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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaacttaagatgctatttatttatataatatcaacagtatatgctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag

Basic information

species Vitis vinifera
transcript Vv13s0019g02360.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 12
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaacttaagatgctatttatttatataatatcaacagtatatgctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
||||||||||| || || ||||| || |||||||| || ||||| ||||| |||||||| ||||  ||||| || ||||||||||| || ||||||||||   |  | |  | |||||||| |  ||   | |  |||    | |   |   ||| | |   |  |    |  ||| || ||| ||  |      || ||  || |                              
CTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTGgtaaatt--ctgtttgaacttaagttcttacc-actcttatggctttattgg---atgttgagttttttttt-ctttttgctatttctgacattccatatttccccactgcag--------------------------

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 13
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacag-----actaaacttaagatgctatttatttatataatatcaacagt-atatgctcaacctggtc-aaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
|||||||||||||| || |||||||| |||||||| |||||||| || ||||| || || || |   |||| || ||||||||||| || |||||||||| | |          | | || |   |   |||  ||||  ||  ||   ||  || || |  |   | |   | || ||   | | |||  |      |  |   | | ||||  |||| || | |      ||      |||
CTTGATGATGTGATTGATCTTGTAATACCAAGAGGTAGCAATAAGCTCGTTTCCCAGATCAAAGCAGCAACCAAGATTCCTGTTCTTGGTCATGCTGgtaagcttgtttttgttattgaattcttgtcactaaatattactagtatgataatggttatttattttgcataaactaagcataatacatttcctttttttattatgatatacatt--gaatgaatgtttt--ttttcttctacag

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaa-----cttaagatgctatttattta-tataatatcaacagtatat-gctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
||| ||||||| || || ||||| || ||||||||||||||||| || ||||| ||||| |||   ||||| || || |||||||| || ||||||||||   | |    | ||       ||  | | | |    || | || |||||||| | |||   |   |   || |     ||| ||   | ||| |                                                 
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaa-aatatgcagactagtttgatttctgaatctttcctctatag-------------------------------------------------

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM2G375504_T03 (Zea mays), 5'ss of exon 12
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaa------acttaagatgctatttattta-tataatatcaacagtatatgc-tcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
||||||||||| || || ||||| || ||||||||||||||||| || ||||| ||||| || |  ||||| || || ||||| || || ||||| ||||   | |    | ||        ||  | | | |    |  | || ||||  || | |||| |        || |     |||||| | | ||| |                                                 
CTTGATGATGTCATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCGCAAATCAAAGCATCAACTAAGATACCTGTCCTCGGTCATGCGGgtaaatttatcttccaatagtttgtttttggtacaaacagtccactacaatactaa-aatatacggactggtttgatttctgaattttttctctatag-------------------------------------------------

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA02G41850.1 (Glycine max), 5'ss of exon 10
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaacttaagatgctatttatttatataatatcaacagtatatgctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
|| |||||||| ||||| || || || |||||||||||||| |||||||||||||| || |||  ||| || |||||||||||| | || |||||||||| ||  |     ||  |||||       |||| ||        |  || || |      |   |||||   ||| ||| ||    | |    |      |||   |||  ||||||                     
CTGGATGATGTAATCGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAGATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCATGCTGgtaagactat----tatgcttaatggcacttttactt--------tggactgtgtg-----attttggtccctcaagttttttcaagttgattaagtccc-tctatttttgaaattaa---------------------

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA14G07120.1 (Glycine max), 5'ss of exon 10
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaacttaagatgctatttatttatataatatcaacagtatatgctcaacctggtc-aaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
|| ||||| || || || || || || |||||||||||||| ||||||||||||||||| |||  ||| || |||||||||||| | || || |||||||       ||||||   |||   |||| | | |||| |||    ||  | | | | ||| |  |  |    ||  | |  |||| ||      |    | |     |    ||||                       
CTGGATGACGTAATTGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAAATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCACGCTGgta-------agacta---tta---tgct-tatgtttaaatataggcataaatttttactctatttaatttggactgtgtgattttgattcctcaagtttttttcaagtc---aatt-----------------------

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT3G55610.2 (Arabidopsis thaliana), 5'ss of exon 13
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaacttaagatgctatttatttatataatatcaacagtatatgctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
|||||||| || || || ||||| ||||||||||||||||| || |||||||||||||||||  | || || ||||| || || || ||||||||||||||| | | |   | |  |       | ||| | || |  | |   |   |  ||     ||| |||   |    ||   | |||   |                                                 
CTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTGgtatgtttataagttcagtt-------ccattaagttcttaagttggattggcctagagagaacatggcttattttttgggtgtttccag-------------------------------------------------

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: AT2G39800.4 (Arabidopsis thaliana), 5'ss of exon 13
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaactt----aagatgctatttatttatataatatcaacagtatatgctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
|||||||| || ||||| ||||| ||||||||||| ||||| || |||||| |||| |||||  || | |||||||| ||||| || || |||||||||||| |  ||   |    ||    |  |   | |||| ||  ||  |   |  ||| |        | |  |     | ||                                                             
CTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAGGTCATGCTGgtatggttgcaagtttgttttttccagaagattctttacttggattgtgctag-agtgtgacgatggcttaattgtgtacttgcag---------------------------------------------------------

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: EFJ29127 (Selaginella moellendorffii), 5'ss of exon 13
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaacttaagatgctatttatttatataatatcaacagtatatgctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
||||| ||||| || ||||| || || |||||||| ||||||||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |||||| |          ||||          || |      | |  | | ||| | | |||    ||   || |  |||       |||| ||   |  |                                       
CTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCGgtatgct----------actt----------ttgtcctcgcattg-cgaaagtttgtcctcgcattgcgaaagctgtttctgacacatggaaaaccctttag-------------------------------------

upper sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: EFJ17662 (Selaginella moellendorffii), 5'ss of exon 13
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaacttaagatgcta---tttatttatataatatcaacagtatatgctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag
||||| ||||| || ||||| || || |||||||| ||||||||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| |||||| |       |   ||     ||| |   ||| |        |   ||   | | |     || |||  || |       |||  |||| |    | |||||| | |                               
CTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCGgtatgctactt--ttgtcctcgcattgcgaaaatttgtcctcgcgttgcgaaagctgtttctgacacatggaaaacc------ttttagatggtatctgccatgtctacgtag-----------------------------

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|33402539|gb|CF208166.1|CF208166
EST:     TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGGCATGCTG                         ATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
genomic: TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgac ... ttgctctcagATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
EST: gi|110362804|gb|EC926359.1|EC926359
EST:     TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG                         ATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
genomic: TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgac ... ttgctctcagATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
EST: gi|110728239|gb|EE103633.1|EE103633
EST:     GTTTCTCAAATAAAGGAATTCA-CAAAAATTCCTGTTCTGGGCCATGCTG                         ATGGCATCTGCCACGTTTATGTCAACAAGTCTGCTAATATGGATACTGCAA
genomic: GTTTCTCAAATAAAGGA-TTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgac ... ttgctctcagATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
EST: gi|110701185|gb|EE078493.1|EE078493
EST:     TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG                         ATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
genomic: TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgac ... ttgctctcagATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
EST: gi|161709197|gb|FC060516.1|FC060516
EST:     TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG                         ATGGCATCTGCC
genomic: TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgac ... ttgctctcagATGGCATCTGCC
EST: gi|110388887|gb|EC953685.1|EC953685
EST:     TGTTTTTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG                         ATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
genomic: TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgac ... ttgctctcagATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
EST: gi|29783302|gb|CB349405.2|CB349405
EST:     TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG                         ATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
genomic: TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgac ... ttgctctcagATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
EST: gi|110414936|gb|EC980800.1|EC980800
EST:     TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG                         ATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA
genomic: TGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgac ... ttgctctcagATGGCATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaacttaagatgctatttatttatataatatcaacagtatatgctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG