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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCTGGTAACGATAAGTCCTGTGTCTGGCATGCCACTGATTTTGCTGATGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataatttgttcattacggtctgttctctgtaactgttttcatattgttttttgaaatagatcaaacgcattttcttgtgattggaactgcttga...

Basic information

species Vitis vinifera
transcript Vv06s0004g06880.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06880.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G30060.1 (Arabidopsis thaliana), 5'ss of exon 3
CATGCTGGTAACGATAAGTCCTGTGTCTGGCATGCCACTGATTTTGCTGATGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtat-aatttgttcattacggtctgttctctgt-aactgttttcatattgttttttgaa-atagatcaaacgcattttcttgtgattggaactgcttga
|| ||||| || |||||||| ||||| ||||| ||   ||||||  | ||||| ||||||||||||||||| ||||||||  | ||||| |||||||| ||||||| | |||||     ||  | | | || | | | |  || ||  || ||  |   | |   | | | | |       |  | ||  | |   |  |   
CACGCTGGGAATGATAAGTCTTGTGTATGGCACGCTCGTGATTTCTCCGATGGTGAATTGAAGGATGAGCTCTTCTGTATCCGGTTTGCTTCAGTTGAGAgtgagtgtgaattttgcttttgtgtttttttatttctcagttgattggatcttactacgtaattgttgcttatagtagcactgctctgtctcgtttttgt---

upper sequence: Vv06s0004g06880.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G07140.1 (Arabidopsis thaliana), 5'ss of exon 3
CATGCTGGTAACGATAAGTCCTGTGTCTGGCATGCCACTGATTTTGCTGATGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtat-aatttg---ttcattacggtctgttctctgtaactgttttcatattgttttttgaaatagatcaaacgcattttcttgtgattggaactgcttga
|| | ||| || || ||||| ||||| ||||| ||   ||| ||||||||||| ||| | ||||||||||||||||||||  ||||||| ||  |||| ||||||||| ||   |   ||  | | ||  |||  | ||   ||  |||  | |   ||  |   ||||||  | || |||   ||     |||| ||      
CACGTTGGGAATGAAAAGTCATGTGTGTGGCACGCTCGTGACTTTGCTGATGGTGAACTCAAGGATGAGCTTTTCTGTATCCGATTTGCTTCTATTGAGAgtgagtatgaaaccgaattttgtaatggcttgtgttttgc--cttatttagtctcagttggtttgatagattca-cggattagattactgatggatcttgacc-
















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|110399769|gb|EC966295.1|EC966295
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110685360|gb|EE063691.1|EE063691
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110694049|gb|EE070825.1|EE070825
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110364054|gb|EC927696.1|EC927696
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|33402476|gb|CF208103.1|CF208103
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110710444|gb|EE086786.1|EE086786
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110686104|gb|EE063409.1|EE063409
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|351042794|gb|FQ431272.1|FQ431272
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCGAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110689315|gb|EE065434.1|EE065434
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|37183761|gb|CF603115.1|CF603115
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCANAAGCTTCATGGANAAGGTTCAAGAGGTTGCTGANATCCCA-CAG
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGA-ATCCCAACAG
EST: gi|110411908|gb|EC977638.1|EC977638
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110362114|gb|EC925626.1|EC925626
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|37184112|gb|CF603466.1|CF603466
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110723271|gb|EE100389.1|EE100389
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110416768|gb|EC982772.1|EC982772
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110724975|gb|EE101275.1|EE101275
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110726623|gb|EE102567.1|EE102567
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110691621|gb|EE069931.1|EE069931
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110717640|gb|EE093673.1|EE093673
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110732314|gb|EE107490.1|EE107490
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110687654|gb|EE065310.1|EE065310
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110687655|gb|EE065311.1|EE065311
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110372303|gb|EC936456.1|EC936456
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
EST: gi|110721265|gb|EE098063.1|EE098063
EST:     TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAA                         ATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA
genomic: TGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataa ... tttgtttcagATTGCAAAAGCTTCATGGAAAAGGTTCAAGAGGTTGCTGAATCCCAACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCTGGTAACGATAAGTCCTGTGTCTGGCATGCCACTGATTTTGCTGATGGAGAATTGAAGGATGAGCTTTTCTGTATAAGATTTGCATCAGTTGAAAgtgagtataatttgttcattacggtctgttctctgtaactgttttcatattgttttttgaaatagatcaaacgcattttcttgtgattggaactgcttga

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaatag