctgtcatttttattttacatgtcatgtgagtgtgtgttcctat---ttgtctctgaggttacttttatt--attgcag
| |||||||| ||||| || ||||| || |||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||| |||| | ||   |||| |  ||||| |||     |  | | |||  ||   || | ||| |   ||    ||    ||| |||
AGTTCTGGACATATGTAGAAAAATCATTTACATGGACAGATCTTCCTTCTAAGTTTCCCACAAAATATGTCCAGTTTCCTgtaagtaacagtttatttt-tggtacatatcaatcatgaatattttctaatttcttatttctaattctagcaatacctaatttcag

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G02690.3 (Glycine max), 5'ss of exon 6
AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagctgtcatttttattttacatgtcatgtgagtgtgtgttcctatttgtctctgaggttacttttatta--ttgcag
| |||||||| ||||| || ||||| || |||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||| |||| |  |  ||||| |  ||||| |||| |||   | | |   |  || | ||| |  |||    ||     || |||
AGTTCTGGACATATGTAGAAAAATCATTTACATGGACTGATCTTCCTTCTAAGTTTCCCACAAAATATGTCCAGTTTCCTgtaagtaacaatttttttt-tggtacatatcat-tgatcttttctaatttcttatttctaattttagcaatacctattttcag

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA13G36310.1 (Glycine max), 5'ss of exon 7
AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagctgtcatttttattttacatgtcatgtgagtgtgtgttcctatttgtctctgaggttacttttattattgcag
| |||||||| ||||| || ||||| | ||||||||| |||||||| || || ||||| ||||||| ||| ||||||||||| || | | ||   |||| |  ||||| |||| |||   | |  |  | | |   |||   | ||| |     ||| |||
AGTTCTGGACATATGTAGAAAAATCATCCACATGGACAGATCTTCCTTCCAAGTTTCCAACAAAATTTGTCCAGTTTCCTgtaagcaacagttcatttt-tggtacatatcat-tgatctttttctaatttctaattctagtgataccta----atttcag

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|161719190|gb|FC065436.1|FC065436
EST:     ATGGACGGATCTTCCAATCTAA-TTTCCGACAAA-TATGTACAGTTTCCT                         ATATTCATAGCATCCGTTCATTCAA-CTATGTTGA
genomic: ATGGACGGATCTTCCA-TCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagct ... attattgcagGTATTCATAGCATCCGTTCATTCAAACTATGTTGA
EST: gi|351053554|gb|FQ459301.1|FQ459301
EST:     CATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT                         GTATTCATGGCATCCGTTCATTCAAACTATGTTGACTGTAATAGGTGGCTG
genomic: CATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagct ... attattgcagGTATTCATAGCATCCGTTCATTCAAACTATGTTGACTGTAATAGGTGGCTG
EST: gi|351036699|gb|FQ457412.1|FQ457412
EST:     CATGGACGGATCTTCCATCTAAATTTCCGGCAAAATATGTACAGTTTCCT                         GTATTCATGGCATCCGTTCATTTCAA-CTATGTTGACTGTAATAGGTGG
genomic: CATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagct ... attattgcagGTATTCATAGCATCCGTTCATT-CAAACTATGTTGACTGTAATAGGTGG
EST: gi|110378718|gb|EC943862.1|EC943862
EST:     CATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT                         ATATTCATAGCATCCGTTCATTCAAACTATGTTGACTGTAATAGGTGGCTG
genomic: CATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagct ... attattgcagGTATTCATAGCATCCGTTCATTCAAACTATGTTGACTGTAATAGGTGGCTG
EST: gi|351043856|gb|FQ452650.1|FQ452650
EST:     ATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTTCCT                         GTATTCATGGCATCCGTTCATTCAAACTATGTTGACTGAAATA
genomic: ATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTT-CCTgtgagtagct ... attattgcagGTATTCATAGCATCCGTTCATTCAAACTATGTTGACTGTAATA
EST: gi|352791431|gb|FQ481010.1|FQ481010
EST:     CATGGACGGATCTTCCATCTAAATTTCCGGCAAAATATGTACAGTTTCCT                         GTATTCATGGCATCCGTTCATTCAAACTATGTTGACTGTAATAGGTGGCTG
genomic: CATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagct ... attattgcagGTATTCATAGCATCCGTTCATTCAAACTATGTTGACTGTAATAGGTGGCTG
EST: gi|351033874|gb|FQ447912.1|FQ447912
EST:     CATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCT                         GTATTCATAGCATCCGTTCATTCAAACTATGTTGACTGTAATAGGTGGCTG
genomic: CATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagct ... attattgcagGTATTCATAGCATCCGTTCATTCAAACTATGTTGACTGTAATAGGTGGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTCTGGACGTATGTGGAGAAATCTTTCACATGGACGGATCTTCCATCTAAATTTCCGACAAAATATGTACAGTTTCCTgtgagtagctgtcatttttattttacatgtcatgtgagtgtgtgttcctatttgtctctgaggttacttttattattgcag

- - - - - - - - - - - - - - - CATGGA