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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtgatgaaagcaatacatcgatccaccttttttccataatattggtgatctaatgttggattgaccatagaatatgcttccttttatgctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTCCCCCCACCTGCAGCTGCACCTCTGCCAGGTCTTTCAGCCACGGACCTCC

Basic information

species Vitis vinifera
transcript Vv09s0002g00880.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 11
tctgtgatgaaagcaatacatcgatccaccttttttccata-----atattggtgatctaatgttggattgaccatagaatatgcttccttttatgctgttg-----tagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTCCCCCCACCTGCAGCTGCACCTCTGCCAGGTCTTTCAGCCACGGACCTCC
          || || |   |   |||  |    ||||| |     | |        ||| |  |   |||  | |  | | ||     |  |||  ||||       ||||||| ||||| |||||||| |||||||| |||||   |||||| || || ||||||||||| |||||| ||||||| || || || || || || ||  
----------aaacattgagttcctccctcaaaattccacatccaaacacaaccaggctatttatttgttgcacttcaactctgaccattgctatcatgttaaaatacagTGCTCTTGGGGGAGCAAGCCCACTCCACCTGGAACTGCTTCAAATCCCCTTCCCCCACCTGCTGCTGCATCTCTGCCTGGCCTGTCTGCAACTGATCTTT

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 11
-----tctgtgatgaaagcaatacatcgatccaccttttttccataatattg---------gtgatctaatgttggattgaccatagaat---atgcttccttttatgctg-ttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTCCCCCCACCTGCAGCTGCACCTCTGCCAGGTCTTTCAGCCACGGACCTCC
     | |  | |      |  ||    | ||  || | ||  ||  || ||         || |  | || |   | | | |||  |||   |   ||  | | ||| |  ||||||||||||||||| | |||||||||||||||||| |||   ||||||||||| |||||||||||  | || ||  | || ||||| || ||  | || ||||
gtacttttaagtttggcttaccactctaaaccctctctatttgatcttactgctcccaaaagttacttcatctgaaacttagcatgcaatctgacatttgttatcatgttaattgtagTGCTCATGGGGAAACAAGCCAACTCCACCAGGTACAGCCTCAAACCCACTTCCCCCACCTGCCCCAGCTCCAGTTCCTGGTCTATCTGCAGCTGATCTCC

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 11
tctgtgatgaaagcaatacatcgatccaccttttttccataatattggtgatctaatgttggattgaccata--gaatatgcttccttttatgctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTCCCCCCACCTGCAGCTGCACCTCTGCCAGGTCTTTCAGCCACGGACCTCC
       | |||  ||   |   |   ||  || ||   |   | |    ||    | |||| |||   ||    ||  || |   ||   || |  |  |||| || ||||| ||||||||||||||| ||||||||  ||||||||| || || ||||| ||  |||||||  | || ||  | ||||| |  || ||| 
------gtaaaactaactaacttaa--actgttcttttgtgggactcaccattcttt-ttggtttgggaatgctaaaattgttgtgttcgttgttcctacagTGTTCTTGGGGAAGCAAGCCAACTCCAGCAGGAACAGCTTCAAACCCGCTTCCTCCACCAGCTCCTGCACCAATCCCGGGATTCTCAGCGAGTGATCTCT

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|110409533|gb|EC975197.1|EC975197
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|33409957|gb|CF215584.1|CF215584
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|30253103|gb|CB970654.1|CB970654
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|37183877|gb|CF603231.1|CF603231
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|110360310|gb|EC923266.1|EC923266
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|110696392|gb|EE072470.1|EE072470
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAAGTACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|110358441|gb|EC922654.1|EC922654
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|110412701|gb|EC978460.1|EC978460
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|110357937|gb|EC921792.1|EC921792
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCCACT
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCC-ACT
EST: gi|110689591|gb|EE065948.1|EE065948
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|71872494|gb|DT021549.1|DT021549
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
EST: gi|71876949|gb|DT026004.1|DT026004
EST:     CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAG                         TGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC
genomic: CTATTCAGATGGGAAATACCCAGTCAATTCTGTGTGGCAAACCAATCAAGgtatgattta ... gctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgatctaatgttggattgaccatagaatatgcttccttttatgctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTCCCCCCACCTGCAGCTGCACCTCTGCCAGGTCTTTCAGCCACGGACCTCC
                gattgac  putative branch site (score: 3)
                                  cttccttttatgct  putative PPT
                        atagaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtgatgaaagcaatacatcgatccaccttttttccataatattggtgatctaatgttggattgaccatagaatatgcttccttttatgctgttgtagTGCTCATGGGGTAGCAAGCCAACTCCACCAGGAACAAGTTCAAACCCACTCCCCCCACCTGCAGCTGCACCTCTGCCAGGTCTTTCAGCCACGGACCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - -aaagcaa
- - - - - - - - - - - - -ccacctt
- - - - - - - - - - - - - - - - - - - - - - -tggtgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgga