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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagaatagatttgatgttacatgtagaaatttatgcttcttgctcaactttatgttttataactctttcttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT

Basic information

species Vitis vinifera
transcript Vv02s0025g01580.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 2
-----------tgaagaatag----atttgatgttacatgtagaaatttatgcttcttgctcaactttatgttttataac-tctttcttactt-----tgtcca----cct----tgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT
           |  | |||||    || |  |  | | | |  |  | | |  | |||    ||        ||| |||| ||| | | |  |     | || |    |||    | | ||   |  || |||||||||||| |||| ||||||||  |||| || || |||||||||||||| || ||||||||||| |||||  | ||  ||  ||| ||||| | |
gtaaaacacgctataaaatagtattatctttttattcctttttacttcttttatacttttcaaaagcagcaatttgtaacatctctgtaaagtaaaagtatctaaattcctaaaatatgtcttttctagATTTGATGCTGTCGTTCATTTTGCTGGTCTGAAAGCTGTGGGTGAAAGTGTGCAGAAGCCATTGCTTTATTATGACCATAATGTTGCTGGGACAATAATT

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g28730.1 (Oryza sativa), 3'ss of exon 2
------------------tgaagaataga--tttgatgttacatgtagaaatttatgcttctt-----gctcaactttatgttttataactctttcttactttgt-ccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT
                  | |   || |    || |  |||  || |    ||| || ||| |     ||  |    |     | || | |  || ||  ||  |   | ||| ||| |  | ||| || ||||||||  |||||||||||||| | || || || || ||||||||||| || ||||||||||| || || |||||  ||| ||| ||| | | |
gtaaaacgtactggttttttagttatggtatctttactttatctggatgcttttctgtttccttgcatgcagaggcatgcccatcatcattacttgttctttattgttagcttctttgcttttcagATTCGATGCTGTAGTTCACTTTGCTGGGCTAAAAGCTGTGGGCGAAAGTGTGCAGAAGCCATTGCTTTATTACGACAACAATGTTAATGGAACAGTAAAT

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
-----------------------------------tgaagaatagatttgatgttacatgtagaaatttatgcttcttgctcaactttatgt-tttataactctttcttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT
                                   |  | |||  |||   | ||  ||||  |   || |  |   ||   |    | ||    |   |||  ||  ||      | ||  ||||  |    ||| ||||||||||| ||||| ||||||||  |||| || ||||| |||||||| ||||| || |||||||| |||||  | ||  || |||||||||| | |
gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagccttgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctc----cagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------------tgaagaatagatttgatgttacatgtagaaatttatgcttcttgctcaactttatgttttataactctttcttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT
                                                                                  | || || ||||||     |   ||    ||| | | ||  |||  || | ||     ||  |||| ||||| || |  |   | ||  ||     |||| |||||||||||||| |||||||||||  |||| ||||| || ||||||||||||||||| || || |||||| | |||||| | | ||| ||||| |||
gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaatattattaaaaaaagatttatctgtcggtg----aatatgttctctttgtacatcattg-accttgcaactttttctcacctctttttcttttctt-----gcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 2
------------------------------------tgaagaatagatttgatgttacatgt-agaaatttatgctt-cttgctcaactttat-gttttataactctttcttactt-tgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT
                                      || |||   | |  | ||   |||  |   || ||| || ||||  | | ||| |    || ||||| ||| | | |  |||     |  ||| | |||||| ||||||||||| || || ||||||||| | |||||||| |||||||| ||| | |||||| |||| |||| ||| |||||| | || || |||||   |
gtaaggatttggcagaaatttttataattgaaaaagaaaaaaatgattgttcttttctttgtcggtgcttcatgttttcttgtactagtttgttaagttgtaactgtttttcattcatgtatgtgtctttttc-ctgcagGTTTGATGCTGTGATACATTTTGCTGGGCTTAAGGCAGTGGGTGAAAGCGTGGATAAACCACTGCTCTACTTTGACAACAACTTGATAGGGACAATCGTT

upper sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------------tgaagaatagatttgatgttacatgtaga--aatttatgcttcttgctcaactttatgttttataactctttcttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT
                                                                     |  | || |   ||| ||| |||| |   ||| | | ||  |||  || | ||| |  ||  |||| ||||| || |  |    ||| | |    ||||| || ||||||||||| || ||||||||  |||| ||||| || ||||||||||||||||| || || |||||| | |||||| | | ||| ||||| |||
gtaaggattatgagagaagcttctttctttttatgattctgatttgagtatgacagaagttatttcaatattattaaaagagat-ttatatgtcggtgaatatgttctctttgtacatcatta-gccttgcaactttttctcacctcctttttcttttct----tgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT

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|110720449|gb|EE096391.1|EE096391
EST:     CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110719820|gb|EE095280.1|EE095280
EST:     ATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: ATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110718272|gb|EE094913.1|EE094913
EST:     CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110731724|gb|EE106396.1|EE106396
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110720256|gb|EE096017.1|EE096017
EST:     CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110720916|gb|EE097257.1|EE097257
EST:     CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110697145|gb|EE073879.1|EE073879
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|161708830|gb|FC060896.1|FC060896
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110718494|gb|EE095391.1|EE095391
EST:     CTAAAGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110720332|gb|EE096162.1|EE096162
EST:     ATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: ATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110727068|gb|EE103430.1|EE103430
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110728721|gb|EE104535.1|EE104535
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110732185|gb|EE107249.1|EE107249
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|71860637|gb|DT009692.1|DT009692
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|71883897|gb|DT032952.1|DT032952
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110727091|gb|EE103475.1|EE103475
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|30125545|gb|CB910884.1|CB910884
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110708350|gb|EE085791.1|EE085791
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|71861707|gb|DT010762.1|DT010762
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110718330|gb|EE095043.1|EE095043
EST:     CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110719030|gb|EE096543.1|EE096543
EST:     CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTC-ACAAA                         TTTTGATGCTGTCATTCACTTAGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: CTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|110709164|gb|EE084386.1|EE084386
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|71856066|gb|DT005121.1|DT005121
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
EST: gi|30126470|gb|CB911809.1|CB911809
EST:     TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAA                         TTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT
genomic: TTGGATCTAAGGGACAAACAAGCGCTTGAACAACTTTTTGCCTCAACAAAgtaagcattt ... tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaactttatgttttataactctttcttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT
                       ttcttac  putative branch site (score: 2)
                   ctctttcttactttgt  CT-rich tract
     tttatgttttataact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaagaatagatttgatgttacatgtagaaatttatgcttcttgctcaactttatgttttataactctttcttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCATTGCTTTACTATGATAACAACCTTATTGGCACAATTACT

- aagaata
- - - - - - - - - - -catgtag
- - - - - - - - - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - - - - -gctcaac