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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgtgcatcataattatttatttcttgataaattgtcacaaagccacatggttttcactaggttttttatttatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA

Basic information

species Vitis vinifera
transcript Vv05s0062g00210.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g05080.1 (Oryza sativa), 3'ss of exon 2
actgtgcatcataattatttatttcttgataaatt---gtcacaaagccacatggttttcactaggttttttatt-----tatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA
         ||||  ||  | | |||  ||   |    ||  |  ||  |  | |   | | | |  | | |        | | |  |         |   | ||||||||||  | |||||||||| | |||||||||| || ||||||||  || ||| ||||||||||||||| ||||||||    |
--------acatatgtaactctctctaaatgtttccaggttccccagtaatttagccatgattggagtatctgacaggagtgttttgtttcctgccctgtgtttgcagGACACGGTGACTGGGTTTTAGTTGGCTGGAGTTGGCAATGTTGATCTGAGGAAAAAGACAAATTATCTTATTGTTGATAACA

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g57854.1 (Oryza sativa), 3'ss of exon 2
actgtgcatcataattatttatttcttgataaattgtcacaaagcca--catggttttcactaggttttttatttatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA
 ||   ||| |   |  | ||    | |  |  ||  |        |  |||| || |    |  |        |||    |         |   | ||||||||||  | |||||||||||| |||||||||| || ||||||||  || ||| |||||||||||| || ||||||||    |
-cttgacataa-gctgctctaagagtagccaggttccccagtgtttaatcatgattatagtcatctgaaaggaatattctgtttcctcccctgtgtttgcagGACACGGTCACTGGGTTTTTGTTGGCTGGAGTTGGCAATGTTGATCTGAGGAAAAAGACAAATTACCTTATTGTTGATAACA

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G26580.1 (Glycine max), 3'ss of exon 2
--actgtgcatcataattatttatttcttgataaattg--tcacaaagccacatggttttcactaggttttttatttatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA
    | |   |  ||||| |||  |  ||| ||   ||  | ||  |   | ||| ||   ||    |  |  |    |   |||  |  |   |  ||  ||||| ||| ||  ||| |||||| ||||||||||||| ||||||||| | || || ||||||||||| |||||||| || ||||
ctgttata-gttgtaattttttcgtaattggtattctgaataactgattgaaatgattaaaac---atcctgaaggcttacaatgactactatattttacacagGATACTGTAGTTGGATTTTTGTTGGCTGGAGTGGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 2
--actgtgcatcataattatttatttcttgataaattg--tcacaaagccacatggttttcactaggttttttatttatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA
    | |   |   | || |||  |  ||| ||   ||  |  |  |   | ||| ||   ||    |  |  |    |   ||| ||  ||  |  ||  ||||| ||| ||  ||| ||| || ||||||||||||| ||||||||| | || || ||||||||||| |||||||| || ||||
ctgttata-gttgcagtttttttgtaattggtattctgaatttctgattgaaatgattaaaac---atcctgaaggcttacaatgaatactttattttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA

upper sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT4G02620.1 (Arabidopsis thaliana), 3'ss of exon 2
----actgtgcatcataattatttatttcttgataaattgtcacaaagccacatggttttcactaggttttttatttatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA
    | ||  ||  ||  |     | || ||    || | || |   |  | |    |||  | |  ||   |     |   | |  | |   ||  | | ||||||||| |   ||| |||||| |||||||||| |||||||||||| |  |||| ||||||||||| ||||| || || ||||
cttaattggcca--atggtggcagaattgtttg-gaactatc-cgttgatataaccctttagcaatcttcaatgccacttacaagacttaaattttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAA

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|110400937|gb|EC967524.1|EC967524
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
EST: gi|110384574|gb|EC949021.1|EC949021
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
EST: gi|110425951|gb|EC992347.1|EC992347
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
EST: gi|51052279|gb|CO819479.1|CO819479
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
EST: gi|26264288|gb|CA815351.1|CA815351
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
EST: gi|34543784|gb|CF512016.1|CF512016
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
EST: gi|26266198|gb|CA817261.1|CA817261
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
EST: gi|27583949|gb|CB006644.1|CB006644
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
EST: gi|110687266|gb|EE064524.1|EE064524
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
EST: gi|37188187|gb|CF607536.1|CF607536
EST:     CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAG                         GACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG
genomic: CTCAAATCCCCACTAAAAGCTCGGCACTCATTGCTATGATTGCTGATGAGgtatggatta ... tcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatggttttcactaggttttttatttatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA
                            atctgat  putative branch site (score: 4)
                  ttttttatttatctga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgtgcatcataattatttatttcttgataaattgtcacaaagccacatggttttcactaggttttttatttatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - tgcatca
- - - - - - - - - - - - - - - - - - tcacaaa
- - - - - - - - - - - - - - - - - - - - - -gccacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggatga