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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgaaagactcaattttataggtgcttcagttattcagttgaagtttatggtcatctcttagtgttaggctcatacttatttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT

Basic information

species Vitis vinifera
transcript Vv12s0028g03130.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os09g15750.1 (Oryza sativa), 3'ss of exon 12
------------acatgaaagactcaattttataggtgc-ttcagttattcagttgaa-gtttatggtcatctcttagtgttaggctcatacttatttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT
             |  ||||  ||   | |  |   ||| |  |  || | | ||    |||||||   |  |  || |  | |  | | |  |   ||||   | |||| ||||  |||||| |||||||||| |    | |  |  | ||| |||| ||||| |||||||| ||||| || || |||||||||||||| || |||||||| |
gttaacttgtttccccgaaatgct--gtctgctgattgcatgtatctacttatttatttgtttatga--acttgctattaat-gattaaaaaatgcatgct---aatttgttagGTTCATTTGATTGATGGCCGAGGGGCTACAAGCTCCAGTCTTGATTCTGCAAGACAGAATCTGGCGGCAACATTTGTCAATGCATTCGTGAATGCTGGAT

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 12
acatgaaagactcaattttataggtgcttcagttattcagttgaagtttatggtcatctc--ttag-tgttaggctcatactt-atttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT
   | | | |   || ||||||| ||    | || ||    | |||| |       | |   | || ||| |  || ||  || | |    | | || | |||||||||||||||||||||||||||||||||||||||||||||||| || || ||||||||||| || || |||||||| |||||||||||||||||||| |
---tcagaaaaaaaagtttatagatgtgctactt-tttgtctcaagtgtgccactttgttgatcagctgtgaaccttatgtttcactctggttgtttctcctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGATTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 12
acatgaaagactcaattttataggtgcttcagttattcagttgaagtttatggtcatctc--ttag-tgttaggctcatactt-atttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT
   | | | |   || ||| | | ||    | || ||    | |||| |       | |   |||  ||| |  || ||  || | |    | | |  | ||||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||||||||| || || |||||||| |||||||||||||||||||| |
---tcagaaaaaaaagtttcttgatgtgctactt-tttgtctcaagtgtgccactttgttgattatctgtgaaccttatgtttcactctgcttgttactcctagGCACACTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCAGCTAGACAGAACCTTGCTGCAACTTTTGTTAATGCATTTGTAAATGCTGGCT

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 10
acatgaaagactcaattttatagg--tgct--tcagttattcagttgaagtttatggtcatctcttagtgttaggctcatacttatttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT
  |    ||  | ||| |  ||||  ||||  ||| ||||| ||||  |  ||||| |  || || ||| || | |     |||      ||| |||||  ||||| || || || || ||| |||||||  | |||||||| || || ||||| ||||||||  |||| ||||| |||||||||||||| |||||||||||||
gtaaatcagttttaatgtgttaggcttgctactcatttatttagttacaaattatgtt--tccctcagtctttgacctgccctt-----tttgaatttta-tagGCTCACTTACTCGACGGCAGGGCTAGCTCCGGTGCAAGCGTGGATTCTGCTAGACAGAATTTGGCTGCTACCTTTGTCAATGCATTCGTAAATGCTGGTT

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 10
--acatgaaa--gactcaattttataggtgcttcag--ttattcagttgaagtttatggtcatctcttagtgttaggctcatacttatttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT
  | || |     | | ||| ||||   || | | |  |||||  |||  ||  |||| | ||     ||||     ||| ||| | |   || | | ||||| |||| || |||||||||||  |||||||  ||||| ||||||| ||||| || || || || ||  | || |||||||| |||||||||||||||||||| |
gtatatcagtttaattgaatattatgtctgttactggtttatttggttacaggatatgtttatgga--agtgc----ctcttacctgtccact-gaaatttgc-agGCTCACTTGCTTGATGGTAGGGCTAGCTCTGGTCCAAGTGTGGACTCAGCTAGGCAAAATCTATCTGCGACTTTTGTGAATGCATTTGTAAATGCTGGAT

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S414_22V6.1 (Physcomitrella patens), 3'ss of exon 12
acatgaaagactcaattttataggtgcttcagttattcagttga-agtttatggtcatct-cttagtgttag-gctcatacttatttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT
   |    | || |||| | |   |        ||||  ||||| ||   ||| || | | |||  |||| |  || |||     ||     | || |   |||| |||||  | ||||| || || ||||| || || || || ||||||||  | || |||||||| || ||||||||||||| |||||| |||||||| |
ttgttgcggtct-aattatttctttatgcagactatt--gttgatagaacatgatcttatactttctgtttgtacttatatcatgttttggtgcttgtctcagGCTCATTTAGTGGATGGTCGTGCCAGTGCAGGAGCTAGCGTAGACTCTGCTCGTCAAAACCTGGCTGCCACTTTTGTCAATGGATTTGTGAATGCTGGCT

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|30304134|gb|CB980928.1|CB980928
EST:     CTCGTGATATAGAGGTGATGGAGGANAAATCTCCTGAAGATATCTATAAG                         GCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
genomic: CTCGTGATATAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAGgtttggactt ... attttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
EST: gi|71864029|gb|DT013084.1|DT013084
EST:     TAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAG                         GCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
genomic: TAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAGgtttggactt ... attttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
EST: gi|30304206|gb|CB981000.1|CB981000
EST:     CTCGTGATATAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAG                         GCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
genomic: CTCGTGATATAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAGgtttggactt ... attttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
EST: gi|71860625|gb|DT009680.1|DT009680
EST:     TAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAG                         GCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
genomic: TAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAGgtttggactt ... attttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
EST: gi|29781461|gb|CB345965.2|CB345965
EST:     CTCGTGATATAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAG                         GCACATTTGCTTGATGATCNGGCTAGTGCTGGTGCAANTGATGACTCTGCC
genomic: CTCGTGATATAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAGgtttggactt ... attttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
EST: gi|71863903|gb|DT012958.1|DT012958
EST:     TAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAG                         GCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC
genomic: TAGAGGTGATGGAGCCCAAATCTCCTGAAGATATCTATAAGgtttggactt ... attttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttatggtcatctcttagtgttaggctcatacttatttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT
                                              ttttgct  CT-rich tract
                             atacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatgaaagactcaattttataggtgcttcagttattcagttgaagtttatggtcatctcttagtgttaggctcatacttatttgcttggattttgctagGCACATTTGCTTGATGGCCGGGCTAGTGCTGGTGCAAGTGTTGACTCTGCCAGACAGAACCTGGCAGCTACTTTTGTCAATGCATTTGTAAATGCTGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - gaaagac
- - - - - - - - - - - - tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgg