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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggattctatcattttcattgtgatggtaactttgtggaagaattggagtattgagcttcaatttccatggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAAATTGAGTGCTAAGCTCATGTTTGGCGCTGACAG

Basic information

species Vitis vinifera
transcript Vv04s0008g03770.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G094712_T04 (Zea mays), 3'ss of exon 3
----gtgaggattcta-tcattttcattgtgatggtaactttgtggaag--------aattggagta----ttgagcttcaatttccatggcattc--agGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAAATTGAGTGCTAAGCTCATGTTTGGCGCTGACAG----------------
    ||| |  | | |  || |         |   |     ||||||||        | ||| ||      || ||   || ||| | |   |||   ||||| || ||||| || || || || ||    || ||||| |||||||||||  |||| |||||||| || ||||||||||||||                
tctcgtgtgtgtacaagccactgatgcgaaaaaactgttggtgtggaagtttatgatacttgaagctgtattttagacacatttttcttcttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAGGTATTCTCTGTTTGAC

upper sequence: Vv04s0008g03770.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G094712_T02 (Zea mays), 3'ss of exon 3
----gtgaggattcta-tcattttcattgtgatggtaactttgtggaag--------aattggagta----ttgagcttcaatttccatggcatt--cagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAAATTGAGTGCTAAGCTCATGTTTGGCGCTGACAG
    ||| |  | | |  || |         |   |     ||||||||        | ||| ||      || ||   || ||| | |   |||   ||||| || ||||| || || || || ||    || ||||| |||||||||||  |||| |||||||| || ||||||||||||||
tctcgtgtgtgtacaagccactgatgcgaaaaaactgttggtgtggaagtttatgatacttgaagctgtattttagacacatttttcttcttatttctagGTCACGTGTCAAGGAGTACCTACCAATCACCGGTCTGGCTGAATTCAATAAGCTGAGCGCTAAGCTTATCTTTGGCGCTGACAG
















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|161712214|gb|FC061588.1|FC061588
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|161714368|gb|FC063209.1|FC063209
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|349822896|gb|FQ398283.1|FQ398283
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|71860471|gb|DT009526.1|DT009526
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|349825792|gb|FQ423087.1|FQ423087
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|161718975|gb|FC067020.1|FC067020
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCACAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|161706860|gb|FC055539.1|FC055539
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|351029008|gb|FQ435009.1|FQ435009
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|110698493|gb|EE076055.1|EE076055
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|110368860|gb|EC932986.1|EC932986
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|110711178|gb|EE087421.1|EE087421
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|71858885|gb|DT007940.1|DT007940
EST:     CTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|71858293|gb|DT007348.1|DT007348
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|349830105|gb|FQ420365.1|FQ420365
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|29783169|gb|CB349167.2|CB349167
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
EST: gi|30306042|gb|CB982836.1|CB982836
EST:     CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAG                         GTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA
genomic: CTTGTTCTGAATGTAGTGAGACGGGCAGAGCAGCTGCTTGTTAATGACAGgtgaggattc ... tggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtaactttgtggaagaattggagtattgagcttcaatttccatggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAAATTGAGTGCTAAGCTCATGTTTGGCGCTGACAG
 tggtaac  putative branch site (score: 2)
                                       tttccat  putative PPT
                                  ttcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggattctatcattttcattgtgatggtaactttgtggaagaattggagtattgagcttcaatttccatggcattcagGTCCCGGGTCAAAGAATATCTTCCTATTGTTGGGCTGGCAGAATTCAATAAATTGAGTGCTAAGCTCATGTTTGGCGCTGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA