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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaatccatactagtgcatattccctccgtcccaaaatataagcattttttgctatgaatctagagaactatgtgtccagattcatagctaaaagttgttatattttgggacggaggtagtatattcataatattgatataaatcttactggagcatgattttcagGAATGCCTTATTGAAGGGGATACTAGTTCTGTTTGGCATGTTGCAAAAGCTATCCATAAGTTAGAG

Basic information

species Oryza sativa
transcript LOC_Os04g14654.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g14654.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G003734_T01 (Zea mays), 3'ss of exon 6
gtactaatccatactagtgcatattccctccgtcccaaaatataagcattttttgctatgaatctagagaactatgtgtccagattcatagctaaaagttgttatattttgggacggaggtagtatattcataatattgatataaatcttactggagc----atgatttt-cagGAATGCCTTATTGAAGGGGATACTAGTTCTGTTTGGCATGTTGCAAAAGCTATCCATAAGTTAGAG
                                                                                                        || | | | |   |  ||| || | | |  |  |  | | ||||| | |  |||     |||||||  ||||||||||||||||||| ||||| |||||| | ||||||||||| ||||| |||||||| ||||||
-------------------------------------------------------------------------------------------------------gtactattgcatatatctagcatgt-ctttctgatattctgaatctcattttagcccttgtgattttatagGAATGCCTTATTGAAGGAGATACAAGTTCTATCTGGCATGTTGCTAAAGCGATCCATAAATTAGAG
















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|33677575|gb|CF305814.1|CF305814
EST:     TTCCATTGGATGAAGATGTGATTTGTTTTGAACTTGATCATTCTCTGCAG                         GAATGCCTTATTGAAGGGGATACTAGTTCTGTTTGGCATGTTGCAAAAGCT
genomic: TTCCATTGGATGAAGATGTGATTTGTTTTGAACTTGATCATTCTCTGCAGgtactaatcc ... tgattttcagGAATGCCTTATTGAAGGGGATACTAGTTCTGTTTGGCATGTTGCAAAAGCT
EST: gi|29641506|gb|CB646513.1|CB646513
EST:     TTCCATTGGATGAAGATGTGATTTGTTTTGAACTTGATCATTCTCTGCAG                         GAATGCCTTATTGAAGGGGATACTAGTTCTGTTTGGCATGTTGCAAAAGCT
genomic: TTCCATTGGATGAAGATGTGATTTGTTTTGAACTTGATCATTCTCTGCAGgtactaatcc ... tgattttcagGAATGCCTTATTGAAGGGGATACTAGTTCTGTTTGGCATGTTGCAAAAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggaggtagtatattcataatattgatataaatcttactggagcatgattttcagGAATGCCTTATTGAAGGGGATACTAGTTCTGTTTGGCATGTTGCAAAAGCTATCCATAAGTTAGAG
                               atcttac  putative branch site (score: 3)
                                                ttttc  putative PPT
      tagtatattcataata  TA-rich tract