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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctctctcccctctgtgtcgttgtgtgtgtgtgtgcacgtgtgcctgcttacactgttagaataaattttagaaaatagttgaactttcgttttccttttttcagtttgtttcaaacctaactggtcctttgttttctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAATACATATGA

Basic information

species Vitis vinifera
transcript Vv09s0002g05250.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G43830.3 (Glycine max), 3'ss of exon 5
--------------------------------------gtctctctctcccctctgtgtcgttgtgtgtgtgtgtgcacgtgtgcctgcttacactgttagaataaattttag---------aaaatagttgaactttcgttttccttttttc---agtttgtttcaaacctaactggtcctttgttttctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAATACATATGA
                                      |    | ||  |     || |  || |     |   ||   |    || | | | | |   | |  | ||  |           | | |||  | | |||  ||||  ||||||    |     ||  |||  |     ||  ||| | || ||| |  ||||| || ||||||||||||  |||||||| |||||||||||||| ||||||||||| ||
gtctctctctctctctctttctctctctctctcccactgaaattatcaacagctagtatgattttagaacttcttgggtggccaccagataatattcccaaagaatatgctgattgaccataacagtagcagtagtttttttttttttttttataaaaaaaattataaaatttctgagtattttctcttatttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAATACATACGA

upper sequence: Vv09s0002g05250.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G01520.1 (Glycine max), 3'ss of exon 6
------------------------------------gtctctctctcccctctgtgtcgttgtgtgtgtgtgtgcacgtgtgcctgct------tacactgttagaataaattt-tagaaaatagttg--aactttcgttttccttttttcagtttgtttcaaacctaactggtcctttgttttctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAATACATATGA
                                      ||    |     |    ||  |  | | |   | | |  ||||| |  |       ||  |    ||||||   |  | ||  |||  ||  || |  | ||||   || |  |  |  ||  |||  |     ||  ||| | || ||| |  ||||| || ||||||||||||  |||||||| |||||||||||||| ||||||||||| ||
gtctctctctctcactctccctctgaatttatcaacagctagtacgattttagaagtgatccttttttaatcttcttgtgtggccaccagataatattccccaagaatatgctgattgaccataactgtaaagtaactttttttgttataaaaatatttataaaatttctgagtattttctcttatttgatcagAGGATTTCAGATCTCTGCAAGAATGCTGGCTCTTGGCTTGTTGTTGATAATACATACGA
















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|161714897|gb|FC064519.1|FC064519
EST:     TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAG                         AGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
genomic: TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAGgtctctctct ... ctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
EST: gi|349816605|gb|FQ399594.1|FQ399594
EST:     TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAG                         AGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
genomic: TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAGgtctctctct ... ctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
EST: gi|110410711|gb|EC976403.1|EC976403
EST:     TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAG                         AGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
genomic: TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAGgtctctctct ... ctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
EST: gi|110378361|gb|EC943489.1|EC943489
EST:     TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAG                         AGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
genomic: TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAGgtctctctct ... ctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
EST: gi|26257746|gb|CA808809.1|CA808809
EST:     AATCCTGGTAACCCATCTGGGACCTACATTCCCAGAGCCTCTGCTTTAAG                         AGGTTTGTAGATCTCTGCAGAAATG
genomic: A-TCCTGGTAACCCATCTGGGACCTACATTCC-AGAGCCTCTGCTT-AAGgtctctctct ... ctttaagtagAGGTTTGCAGATCTCTGCAGAAATG
EST: gi|110693324|gb|EE069456.1|EE069456
EST:     TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAG                         AGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
genomic: TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAGgtctctctct ... ctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
EST: gi|110394684|gb|EC959919.1|EC959919
EST:     TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAG                         AGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT
genomic: TGAATCCTGGTAACCCATCTGGGACCTACATTCCAGAGCCTCTGCTTAAGgtctctctct ... ctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccttttttcagtttgtttcaaacctaactggtcctttgttttctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAATACATATGA
                        acctaac  putative branch site (score: 2)
                                  tcctttgttttcttt  putative PPT
                                     tttgttttctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctctctcccctctgtgtcgttgtgtgtgtgtgtgcacgtgtgcctgcttacactgttagaataaattttagaaaatagttgaactttcgttttccttttttcagtttgtttcaaacctaactggtcctttgttttctttaagtagAGGTTTGCAGATCTCTGCAGAAATGCTGGATCTTGGCTTGTTGTAGATAATACATATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA