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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttttgttcaagcatctacttactttttcatgaaccttattagtttttagggagacatattctgaagtggcattcttttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGATGATATTTCTATAGTTAGAGAGTTGCCTTATGACTTCTCTTGGAGCACA

Basic information

species Vitis vinifera
transcript Vv00s0313g00030.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G02850.1 (Glycine max), 3'ss of exon 5
gtagttttttgttcaagcatctacttactttttcatgaaccttattagtttttagggagacatattctgaagtggcattcttttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGATGATATTTCTATAGTTAGAGAGTTGCCTTATGACTTCTCTTGGAGCACA
        |  || |     | | |    | || ||    |  ||   || |  | ||   | ||  ||| || || |   |||  ||||||||| |||||||||||||||||||| ||||| || ||| ||||  |||||||||||||||||||||||| |||||||||  | || ||| | |||||||||
-------gtaattgacaacaccattattatatttatttgtccgatggattgtgtgcgatgaa-atgttgaggttgcttatgtttgactgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGATGATATTTCTATAGTTAAAGAGTTGCCCAAAGAGTTCGCCTGGAGCACA

upper sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G33160.1 (Glycine max), 3'ss of exon 5
gtagttttttgttcaagcatc-tacttactt-tttcatgaaccttattagtttttagggagacatattctgaagtggcattcttttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGATGATATTTCTATAGTTAGAGAGTTGCCTTATGACTTCTCTTGGAGCACA
||| ||       | | |||     ||| || |  |||| |        || | |   || | ||    ||| || ||||   ||| | |||||||| |||||||||||||||||||| ||||| || ||| ||||  |||||||||||||||||||||||| |||| ||||| | || |||   |||||||||
gtaattgccgacaccatcattgcgtttatttgtcccatggatt------gtgtgtgatgaaatat----tgaggttgcatatgtttgtttgcagCTCCTTCATGGATATATTTGATGTGGATCATTTCATTGATGTATTGAAGGATGATATTTCTATAGTTAAAGAGCTGCCTAAAGAGTTCAGCTGGAGCACA
















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|34549653|gb|CF517885.1|CF517885
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|30128462|gb|CB913801.1|CB913801
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|352764443|gb|FQ472800.1|FQ472800
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|34549133|gb|CF517365.1|CF517365
EST:     CTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: CTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|161716901|gb|FC068123.1|FC068123
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|110724909|gb|EE101147.1|EE101147
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|110710320|gb|EE086550.1|EE086550
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCNAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|161714330|gb|FC062631.1|FC062631
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|33409871|gb|CF215498.1|CF215498
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|351032719|gb|FQ462433.1|FQ462433
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|30136929|gb|CB922267.1|CB922267
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|352782495|gb|FQ470398.1|FQ470398
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|352794755|gb|FQ475253.1|FQ475253
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|352785495|gb|FQ477709.1|FQ477709
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|351016529|gb|FQ423956.1|FQ423956
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|351018711|gb|FQ425613.1|FQ425613
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|351013796|gb|FQ433948.1|FQ433948
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
EST: gi|161718121|gb|FC068890.1|FC068890
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTTGATGTTGATCAC
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTT-GATGTTGATCAC
EST: gi|352773927|gb|FQ473059.1|FQ473059
EST:     ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG                         CTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA
genomic: ACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAGgtagtttttt ... ttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccttattagtttttagggagacatattctgaagtggcattcttttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGATGATATTTCTATAGTTAGAGAGTTGCCTTATGACTTCTCTTGGAGCACA
                                      cattcttttttctgc  CT-rich tract
     tattagttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttttgttcaagcatctacttactttttcatgaaccttattagtttttagggagacatattctgaagtggcattcttttttctgcagCTCATTCATGGATATATTTGATGTTGATCACTTTATTAATGTCCTGAAGGATGATATTTCTATAGTTAGAGAGTTGCCTTATGACTTCTCTTGGAGCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA