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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacctttttctgttgacatgataagctatagttgtaatccatttcaaaattgatataggtgactgaatatgtgccctggatcttgaactctcttaactgctgcag

Basic information

species Vitis vinifera
transcript Vv03s0038g04470.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 5
GGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacctt-----tttctgt-tgacatgata--agctatagttgtaatccatttcaaaattgatataggtgactgaatatgtgccctg-gatcttgaactctcttaactgctgcag--------------------------
||  |||||||| | |||||| |||| ||||| |||||||||||| | || ||||||||||| |||||||||||||||||    |||  |     ||||||| |   |||        | |  ||  |  | || |   || | | |   || |   |  |  ||  ||  | |||  |  | |  | | |  ||                             
GGCCTTAAGAACTTTACAAAGTCTGCCCGGGACCTCATTATGCGGTTACAAAAGATTGATGGTGATAATTACCCTGAGgtgagtaacactgccggtttctgtgtattatggcccttattttgatttcatccgatataggaaattaaaattgtaaagaagaacatgtactaaggtctcaactttttctgattattgatttgttatttctcttcttaatgatacag

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G04460.1 (Glycine max), 5'ss of exon 5
GGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacctt-----tttctgt-tgacatgataagctatagttgtaatcc--atttcaaaattgatataggtgactgaatatgtgccctggatcttgaact---ctcttaactgctgcag------------------------------------
||  | |||||| | |||||| |||| |||||||||||||||||| | || ||||||||||| || |||||||||||||| |  |||  |     ||||||| |    || ||   ||      |  |    ||||||    | ||||         | | | |      ||   || |||    ||| ||||  ||| |                                    
GGCCTCAAGAACTTTACAAAGTCTGCTCGGGATCTCATTATGCGGTTACAAAAGATTGATGGTGACAATTACCCTGAGgtgtgtaacactgtcggtttctgtgtattttgttacattacgccccttgttttgatttcatcggttatatgaaattaaaagtttttaaagaagaatatgtactaaggtctcaactattgctgattttttattttttatttctttttttaatgatacag

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G01260.1 (Glycine max), 5'ss of exon 5
GGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacctttttc----------tgttgaca---------tgataagctatagttgtaatccatttcaaaattgatataggtgactgaatatgtgccctggatcttgaactctctta--actgctgcag
||  |||||||| | |||||| |||| ||||| |||||||  ||  |||||||||||||||| || |||||||||||||| |     ||| |||          ||||  |          ||  | ||||   |||| |   ||| |||| |  |   | |  |    |||       |||| |    | ||| |||  | |  | |||
GGCCTTAAGAACTTTACAAAGTCTGCCCGGGAACTCATTACCCGATTGCAGAAGATTGATGGTGACAATTACCCTGAGgtgtgttgtcttgttccctgtgtaattgtttgctattttcttttggaatgctagttttgtcagttattgcaaattcaaatgatgatatcctatagtcagaatggaccaatgattcttttattaataatacag

upper sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G01220.1 (Glycine max), 5'ss of exon 5
GGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacctttttctgt-tgacatgataagctatagttgtaatccatttcaaaattgatataggtgactga-atatgtgccctggatcttgaactctcttaactgctg-cag------------------------
||  |||||||| | |||||| |||| ||||| || ||||  ||  |||||||||||||||| ||||||||||||||||| |     ||| |||  | | || || |||   || | | |  ||  ||  ||   || | | |     |     |  | |    |||  |  ||| |  |||| |  | | |                        
GGCCTTAAGAACTTTACAAAGTCTGCCCGGGAACTTATTACCCGATTGCAGAAGATTGATGGTGATAATTACCCTGAGgtgtgttgtcttgttccctgtcacgtg-taattaattgctattttcttttggaatgctggttttgtcagttattgcaaattcgaaagatgatatactatggtaacagtggactgatgattcttttattaatgatacag

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|351015523|gb|FQ447352.1|FQ447352
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|351026236|gb|FQ428248.1|FQ428248
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|349822502|gb|FQ412766.1|FQ412766
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|351026103|gb|FQ428115.1|FQ428115
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|30296909|gb|CB973703.1|CB973703
EST:     TGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: TGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|351027625|gb|FQ446789.1|FQ446789
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|351055947|gb|FQ453408.1|FQ453408
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|294964977|gb|GW838780.1|GW838780
EST:     GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|349828849|gb|FQ419182.1|FQ419182
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|161709016|gb|FC058796.1|FC058796
EST:     GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|351040873|gb|FQ438417.1|FQ438417
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|349819344|gb|FQ412238.1|FQ412238
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|349817039|gb|FQ399786.1|FQ399786
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|30296834|gb|CB973628.1|CB973628
EST:     GCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|32270608|gb|CD719767.1|CD719767
EST:     GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|351024179|gb|FQ423602.1|FQ423602
EST:     GGGAGCTCATTATGCGGCTGCAGGAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|30299808|gb|CB976602.1|CB976602
EST:     GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
EST: gi|351021812|gb|FQ437197.1|FQ437197
EST:     GGGAGCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAG                         ACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC
genomic: GGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacc ... actgctgcagACTCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTTTAAGAACCTAACAAAGGCTGCACGGGATCTCATTATGCGGCTGCAGAAGATTGATGGGGATAATTACCCTGAGgtattcaacctttttctgttgacatgataagctatagttgtaatccatttcaaaattgatataggtgactgaatatgtgccctggatcttgaactctcttaactgctgcag

- - - - - - - - - - - - - - - - - - - - - -  CTGCAG