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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctggttttttgtgaaacccatttccatggttttgtgcatgccttgtttcttataccccaattttcagttttttcacttattaaaattatgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCTTGCTATAAACTTTTGTGTTCCAA

Basic information

species Vitis vinifera
transcript Vv02s0025g04580.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g04580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G27380.1 (Glycine max), 3'ss of exon 5
-----gtgctggttttttgtga-aacccatttccatggttttgtgcatgccttgtttcttataccccaattttcagttttttcacttattaaaattatgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCTTGCTATAAACTTTTGTGTTCCAA
      || || |   || ||  || ||| |   || |||  |  ||       ||    | | |     ||| | |||  |   | |||    ||     |  ||||||||||||| || || |||||||| |||||||| |||||||||||||| || ||| | ||||  |||   ||
agtgcttgttgatgccttctgtcaatccacta--atagttcagcacacattagtttagacagatcttctctttaattttaattggtcatt----ttcctgctatagGTTGTTGATGGAAAACTCTCACAGACCTGTTATCTCATGGCACTTGATTCCTGTTATCAGCTTTACTGTAAGAA

upper sequence: Vv02s0025g04580.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G32480.1 (Glycine max), 3'ss of exon 5
-----gtgctggttttttgtgaaacccatttccatggttttgtgcatgccttgtttcttataccccaattttcagttttttcacttattaaaattatgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCTTGCTATAAACTTTTGTGTTCCAA
      ||  | |   || ||  |  ||  |  | |   ||  |||  | ||  ||   | |   |  || ||  | |||| | ||  | |  ||     |  || |||||||||| || || |||||||| |||||||| |||||||||||||| || ||    ||||  |||   ||
agtgattgtggatgccttctgtcaatcaactaaaag---ttcagcacacattaatttagacagatc--ttctctttatttttaattggtcattttcctgctgtagATTGTTGATGGAAAACTCTCACAGACCTGTTATCTCATGGCACTTGATTCCTGTTACCGGCTTTACTGTGAGAA
















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|110387333|gb|EC951991.1|EC951991
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110698402|gb|EE075860.1|EE075860
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|351015524|gb|FQ447353.1|FQ447353
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGAACT-GTTATCTGATGGCACTTGATTC
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGA-CTTGTTATCTGATGGCACTTGATTC
EST: gi|110390437|gb|EC955346.1|EC955346
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110729426|gb|EE105370.1|EE105370
EST:     TGTCACATGCATATGATATTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCT
EST: gi|110699371|gb|EE076321.1|EE076321
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110691612|gb|EE069914.1|EE069914
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAA
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAA
EST: gi|294966823|gb|GW837842.1|GW837842
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110374042|gb|EC938533.1|EC938533
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110718761|gb|EE095962.1|EE095962
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110377475|gb|EC942541.1|EC942541
EST:     TGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|34545276|gb|CF513508.1|CF513508
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110699704|gb|EE076934.1|EE076934
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|30297572|gb|CB974366.1|CB974366
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTTGATGGGAAGCTGACAGANACTTGTTATCTGAT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGAT
EST: gi|110383242|gb|EC947601.1|EC947601
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110730120|gb|EE106836.1|EE106836
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110357104|gb|EC920414.1|EC920414
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|33402990|gb|CF208617.1|CF208617
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110698626|gb|EE076340.1|EE076340
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GNTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|30255111|gb|CB971558.1|CB971558
EST:     GTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGGAGAATATCCG                         GTTGTCGATGGGA
genomic: GTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGT-GAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGA
EST: gi|71862577|gb|DT011632.1|DT011632
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110379517|gb|EC944717.1|EC944717
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110698484|gb|EE076038.1|EE076038
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110385868|gb|EC950425.1|EC950425
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|27580267|gb|CB002962.1|CB002962
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|110727089|gb|EE103473.1|EE103473
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|30251422|gb|CB969155.1|CB969155
EST:     TGTCACGTGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|349823636|gb|FQ415046.1|FQ415046
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|71864669|gb|DT013724.1|DT013724
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|71864506|gb|DT013561.1|DT013561
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTCGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTC
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTC
EST: gi|30255107|gb|CB971554.1|CB971554
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCG                         GTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCT
EST: gi|351020029|gb|FQ439846.1|FQ439846
EST:     TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCTG                         GTTGTTGATGGG
genomic: TGTCACATGCATATGATTTTTACAAGCCTAATCTTGCTAGTGAATATCCGgtaatacttc ... atgtttccagGTTGTTGATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttcttataccccaattttcagttttttcacttattaaaattatgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCTTGCTATAAACTTTTGTGTTCCAA
                                              tgtttcc  CT-rich tract
                aattttcagttttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctggttttttgtgaaacccatttccatggttttgtgcatgccttgtttcttataccccaattttcagttttttcacttattaaaattatgtttccagGTTGTTGATGGGAAGCTTTCACAGACTTGTTATCTGATGGCACTTGATTCTTGCTATAAACTTTTGTGTTCCAA

gtgctgg
- - - - - - - - aaaccca
- - - - - - - - - - - - - ccatggt
- - - - - - - - - - - - - - - - - - - -catgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tacccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attaaaa