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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttgaggaattgctcttcattgcaatttgatttatctggtgagttcagttgtacaatatttttccaattttcactaattggagctgcatattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA

Basic information

species Vitis vinifera
transcript Vv08s0040g00020.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G44840.1 (Glycine max), 3'ss of exon 3
-tgcttgaggaattgctcttcattgcaatttgatttatctggtgagttcagttgtacaatatttttccaattttcactaattggagctgcatattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA-
 || ||     ||   | | | | |   | | | |||     |||||  | || |      |   | ||||  |     | |     | ||| ||| |||||||||||||||||| |||||| ||||||||||||||||||| |||||||||||||  ||||| ||  ||||||||  | || ||||| |||||||  |   
ttgtttccttgataagtgtcc-tcggggtcttagttagaatttgagta-atttattttccttcggtacaataatttaatactatgaatccatcttcaacaggTGATTGCAAATTTCAGTGCAGCATGGTGTGGTCCTTGTAAGATGATTGCACCATATTACTGTGAGTTATCTGAGAAATACACTTCTATGATGTTCTTGGT

upper sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G40970.1 (Glycine max), 3'ss of exon 3
-----tgcttgaggaatt-------gctcttcattgcaatttgatttatctggtgagttcagttgtacaatatttttccaattttcactaattggagctgcatattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA
     | |||||  | |        | ||||  ||  ||||||| | || || |    |  |  |||||||| |||   |||    ||||  |  | |    | |   |||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||||  ||| ||||  ||||||||  | || | ||| |||||||  |  
ttgtttccttgataagtgtcctcagggtcttagttagaatttgactaatttgttttccttgg--gtacaataattt---aat----acta--taaatccttgt-tcaaacagGTGATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGATGATTGCGCCATATTACAGCGAGTTATCTGAGAAATACACATCTATGATGTTCTTGT

upper sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G00410.2 (Glycine max), 3'ss of exon 3
tgcttgaggaattgctcttcattgcaatttgatttatctggtgagttcagttgtacaatatttttccaattttcactaatt------ggagctgcatattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA
  ||||| || ||    |||| |  |  ||  |||| |             |||||  |||||        | || || ||        |||| ||| ||  |||||| ||||||||||| ||||| |||||||||||||||||||| |||||||||||||  || |||||  | || |||  | |||| ||| | |||||  || 
--cttgaagattt----ttcagtatatctttttttacccccctttcctgagtgtactgtatttcctttgggtgcaatagttaattctaaagcttcatgtttaacagGTTATTGCAAATTTCAGTGCCACATGGTGTGGTCCTTGTAAGATGATTGCACCATATTATTGCGAGTTGTCCGAGAAATACCCATCTATCATGTTCTTAT

upper sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G34660.1 (Glycine max), 3'ss of exon 3
tgcttgaggaattgctcttcattgcaatttga----tttatctggtgagttcagttgtacaatatttt--tccaattttcactaattggagctgcatattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA
  ||| |  | ||  | |  |   | |         ||| | |  |||||  |  ||||     |||   | ||||  | | |   |  |||| ||| ||  |||||| ||||||||||| ||||||||||||||||||||||||||  |||||||||||   || |||||  | || | |  | |||| ||| | |||||  || 
--cttaa--atttcttttaaacccccacccagcccctttctttcatgagtata-ctgtatttcctttgggtgcaatagttaatt-ctaaagcttcatttttaacagGTAATTGCAAATTTCAGTGCAACATGGTGTGGTCCTTGTAAGGTGATTGCACCACATTATTGCGAGTTGTCCGTGAAATACCCGTCTATCATGTTCTTAT

upper sequence: Vv08s0040g00020.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G08710.1 (Arabidopsis thaliana), 3'ss of exon 3
tgcttgaggaattgctcttcattgcaatttgatttatctggtgagttcagttgtacaatatttttccaattttcactaattggagctgcatattcga--cagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA
         | ||   | |  |||  ||||   || |||  ||   |  |||||    | ||| || |  |    |||||     ||      | ||  |||||| ||||||| || ||||| |||||||||||||| ||||||||  | |||||||| | |  ||| || || |||  |||  ||||||| ||||| ||  
------gtaatttttccctttttgatatttctcttctctcatgtagt--gttgtgtt-tgtttctcaatctcatgctaatatcttctcttctcttgaaacagGTGGTTGCAAACTTCAGTGCGACATGGTGTGGTCCGTGTAAAATTGTGGCACCATTTTTCATCGAGCTCTCAGAGAAACATTCTTCTCTTATGTTCCTTC

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|32244946|gb|CD710765.1|CD710765
EST:     AGAAAATTGGGAGGAGAAGTTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AGAAAATTGGGAGGAGAAG-TTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|110374147|gb|EC938715.1|EC938715
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|34547173|gb|CF515405.1|CF515405
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|27581758|gb|CB004453.1|CB004453
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|110726854|gb|EE103001.1|EE103001
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|32245165|gb|CD710984.1|CD710984
EST:     AGAAAATTGGGAGGAGAAGTTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AGAAAATTGGGAGGAGAAG-TTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|34547261|gb|CF515493.1|CF515493
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|32245155|gb|CD710974.1|CD710974
EST:     AGAAAATTGGGAGGAGAAGTTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AGAAAATTGGGAGGAGAAG-TTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|27580823|gb|CB003518.1|CB003518
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|32250353|gb|CD716172.1|CD716172
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|161715399|gb|FC064896.1|FC064896
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|110368898|gb|EC933032.1|EC933032
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
EST: gi|110701721|gb|EE079613.1|EE079613
EST:     AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATT                         GTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA
genomic: AAGAAAATTGGGAGGAGAAGTTGGCAGAAGCAAGCAAAGATGGAAAGATTgtaagttctt ... tattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagttgtacaatatttttccaattttcactaattggagctgcatattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA
                            cactaat  putative branch site (score: 2)
           aatatttttccaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttgaggaattgctcttcattgcaatttgatttatctggtgagttcagttgtacaatatttttccaattttcactaattggagctgcatattcgacagGTGATTGCAAATTTTAGTGCAACATGGTGTGGTCCTTGTAAAATGATTGCACCATTCTACTGCGAACTATCTGAGGCACACCCTTCTCTGATGTTTCTAA

tgcttga
- - - - - - - - - -cattgca
- - - - - - - - - - - - - - - - - - -ctggtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggagct