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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGATGGTAGTGGATGCGTTTCCATCTATGGAAGCAAGTTCGAGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcatttttccttcctcatgttgcttctttgttggtactttttcttcaaataaatttcagcaattagattccagatttatttcatgatttaactatt...

Basic information

species Vitis vinifera
transcript Vv13s0084g00620.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0084g00620.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA15G37190.1 (Glycine max), 5'ss of exon 4
GGTGATGGTAGTGGATGCGTTTCCATCTATGGAAGCAAGTTCGAGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcatttttccttcctcatgttgcttctttgttggtactttttcttcaaataaatttcagcaattag--attccagatttatttcatgatttaactatt
||||||||||||||||| |||||||||||||||  |||||| || |||||||| |||| ||| ||||||||||||||||| ||  |||| |||||||   |||    || ||    |||    ||||  |||| | |     |||| |   || |   | | |  | || ||  | | |   |      |   | 
GGTGATGGTAGTGGATGTGTTTCCATCTATGGACTCAAGTTTGATGATGAAAACTTTACTGCGAAACACACTGGTCCTGGCCTTCTGTCCATGgtatgtgtttgctgtttctacctttgtcattttg--ggtaatatgaaaacaaagactgttaatggaatggccactcaaggataaatatgtaccagtatggta

upper sequence: Vv13s0084g00620.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA09G11960.1 (Glycine max), 5'ss of exon 4
GGTGATGGTAGTGGATGCGTTTCCATCTATGGAAGCAAGTTCGAGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt-ttccttcctcatgttgcttc------tttgttggtactttttcttcaaataaatttcagcaattagattccagatttatttcatgatttaactatt
|| |||||||||||||| |||||||||||||||  |||||| || |||||||| ||||  || ||||||||||||||||| ||  ||||||||||||   |||  |  |||  | ||||  ||       | ||    ||     | || |   ||   ||| ||    |||   | || | |  ||  ||   | |   
GGAGATGGTAGTGGATGTGTTTCCATCTATGGACTCAAGTTTGATGATGAAAACTTTACGGCCAAACACACTGGTCCTGGCCTTCTGTCAATGgtatgtgtttgctatttctacctgttattttgggtaatatgaaaataggcactgttaatggaatgatca-cacaaggat---aaatatgtaccagtatggtatt---

upper sequence: Vv13s0084g00620.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G26260.1 (Glycine max), 5'ss of exon 4
GGTGATGGTAGTGGATGCGTTTCCATCTATGGAAGCAAGTTCGAGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcatttttccttcctcatgttgcttctttgttggtactttt-tcttcaaataaatttcagcaattagattccagatttattt-catgatttaactatt
|| |||||||||||||| |||||||||||||||  |||||| || |||||||| ||||  || ||||||||||||||||| ||  |||| |||||||   |||    || || |  |  | | || | |  ||      |   ||     | |  |   || | ||    |||  || |  |  | |    ||||
GGAGATGGTAGTGGATGTGTTTCCATCTATGGACTCAAGTTTGATGATGAAAACTTTACGGCCAAACACACTGGTCCTGGCCTTCTGTCGATGgtatgtgtttgctatttct-acctgtcattttgggtaatatgaaaatagacacggttaatggaatgatcacataa-ggataaatatgtaccagtatggtatt

upper sequence: Vv13s0084g00620.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT2G38730.1 (Arabidopsis thaliana), 5'ss of exon 3
GGTGATGGTAGTGGATGCGTTTCCATCTATGGAAGCAAGTTCGAGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcatttttccttcctcatgttgcttctttgttggt---actt--------tttcttcaaataaatttcagcaattagattccagatttatttcatga-tttaactatt------------------------------
  |||||||||||||||| | || ||||| ||   |||||| |||||||| ||||||| ||||||||| ||||| || ||  |  | || |||||||  | ||| | ||    || |   || |   || ||   ||||           |||   ||    || | | || ||  || |   ||| | ||||| ||| |  | |                              
AATGATGGTAGTGGATGCATGTCAATCTACGGCCACAAGTTTGAGGATGAGAATTTTACTGCTAAACATACTGGACCAGGATTGCTCTCCATGgtatgtaatttgctttatgaatctgagttataaatttgtgtaacttgaatcagcccccttgtgattttctttatccatgagtctctattattact-catgactttgatcactaatattatggttctcattcttttgttgtag

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|110689345|gb|EE065486.1|EE065486
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|110369676|gb|EC933841.1|EC933841
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|32459581|gb|CD800755.1|CD800755
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|30330499|gb|CD013761.1|CD013761
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|30330447|gb|CD013709.1|CD013709
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|22009195|gb|BQ794229.1|BQ794229
EST:     TGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: TGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|71890647|gb|DT039702.1|DT039702
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|27586714|gb|CB009409.1|CB009409
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|110397718|gb|EC963561.1|EC963561
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|110377315|gb|EC942381.1|EC942381
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|71875212|gb|DT024267.1|DT024267
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|71871923|gb|DT020978.1|DT020978
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|110421609|gb|EC987908.1|EC987908
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|110408091|gb|EC973714.1|EC973714
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|32459126|gb|CD800300.1|CD800300
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
EST: gi|71876171|gb|DT025226.1|DT025226
EST:     AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATG                         GCAAATAGTGGGCCAGGTACCAATGGTTGTCAG
genomic: AGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcattt ... ccttttgcagGCAAATAGTGGGCCAGGTACCAATGGTTGTCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGATGGTAGTGGATGCGTTTCCATCTATGGAAGCAAGTTCGAGGATGAAAATTTTATTGCTAAACACACTGGTCCTGGTCTCTTGTCAATGgtattcatttttccttcctcatgttgcttctttgttggtactttttcttcaaataaatttcagcaattagattccagatttatttcatgatttaactatt

- - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa