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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT

Basic information

species Vitis vinifera
transcript Vv09s0018g02130.t01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 9
ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaat-tttatttgtttttgccatg-tagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
                  | | |      | ||| |  ||   | |  | || | ||| |  |     ||     ||  |||||   | | |  | |  ||||| || |||||||| ||||| || ||||||||||| ||||| ||||| || |||||||| ||||| |||||||| |||||||| || ||||| |||||  
-----------------gttaggga----agttggagcttaataatcttacacaatta-atttaacaaatgccttaacatttatccatatgtaacgttctagGTGGTCCGCTGGGGTCGTTCGGTTTATGCAAATATCCAAAAGTTTATTCAATTCCAGCTTACTGTAAATGTTGCGGCTCTTATAATCAATGTGGTTGCTG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 5
ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
  |    |  |   ||||  |          |||| ||| | |    || | ||   ||||   || | | | |||  ||  ||   ||||    | ||||| ||||||||||| || ||||| ||||||||||| ||||| ||||| ||||||||||| || || ||||||||||||||| | || |||||||||||  
--gtttggcctatttttagaatctaaggatcttgataatacgcgcacatgccta---atacaacgt-tgtcttacatgttctttatcttttatattctagGTGGTTCGCTGGGGTCGCTCTGTTTATGCAAATATCCAAAAGTTTATTCAGTTCCAGCTTACCGTAAATGTTGCAGCTCTTGTCATCAATGTTGTTGCTG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA15G00340.1 (Glycine max), 3'ss of exon 27
-----ttgccatgtat-gcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
     | ||    | | | ||| |   | |   |||||| |      |    ||  |     |  | | | | ||| ||| |  | || ||   ||||   ||||||||||||||||||| |||||||| |||||||||||||| |||||||| ||||||||||||||||||||||| || |||||| | ||||||||||| ||  
gattttggcttcatcttggattaagagataaatttatttcatggagac--acaacacgagcattcagcagat-tatctgagatgtgtagttcactttg---tgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAGCTCACTGTTAATGTAGCTGCTCTTGTAATAAATGTTGTGGCCG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA13G44990.1 (Glycine max), 3'ss of exon 27
--ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctg-gtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
    |     | |    ||  ||||||    ||||      |      |   ||     || | |  |  ||| | | |  | || || | ||||   ||||||||||||||||||| |||||||| |||||||||||||| |||||||| |||||||| ||||||||||||||||| |||||| | |||||||| || ||| 
cacggattgatcttggattgagaagagataaatttatttcgtggagacacaacacgagcattcataagattatctaagatgtgtagttctctttg---tgtagGTTGTTCGCTGGGGCCGTTCTGTATATGCAAATATTCAGAAATTTATTCAGTTCCAACTCACTGTTAATGTTGCTGCTCTTGTAATAAATGTAGTGGCAG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 28
ttgccatgtatgcatttatgaagaggcttatttga--aaattcccagtaattcatatttat--acctg--gtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
       || |    ||| | ||||  |||||| |  ||    |  ||  |    |||  |  |||||   | | | | | | || |||||  || |    |||||||||| |||||||| || ||||| |||||||||||||| |||||||||||||||||||| || ||||||||||| |||||| | ||||||||||| ||| 
-----gggttttggcttaaggagagatttatttcaccaagacacgtgtcctatggattgctcaacctgtaatttgtgtaagatttctatttcattct-ttgtgtagGTTGTCCGCTGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTCCAGCTTACAGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 25
ttgccatgtatgcatttatgaagaggcttatttga--aaattcccagtaattcata-----tttatacc-tggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
       || |    ||| | ||||  |||||| |  ||    |  |||    ||       | ||    |  | | | ||| |  | |||||  || |    |||||||||| || ||||| || ||||| |||||||||||||| |||||||||||||| |||||||| ||||||||||| |||||| | ||||||||||| ||| 
-------gttttggcttaaggagagatttatttcaccaagacacatgtatcctatggattgctcatcttgtaatttgtctgagatgtctatttcattct-ttgtgtagGTTGTCCGATGGGGCCGCTCTGTATATGCAAATATTCAGAAATTTATCCAGTTTCAGCTCACGGTTAATGTTGCTGCTCTTGTAATAAATGTTGTGGCAG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 22
ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
                                            ||||   |||        |||||    |   ||   |     || ||||     ||||||| |||||||| || || || ||||| |||||||| || ||||||||||||||||| ||||| |||||||  || ||  || | || || || ||  
--------------------------------------------gtaa--gataacagcttttggtgcgagtctgaaggatcgaaattcttgc-----agGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTTGTTGCGCTGGTTCTCAACGTCGTGGCCG

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: EFJ25508 (Selaginella moellendorffii), 3'ss of exon 23
ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
                                            ||||   |||        |||||    |   ||   |     || ||||     ||||||| |||||||| || || || ||||| |||||||| || ||||||||||||||||| ||||| ||||| |  || ||  || | || || || ||  
--------------------------------------------gtaa--gataacagcttttggtgcgagtctgaaggatcgaaattcttgc-----agGTTGTACGCTGGGGTCGGTCCGTGTATGCCAATATTCAGAAGTTTATCCAGTTCCAGCTGACTGTAAATGTAGTTGCGCTGGTTCTCAACGTCGTGGCCG

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|110357398|gb|EC920911.1|EC920911
EST:     AAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAG                         GTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAG
genomic: AAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAGgttagtgtaa ... tgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattcatatttatacctggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT
                                ttttatttgttttt  CT-rich tract
                      tatatgacaattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgccatgtatgcatttatgaagaggcttatttgaaaattcccagtaattcatatttatacctggtgtatatgacaattttatttgtttttgccatgtagGTTGTTCGCTGGGGGCGTTCTGTCTATGCAAATATTCAAAAATTTATCCAGTTCCAGCTCACTGTTAATGTTGCAGCTCTTATTATAAATGTTGTTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- -ccatgta
- - - - - - - - - - - - - - - - - - -attccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacctgg