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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgtatttgcgcaggcataattactgcatatggcagctcaattgaaaattttaaatgattgtttgtttcttgcag

Basic information

species Vitis vinifera
transcript Vv03s0063g01080.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os03g41460.1 (Oryza sativa), 5'ss of exon 5
AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgtat---ttgcg--caggcataattactgcat---------atggc-agctcaattgaaaattttaaatgattgt-ttgtttcttgcag
 ||||| ||||| ||||| |||||| | || ||||||||||| ||||| || || |||||||| || || || |||||||| |||   |||||||| ||||| |   |||||  ||  ||  || || |  |         ||  | |  |  |||  |||   | |  |||  | ||  || | ||||
TGATGTGTGGTCGTGTGGAGTAACCCTCTACGTAATGCTGGTTGGTGCATATCCTTTTGAGGATCCAGATGAGCCTAAGAATTTCAGGAAGACAATTCAGgtttccattgcggtcatccaacatcacggtctcaaaatttcataaccattttgattacaaaaactgatcgatgatcttcattttcgcag

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G171435_T02 (Zea mays), 5'ss of exon 7
AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgtatttgcgcaggcataattactgcatatggca-gctcaattgaaaa-----ttttaaatgat-tgtttgtttcttgcag--------------------
 ||||| ||||| ||||| |||||| | |||||||||   || ||||| || || ||||| ||||| || || ||||||||||||| ||||||||| |||||  ||         | ||   | ||  | | | || ||   ||  |     || |  |   | | | |||   |  |||                    
TGATGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGCTGTTGGTGCATATCCTTTTGAAGACCCAGAAGAGCCTAAGAACTTCCGCAAGACAATTCAGgttattttttttctttcatggatacaagttgaatgcacaccagagcacgcgcttgtgtacagtgtatgtgtcaatcacagcacatatgtgtcctagcaca

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G066867_T01 (Zea mays), 5'ss of exon 6
AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgtatt-tgcgcaggcataattactgcatatggcagctcaattgaaaattttaaatgattgtttgtttcttgcag-----------
 ||||| ||||| ||||| |||||  | || || |||||||| ||||| || |||||||||||||| || || |||||||| |||   |||||||| ||||| |  |  |||| |    ||||  ||    |   |||||||||    |     ||||     | |      |            
TGATGTGTGGTCATGTGGAGTAACGCTGTACGTGATGCTGGTCGGTGCATATCCATTTGAGGACCCAGATGAGCCTAAGAATTTCAGGAAGACAATTCAGgtttcctttgcagactggtttacaccagc--gtctctcaattgactgctcatcctgatcaaacgctgacgagatctgcttggcag

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA07G33120.1 (Glycine max), 5'ss of exon 7
AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgtatttgcgcaggcataattactgc--atatggcagctc-aattgaa--aatttt---aaatgattgtttgtttcttgcag
|||||| |||||||| ||||| ||||||||||| ||| |||||||||| || || |||||||| || ||||||||||| || |||| |||||||||||| |||  |    |  | |  || |  |  || ||| |  |   ||||||  | ||||   ||||   ||  ||||  ||||||
AGATGTGTGGTCTTGCGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAATACATgtaactaatgacactttttttcaaccaatgtggtacttttgattgaattagttttcctaaattgatgaatgttggttgcag

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA02G15330.1 (Glycine max), 5'ss of exon 7
AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgtatttgcgcaggcataatt---actgcatatggcagctcaattgaa--aatttt---aaatgattgtttgtttcttgcag
|||||| |||||||||||||| ||||||||||| ||| |||| ||||| || || |||||||| || ||||||||||| || |||| |||||||||||| |||  |       | |  ||   | |   | ||  |  |  ||||||  | ||||   |||    ||  || || ||||||
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTTGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGCAAGACAATACATgtaactaattgcacctttttttcaatcagtgtgttactttgattgaattagttttcctaaactgatgcatgcttgttgcag

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA20G01240.1 (Glycine max), 5'ss of exon 7
AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgta-tttgcgcaggcataattac-tgcatatggcagctcaattgaaaattttaaatgattgtttgtttcttgcag
|||||| |||||||||||||| ||||||||||| ||| |||||||||| || || |||||||| || ||||||||||| || ||||  |||||||| || |||   | |     |||  |||  |  |  | | |     ||||||    |||||   |||  | || |||||||
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaacgtagtaataatattgaattacttaaactgttggattttgcttgcag

upper sequence: Vv03s0063g01080.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA07G29500.1 (Glycine max), 5'ss of exon 7
AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgta-tttgcgcaggcataattactgca-tatggcagctcaattgaa-----aattttaaatgattgtttgtttcttgcag
|||||| |||||||||||||| ||||||||||| ||| |||||||||| || || |||||||| || ||||||||||| || ||||  |||||||| || |||   | |     |||  |||   || | | | |     ||||||       | |||||   |||  |  | |||||||
AGATGTGTGGTCTTGTGGGGTGACCTTATATGTCATGTTGGTGGGTGCATATCCTTTTGAGGATCCAGAGGAACCTAAAAATTTCCGGAAGACAATTCATgtaacctactgcaccatttttaggtcaatgtagtaataatattgaattacttttcttaaactgttggattatgcttgcag

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|71872877|gb|DT021932.1|DT021932
EST:     ACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAG                         AGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCT
genomic: ACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgtatttgcgc ... tttcttgcagAGAATTTTGAAAGTCCAGTATTCTATTCCAGATTATGTTCATATATCTCCT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATGTATGGTCTTGTGGGGTAACCTTATATGTAATGCTGGTGGGTGCTTACCCATTTGAGGACCCTGAGGAACCTAAGAACTTCCACAAGACAATACAGgtatttgcgcaggcataattactgcatatggcagctcaattgaaaattttaaatgattgtttgtttcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC