Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCAGTCTTTCTTTGCTGCATTGAAGGCATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtgggtattgtaaaagaaaaaaaaaataatggacttgagataaatagttgtcataatattaaattccatgcctacaaataacatcctccatcttg...

Basic information

species Vitis vinifera
transcript Vv08s0056g00440.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00440.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os05g25180.1 (Oryza sativa), 5'ss of exon 6
GTCCAGTCTTTCTTTGCTGCATTGAAGGCATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgta---gtgtgggtattgtaaaa--gaaaaaaaaaataatg-gacttgagataaatagttgtca-taatattaaattccatgcctaca-aataacatcctccatcttg
|| ||||| ||||| |||||| |||| ||||||||||| ||||| || ||||||||  ||||||| ||  |||| ||||||   ||     || ||  ||   |   ||   || ||||  |  ||  |||| || |  | | |  ||   | ||  | |  |    ||||  |   |        
GTTCAGTCATTCTTGGCTGCAGTGAAAGCATTGTCACGTAAAGATGTGCATTATGGGTCTTATGCGACAGCAGAACAGgtaaacgttcatctactggcaagttgctcaacttaaaaatgcaatatgccataactattgataaatcgtaagcatttgtaggattttgtaatagtacaat--------

upper sequence: Vv08s0056g00440.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA18G45010.1 (Glycine max), 5'ss of exon 6
GTCCAGTCTTTCTTTGCTGCATTGAAGGCATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtgggtattgtaaaagaaaaaaaaaataatggacttgagataaatagttgtcataatattaaattccatgcctacaaataacatcctccatcttg-
|| || || |||||||||||| |||| |||||||| || |||||  | || ||||| |||||||| || ||||||||||||  |||||| |  |      |  |   | |  |||| ||| |  || ||  |     ||| | |   || || | |    |    |   | ||| |   
GTGCAATCCTTCTTTGCTGCAGTGAAAGCATTGTCGCGTAAAGAAATGCACTATGGGGCTTATGCAACATCAGAGCAGgtacagtgggtgtcttcttttgatcactgatttttggagttg-gtcaattaactactgaaatttcagtgtctatccattttcactctaatttacatttgtt
















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|110730035|gb|EE106655.1|EE106655
EST:     CATTGTCACGGAAAGAAGTTCATTATGGAGCTTATGCTACGTCAAAGCAG                         GTCAATGCACCTGGGGATTTGTGCGCTATTTGCCAGGAGAAGATGAAGGCT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
EST: gi|37184416|gb|CF603770.1|CF603770
EST:     CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAG                         GTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
EST: gi|30253236|gb|CB970787.1|CB970787
EST:     CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAG                         GTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
EST: gi|110729839|gb|EE106235.1|EE106235
EST:     CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAG                         GTCAATGCGGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
EST: gi|110368592|gb|EC932580.1|EC932580
EST:     CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAG                         GTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
EST: gi|161721710|gb|FC071108.1|FC071108
EST:     CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAG                         GTCAATGCAGCTGGGGATCTGT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGT
EST: gi|22011953|gb|BQ796987.1|BQ796987
EST:     CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAG                         GTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
EST: gi|110390287|gb|EC955189.1|EC955189
EST:     CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAG                         GTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
EST: gi|110396248|gb|EC961929.1|EC961929
EST:     CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAG                         GTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
EST: gi|30253079|gb|CB970630.1|CB970630
EST:     ATTGTCACGGAAAGAGGTTCATTTATGGAGCTTATGCTACGTCAGAGCAG                         ANCAATGCAGCTGGANATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
genomic: ATTGTCACGGAAAGAGGTTCATT-ATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGTGCGCTATTTGCCAGGAGAAGATGCATGCT
EST: gi|161719084|gb|FC069337.1|FC069337
EST:     CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAG                         GTCAATGCAGCTGGGGATCTGT
genomic: CATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtggg ... tctaatgtagGTCAATGCAGCTGGGGATCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCAGTCTTTCTTTGCTGCATTGAAGGCATTGTCACGGAAAGAGGTTCATTATGGAGCTTATGCTACGTCAGAGCAGgtagtgtgggtattgtaaaagaaaaaaaaaataatggacttgagataaatagttgtcataatattaaattccatgcctacaaataacatcctccatcttg

- - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccatc