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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_Os01g68320.4
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|14980905|gb|BI305583.1|BI305583
EST:     GAACTGAACTTGTGGATTGATGGTGTATGCAAGGTGCCATCATGTCAGAG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: GAACTGAACTTGTGGATTGATGGTGTATGCAAGGTGCCATCATGTCAGAGgtagatcgtc ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|25801286|gb|CA757247.1|CA757247
EST:     TGTATGCAAGGTGCCATCATGTCAGAG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: TGTATGCAAGGTGCCATCATGTCAGAGgtagatcgtc ... atttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
EST: gi|14981748|gb|BI306426.1|BI306426
EST:     GAACTGAACTTGTGGATTGATGGTGTATGCAAGGTGCCATCATGTCAGAG                         ATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTG
genomic: GAACTGAACTTGTGGATTGATGGTGTATGCAAGGTGCCATCATGTCAGAGgtagatcgtc ... 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
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagatcgacaatgttgatatcccagtttggtctgctgtggtcttcagggcaaaagtattatcttgattacatactcatcattttcttgttatttttgcagATGTCAAGGATATTAAGTGTGTGATAAATTTTGATTTTCCAACAACTCTTGAAGATTATATTCACAGAATAGGTCGAACTGGCCGCGCTGGTGCTAGTGG

- - - - - atgttga
- - - - - - - - - - - - - - - tctgctg
- - - - - - - - - - - - - - - - - - - - - - - -ggcaaaa