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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTGGTGAAAAGGGTGATGACTTGATAAGGGTTTTAAGAGAACTTACCACCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatcccatattctaatccttgttttaattcattatttcattcactagagactgtcacaattatattctttgagggatgtacatgttgtcagctt...

Basic information

species Vitis vinifera
transcript Vv12s0059g01290.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g01290.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA10G38820.1 (Glycine max), 5'ss of exon 2
TACTGGTGAAAAGGGTGATGACTTGATAAGGGTTTTAAGAGAACTTACCACCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatcccatattctaatccttgttttaattc-attatttcattcactagagactgtcacaattatattctttgagggatgtacatgttgtcagctt-----------------------------------------------------------
 ||||| ||||||||||| |||||||| |||||||| |||||||| || ||||| ||||||||||| |||||||||||||| |||||||||||||||||||| |      || | |    || |  ||| ||  |  |  || | ||       ||   || |  | |  ||| | |||   | ||| |     |    |                                                            
AACTGGGGAAAAGGGTGAGGACTTGATCAGGGTTTTGAGAGAACTGACTACCGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAGgttag-----ccttttagccattccagttgtatctggaccatctgatgtttcctagttggttaagaattaattttctgacataagtaaaaccaattccttcttttgatgttattttaacttgtatctgtctactcatctagagatttgtaaaatttttag

upper sequence: Vv12s0059g01290.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA20G28950.2 (Glycine max), 5'ss of exon 3
TACTGGTGAAAAGGGTGATGACTTGATAAGGGTTTTAAGAGAACTTACCACCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatcccat-attctaatccttgttttaattcattatttcattcactagagactgtcacaattatattctttgagggatgtaca--tgttgtcagctt---------------------------------------------------------
 ||||| ||||||||||| |||||||| |||||||| |||||||| || || || ||||||||||| |||||||||||||| |||||||||||||||||||| |    |      |||| | |  |   | |    |||  |  | || |||||      | | ||||| ||| | |||   | ||| |     || |  |||                                                         
AACTGGGGAAAAGGGTGAGGACTTGATCAGGGTTTTGAGAGAACTGACTACTGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAGgttagccttttagccattccagttgta--tctggaccatc-tgacgtttactagttggc-taagaatta-attttctgacataagtaaaaccaatgccttcttttgatgttattttaacttatatctgtctactcatctagagatttgtaaaatttttag
















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|349826040|gb|FQ415845.1|FQ415845
EST:     CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAG                         GAAGATAAGAATGTGGCGCATCTCACGCATGTAAGTGAAATGGAAAAGAAG
genomic: CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatc ... gattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAG
EST: gi|110365436|gb|EC928421.1|EC928421
EST:     CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAG                         GAAGATAAGAATGTGGCGCATCTCACGCATGTAAGTGAAATGGAAAAGAAG
genomic: CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatc ... gattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAG
EST: gi|110386241|gb|EC950822.1|EC950822
EST:     CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAG                         GAAGATAAGAATGTGGCGCATCTCACGCATGTAAGTGAAATGGAAAAGAAG
genomic: CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatc ... gattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAG
EST: gi|351019910|gb|FQ439727.1|FQ439727
EST:     CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAG                         GAAGATAAGAATGTGGCGCATCTCACGCATGTAAGTGAAATGGAAAAGAAG
genomic: CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatc ... gattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAG
EST: gi|161721680|gb|FC069810.1|FC069810
EST:     CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAG                         GAAGATAAGAATGTGGCGCATCTCACGCATTTAAGTGAAATGGAAAAGAAG
genomic: CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatc ... gattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAG
EST: gi|110401450|gb|EC968060.1|EC968060
EST:     AAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAG                         GAAGATAAGAATGTGGCGCATCTCACGCATGTAAGTGAAATGGAAAAGAAG
genomic: AAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatc ... gattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAG
EST: gi|110382053|gb|EC938357.1|EC938357
EST:     CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAG                         GAAGATAAGAATGTGGCGCATCTCACGCATGTAAGTGAAATGGAAAAGAAG
genomic: CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatc ... gattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAG
EST: gi|110374049|gb|EC938544.1|EC938544
EST:     CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAG                         GAAGATAAGAATGTGGCGCATCTCACGCATGTAAGTGAAATGGAAAAGAAG
genomic: CCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatc ... gattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTGGTGAAAAGGGTGATGACTTGATAAGGGTTTTAAGAGAACTTACCACCGTACAAAGAAAAATAGCAGATTTGCAAGTGGAACTTCAAGGTCGAAAGgtgaagtatcccatattctaatccttgttttaattcattatttcattcactagagactgtcacaattatattctttgagggatgtacatgttgtcagctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA