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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagatcgacaatgttgatatcccagtttggtctgctgtggtcttcagggcaaaagtattatcttgattacatactcatcattttcttgttatttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTGAAGATTATATTCACAGAATAGGTCGAACTGGCCGCGCTGGTGCTAGTGG

Basic information

species Oryza sativa
transcript LOC_Os01g68320.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G362850_T01 (Zea mays), 3'ss of exon 9
--gagatcgacaatgttgatatcccagtttggtctgctgtggtcttcagggcaaaagtattatcttgattacatactcatcattttcttgttatttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTGAAGATTATATTCACAGAATAGGTCGAACTGGCCGCGCTGGTGCTAGTGG
  | |||||||||||||||| | ||||  |||||     |||| |||||| ||| |     || |||||||  |||| || || ||  ||||  |||||||||||| ||||| || |||||||||||||||| |||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||| ||
tggggatcgacaatgttgatgttccagcgtggtccagcatggtattcaggacaacacatcaattttgattaagtactgataatatt--tgttgattttgcagATGTGAAGGACATAAAGTGTGTGATAAATTATGATTTTCCAACAACTCTTGAAGATTATATTCACAGGATAGGTCGAACTGGCCGTGCTGGTGCTAGCGG

upper sequence: LOC_Os01g68320.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA05G02590.1 (Glycine max), 3'ss of exon 8
-----gagatcgacaatgttgatatcccagtttggtctgctgtggtcttcagggcaaaagtattatcttgattacatactcatcattttcttgttatttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTGAAGATTATATTCACAGAATAGGTCGAACTGGCCGCGCTGGTGCTAGTGG
     ||     |||     |  ||     |||    ||| ||  ||| ||     |||   |   ||| ||| | ||       |||| || |  |  | | |||||| || || || || |||||||| |||| |||||||||| |||  || ||||||||| | |||||||| ||||||||||| || || || ||||  ||
ctctagaatcttacagcacagggataaggattt---ttgcagttttctccatttttaaaccttacacttaattcctta--tgatgttttgttttgttgctcgtagATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCATCAAGCCTGGAAGATTATGTCCACAGAATTGGTCGAACTGGTCGTGCAGGGGCTAAAGG

upper sequence: LOC_Os01g68320.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G09270.1 (Glycine max), 3'ss of exon 8
----gagatcgacaatgttgatatcccagtttggtctgctgtggtcttcagggcaaaagtattatcttgattacatactcatcattttcttgttatttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTGAAGATTATATTCACAGAATAGGTCGAACTGGCCGCGCTGGTGCTAGTGG
    ||     ||| ||  |  ||     |||  | ||| ||  ||| ||     |||   |   ||| ||| | ||       |||| || |  |  ||| |||||| || || || || |||||||| |||| ||||||||||||||  || ||||||||| | |||||||| ||||||||||| || || || ||||  ||
tctagaatcttacagtgcagggataaggattt--tttgcagttttctccatttttaaaacctacacttaattcctta--tgatgttttgttttgttgcttgtagATGTGAAAGACATAAAATGTGTGATCAATTATGATTTTCCAACAAGCCTGGAAGATTATGTCCACAGAATTGGTCGAACTGGTCGTGCAGGGGCTAAAGG

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|29643632|gb|CB648639.1|CB648639
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29678104|gb|CB674379.1|CB674379
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29661778|gb|CB658053.1|CB658053
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAA
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAA
EST: gi|29629642|gb|CB634651.1|CB634651
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29643631|gb|CB648638.1|CB648638
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|88980895|gb|CI021022.1|CI021022
EST:     ATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: ATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29662446|gb|CB658721.1|CB658721
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|29669297|gb|CB665572.1|CB665572
EST:     TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGGGAAAAGTCCTATAATGGCTGCCACAGATGTAGCGGCACGTGGTCTTGgtatggtgac ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggcaaaagtattatcttgattacatactcatcattttcttgttatttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTGAAGATTATATTCACAGAATAGGTCGAACTGGCCGCGCTGGTGCTAGTGG
               tcttgat  putative branch site (score: 4)
                                   ttttcttgttattttt  putative PPT
                                  attttcttgttatttt  TA-rich tract