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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacttttttataacagtgcgattgattgtgccctttaataaaattcagcatacatgccttgtattgttcataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG

Basic information

species Vitis vinifera
transcript Vv14s0066g00210.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g19350.1 (Oryza sativa), 3'ss of exon 5
aacttttttataacagtgcgattgatt--gtgccctttaataaaattcagcatacatgccttgtattgttcataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG
    | | | |    ||| | |||     | |      | |    ||| | | | ||  ||  | |||     ||  ||| ||| |   | |  || ||||||| ||| |||||||||||||| || ||||| ||||||||||||   | ||||| 
tgtgtgtgtgtgtgtgtgtgtttggggaggggggggggagtggggttctgta-atattgctattcttgaagg-aagcattcatgaattcattgaatttgcagATATGAGGTACTTGATGAGGAGCCAGGTGACGATGAAGAGAGT---GCCCAAAA

upper sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G862959_T04 (Zea mays), 3'ss of exon 6
aacttttttataacagtgcgattgattgtgccctttaataaaattcagcatacatgccttgtattgttcataaatattgatggaacaac--tatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG
 | |    | ||   |  |  ||   ||||||  ||| |          ||     | |  |  |||   ||   | | ||  || |    |  |  ||||| | ||||||||||||||| ||||| |||||||| |||||||| | |   |||| 
-attaccatgtacatgcacattttcgtgtgcctgttactgttgccttatatgtgaccatcatcctgtaagtat-cactcatttaatattgatgcacgtgcagGTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACT---CAAAA

upper sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G08050.1 (Glycine max), 3'ss of exon 6
aacttttttataacagtgcgattgattgtgccctttaataa-aattcagcatacatg-ccttgt-attgttc-ataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG
   |  |   | ||||   || |  |  | |  ||| | |  |||      ||  || |||||| ||| ||  ||   |  |  ||  |||  |   |   ||||||||||||||| ||||||||||| |||||||||||||| || |||||||||||
-tgtaatcattgacagaaagagtagt-atccattttgacattaatcttttgtaattgtccttgtcattattttatttgttctcctgtgaca--tgatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG

upper sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G07460.1 (Glycine max), 3'ss of exon 5
---aactttt--ttataacagtgcgattgattgtgccctttaataaaattcagcatacatgccttgtattgttc-ataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG
   ||   ||      || | |   |   ||| || | || |      ||  | |    | | ||  ||| ||  ||   |  |  || ||||  |   | | ||||||||||||||| ||||||||||| || ||||||||||| || |||||||||||
tgtaatcattgacagaaagaatagtacccattatgacattgatc----ttttgtaattgtccttttcattattttatttgttctcctgtaaca--tgattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAG

upper sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G40550.2 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------------------aacttttttataacagtgcgattgattgtgccctttaataaaattcagc-atacatgccttgta--------ttgttcataaatattgatgga---acaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG
                                                                        |  ||  |      |      ||| |  ||||     | | ||   ||   | | ||    ||         |  |  || ||| |  ||      | |||| | ||| |||| |||||||||||||||| ||||| || |||||||||||  | || || || ||
gtaagccttcgaacctttcttctgtatgatgttatgcctaatttttgaatatcacacaaatgcatatctgatagtttagtagctgaaacttatttgttgctgccaacacacacaaaagagttgtgcttgttaagtgcaaaggcttcatctatgaatctaaatatgtttaaaactttttatccagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAAGCGGTCAGAG

upper sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G27460.2 (Arabidopsis thaliana), 3'ss of exon 5
--aacttttttataacagt-gcgat-tgattgtgccctttaataaaattcagcatacatgccttgtattgttcataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG
  ||||  |  ||| | ||   ||     || ||     ||      |    |||| ||  | | ||| | || ||||||  | |  ||  ||| | |   |||| |||||||||||||||| ||||| || |||||||||||  |  ||||||| ||
taaactggtagatagccgttatgacgcagttatggtaaatatgttgctcttccatagat-tcatatatgggtc-taaataaagtttcaa--acttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG

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|349827292|gb|FQ421565.1|FQ421565
EST:     GATGAATGGTTTGTTGTAAAAGTAATACATTTTGATCGGGAGGCAAGAGA                         ATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCA
genomic: GATGAATGGTTTGTTGTAAAAGTAATACATTTTGATCGGGACGCAAGAGAgtaagtttta ... atatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCA
EST: gi|83274402|gb|DV938499.1|DV938499
EST:     GATGAATGGTTTGTTGTAAAAGTAATACATTTTGATCGGGACGCAAGAGA                         ATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCA
genomic: GATGAATGGTTTGTTGTAAAAGTAATACATTTTGATCGGGACGCAAGAGAgtaagtttta ... atatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcatacatgccttgtattgttcataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG
                             tattgat  putative branch site (score: 3)
                tattgttcataaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacttttttataacagtgcgattgattgtgccctttaataaaattcagcatacatgccttgtattgttcataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - -ataacag
- - - - - - - - - - - - - - tgccctt
- - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - -ttcagca
- - - - - - - - - - - - - - - - - - - - - - - - - - catgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaacaa