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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atactgaagattttccattttcttttctgagtcaactctctgtttgtttgcggatttgaactagaacttaactttgtgttgcatggtggggtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGCCTTACTGAATCCCACATCAGCAGAGCCTCTTGTTTGGCCATCTCCCTTG

Basic information

species Vitis vinifera
transcript Vv06s0004g04550.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g02130.1 (Oryza sativa), 3'ss of exon 6
atactgaagattttccattttcttt--tctgagtcaactctctgtttgtttgcggatttgaactagaacttaactttgtgttgcatggtggggtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGCCTTACTGAATCCCACATCAGCAGAGCCTCTTGTTTGGCCATCTCCCTTG
  ||   || ||     | ||||      |||     |  | || |   ||||  ||  |  ||   ||| |  ||  | ||    | |   || ||  ||||||||| || ||    ||||| || || |  || ||||||||||||||||| || ||||| || ||||||||||||||  | || |||||||| ||  | 
tcacatgagcttgctgttcttctcaaacttgacctgtccttttgctgaattgcccat--gctctgccactgattttaattttaatggtttttgtttccccagGAGAATTCCCTATTCTGTTGCGCTGAAACGGAACCATGGAGCATGTGCAGCTTTGCTGAACCCTACATCAGCAGAGCCCATGGTGTGGCCATCCCCACTT

upper sequence: Vv06s0004g04550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G14900.1 (Glycine max), 3'ss of exon 6
atactgaagattttccattttcttttctgagtcaactctctgtttg-tttgcggatttgaactagaacttaactttgtgttgcatggtggggtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGCCTTACTGAATCCCACATCAGCAGAGCCTCTTGTTTGGCCATCTCCCTTG
| |        | |  |||    |   |     | |  | | || | ||     |||       ||| ||  |||  || || ||| || | | | |||||| |||||||||| || |||||||| || ||||  ||||||||||||||||| || |||||||   | || || ||||||||||| ||||||||  | |||
acaacacgaggtcttaattactataatttgactagcaatgttttagattcttatattaatttctgaatttgccttcatgctgtatgttgtg-tttatgcagGCGAATACCGTATGTAGTTGCTCTGAAACACAGACATGGAGCATGTGCAGCATTGCTGAATCTTTCGTCTGCTGAGCCTCTTGTATGGCCATCATCTTTG

upper sequence: Vv06s0004g04550.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G28840.1 (Arabidopsis thaliana), 3'ss of exon 6
atactgaagattttccattttcttttctgagtcaactctctgtttgtttgcggatttgaact-agaacttaactttgtgttgcatggtggggtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGCCTTACTGAATCCCACATCAGCAGAGCCTCTTGTTTGGCCATCTCCCTTG
                       | | |   | || | | ||      |   | ||||   | ||||| ||||||         | |     ||| | |||||||||||| || ||||||||  | ||||| |||||||||||||||| ||||||||| |||||  | || |||||||| |||||||||||||| || || 
----------------------gtatatatataaattttgtggaaaagtcttgttttggtttcagaacataacttga----atcttgaaatatcttttcagGAGAATACCTTATGTGGTTGCGATGAAGCATAAGCATGGAGCATGTGGAGCCTTACTTAATCCGTCCTCTGCAGAGCCACTTGTTTGGCCATCACCATTA

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|37188493|gb|CF607842.1|CF607842
EST:     GAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGG                         GAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGC
genomic: GAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGGgtattgtctg ... gtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGC
EST: gi|294965069|gb|GW838872.1|GW838872
EST:     AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGG                         GAGAATACCGTACGTGGTTGCACTTAAGCACAAGCATGGAGCATGTGCAGC
genomic: AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGGgtattgtctg ... gtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGC
EST: gi|110712240|gb|EE089633.1|EE089633
EST:     AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAAAAAGATTCATCAAG                         AAGAATACCGTAC-TGGTTGCTCTTAA
genomic: AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGGgtattgtctg ... gtctctgcagGAGAATACCGTACGTGGTTGCTCTTAA
EST: gi|110699327|gb|EE076228.1|EE076228
EST:     AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGG                         GAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGC
genomic: AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGGgtattgtctg ... gtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGC
EST: gi|37186435|gb|CF605788.1|CF605788
EST:     AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGG                         GAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGC
genomic: AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGGgtattgtctg ... gtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGC
EST: gi|27585102|gb|CB007797.1|CB007797
EST:     AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGG                         GAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGC
genomic: AGGGAATTGCTGGCTTGGGGTGCTGATCGTCTTCAGAGAGATTCATCAGGgtattgtctg ... gtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgcggatttgaactagaacttaactttgtgttgcatggtggggtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGCCTTACTGAATCCCACATCAGCAGAGCCTCTTGTTTGGCCATCTCCCTTG
                    acttaac  putative branch site (score: 3)
                                              tctctgc  putative PPT
                      ttaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atactgaagattttccattttcttttctgagtcaactctctgtttgtttgcggatttgaactagaacttaactttgtgttgcatggtggggtctctgcagGAGAATACCGTACGTGGTTGCTCTTAAGCACAAGCATGGAGCATGTGCAGCCTTACTGAATCCCACATCAGCAGAGCCTCTTGTTTGGCCATCTCCCTTG

- - - - - - - ccatttt
- - - - - - - - - - - - - - - - caactct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggg