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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttttatgtttttgtctcttttttatttattatttatttatttttcttttatcctaaactaacctggtgtgcttgtctctgcaattttgtctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG

Basic information

species Vitis vinifera
transcript Vv18s0076g00260.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 13
------gtttttatgtttttgtctcttttttatttattatttatttatttttcttttatcctaaactaacctggtgtgcttgtctctgcaattttgtctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
       |||||||||| |  ||| || || | |||  ||| |  | | | | || |   || ||   |  |    |   | ||| |   | || |  |   |||||||||||||||||||||| |||||||| |||||||| || || ||
attagcttttttatgttctcttctattattcaattaccattaacctctatatgttctgctctcaa---atttaacat---tttctttttcacttggattaattcagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAACACAGG

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 13
gtttttatgtttttgtctcttttttatttattatttatttatttttcttttatcctaaactaacctggtgtgcttgtctctgcaattttgtctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
 |   |||||| || ||| || || | |||  ||| |  | |   | || |   || ||    |    |   | | ||| |   | || |  |   | |||||||||||||||||||| |||||||| |||||||| ||||| ||
ttcgatatgttcttttctattattcaattaccattaacctctacatgttcttctctcaaagctcaatttaaccatatctttttcacttggattaatttagAGCTCATCATGGCTTTGGATGGGTTGGAGAATGGGCTAATACAGG

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: EFJ35129 (Selaginella moellendorffii), 3'ss of exon 9
gtttttatgtttttgtctcttttttatttattatttatttatttttcttttatcctaaactaacctggtgtgcttgtctctgcaattttgtctgtgtc-agAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
                                 || ||| || |    |  | |       |||   |    |  | |||  |  |||| ||  | || ||||||||||| || ||||| ||||||||||||||||| ||| | ||
--------------------------------gttaattcatatg--gtcaagctcgtgtgaac---gctaaccagcctcctcttttttatcaatctctagAGCTCATCACGGATTTGGATGGGTTGGCGAATGGGCAAATTCTGG

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|110719053|gb|EE096590.1|EE096590
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110720867|gb|EE097166.1|EE097166
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110720638|gb|EE096734.1|EE096734
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110718519|gb|EE095448.1|EE095448
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110696366|gb|EE072430.1|EE072430
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110720216|gb|EE095942.1|EE095942
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110720676|gb|EE096807.1|EE096807
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110720592|gb|EE096647.1|EE096647
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110719214|gb|EE096935.1|EE096935
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110713860|gb|EE090149.1|EE090149
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110718805|gb|EE096054.1|EE096054
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110719766|gb|EE095191.1|EE095191
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|30302844|gb|CB979638.1|CB979638
EST:     GGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGATTGGGTTGGCGAATGGGCCAATACCGG
genomic: GGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
EST: gi|110720643|gb|EE096746.1|EE096746
EST:     ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA                         AGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
genomic: ATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAAgtaaaactgc ... tctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttatcctaaactaacctggtgtgcttgtctctgcaattttgtctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG
            aactaac  putative branch site (score: 1)
                                        ttttgtct  putative PPT
          taaactaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttatgtttttgtctcttttttatttattatttatttatttttcttttatcctaaactaacctggtgtgcttgtctctgcaattttgtctgtgtcagAGCTCATCATGGCTTTGGTTGGGTTGGCGAATGGGCCAATACCGG

- - - - - - -tgtctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctctgc