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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcttatggcttctgatattttgtgatcttatgtttctgctatgtgtgcatgcttgcaattgctctaatatgaaccttgattatgacatttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAACTATGACTGG

Basic information

species Vitis vinifera
transcript Vv10s0405g00020.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0405g00020.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G351417_T03 (Zea mays), 3'ss of exon 1
attcttatggcttctgatattttgtgatcttatgtttctgctatgtgtgcatgcttgcaattgctctaatatgaaccttgattatgacatttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAACTATGACTGG
             |   |  |||    | |||  |||| |     | | |||  | |    || |||||| ||  | |  |||||| | ||||   ||||||||||||||| || |||||| | || |||||||||||||| || || || ||||| |||
------------gcgagttgtttcactttttacctttcagagtacttttcata-tagtg--tggtctaatctggtcat--attatg-cttttgtaagcagGAACTATTGACAAGACATAAAGCAACCGTTGCTGAATTTCTCTCCAACAATTATGATTGG
















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|110718449|gb|EE095298.1|EE095298
EST:     CA-CTTNCCAAATTT-GACATTGCTGCAGATGCTGCTGNCA-CTTTTA-G                         GAACTATTGACGA
genomic: CAACTT-CCAAATTTTGACATTGCTGCAGATGCTGCTG-CAACTTTTAAGgtttgtggat ... ttgcttgcagGAACTATTGACGA
EST: gi|30136804|gb|CB922142.1|CB922142
EST:     TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAG                         GAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
genomic: TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGgtttgtggat ... ttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
EST: gi|161715770|gb|FC066174.1|FC066174
EST:     TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAG                         GAACTATTGAC
genomic: TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGgtttgtggat ... ttgcttgcagGAACTATTGAC
EST: gi|110397538|gb|EC963286.1|EC963286
EST:     TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAG                         GAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
genomic: TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGgtttgtggat ... ttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
EST: gi|110712226|gb|EE089603.1|EE089603
EST:     TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAG                         GAACTATTGACGAAGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
genomic: TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGgtttgtggat ... ttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
EST: gi|33403466|gb|CF209093.1|CF209093
EST:     TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAG                         GAACTATTGACGAGGCATAAATCTACGGTTGCTGGATTTCTTTCTAAGAAC
genomic: TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGgtttgtggat ... ttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
EST: gi|110699863|gb|EE077248.1|EE077248
EST:     TCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGNCA-CTTTTAAG                         GAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
genomic: TCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTG-CAACTTTTAAGgtttgtggat ... ttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
EST: gi|110381120|gb|EC946437.1|EC946437
EST:     TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAG                         GAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
genomic: TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGgtttgtggat ... ttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
EST: gi|110724431|gb|EE100255.1|EE100255
EST:     TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAG                         GAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC
genomic: TTCAACTTCCAAATTTTGACATTGCTGCAGATGCTGCTGCAACTTTTAAGgtttgtggat ... ttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcatgcttgcaattgctctaatatgaaccttgattatgacatttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAACTATGACTGG
                                            tttgctt  CT-rich tract
                     taatatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcttatggcttctgatattttgtgatcttatgtttctgctatgtgtgcatgcttgcaattgctctaatatgaaccttgattatgacatttgcttgcagGAACTATTGACGAGGCATAAATCTACGGTTGCTGAATTTCTTTCTAAGAACTATGACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - -tatggct
- - - - - - - - - - - - - - - - - - -ctgctat
- - - - - - - - - - - - - - - - - - - - - - - - gcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgaac