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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggcatgttgatctaattagaaatgtgctcattgtatagcttccttgtatttatttcccatcaactgatgcacaggataatcctgatatatgttgttagGTTGTCCATTTCAAGGGTTCAAGGAAGCGTTTGATGCTTGAAGCATGGAATTTCTACAACTCAACCTCTGAATTATCTGATATGTTGTGCCTAATTTTAA

Basic information

species Oryza sativa
transcript LOC_Os06g37430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G038667_T02 (Zea mays), 3'ss of exon 8
--ggggcatgttgatctaattagaaatgtgctcattgtatagcttccttgtatttatttcccatcaactgatgca--caggataatcctgatatatgttgttagGTTGTCCATTTCAAGGGTTCAAGGAAGCGTTTGATGCTTGAAGCATGGAATTTCTACAACTCAACCTCTGAATTATCTGATATGTTGTGCCTAATTTTAA
  ||  |||  | ||  |||   ||||||||   |||| || | |  |||||| |  || | ||  ||||   ||  |||  |||| ||  ||    || | ||||||| |||||||| ||||| || ||||| ||||||||||| |||||||||||||||| |||||||||| |  | ||||||||| | |||||||| || |
atggatcatactaattcaat---aaatgtgcatgttgtgtaacattgttgtatatgctttctatttactgtgacatccagagtaattcttgtac-cattttcagGTTGTTCATTTCAAAGGTTCCAGAAAGCGATTGATGCTTGAGGCATGGAATTTCTACAGCTCAACCTCTAAGCTGTCTGATATGCTATGCCTAATCTTGA

upper sequence: LOC_Os06g37430.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G143688_T01 (Zea mays), 3'ss of exon 5
ggggcatgttgatctaattagaaatgtgctcattgtatagcttccttgtatttatttcccatcaactgatgcac--aggataatcctgatat-atgttgttagGTTGTCCATTTCAAGGGTTCAAGGAAGCGTTTGATGCTTGAAGCATGGAATTTCTACAACTCAACCTCTGAATTATCTGATATGTTGTGCCTAATTTTAA
||   ||  | ||  |||   ||||||||    ||| || | |  |||||| | ||| | ||  ||||   ||   || ||||| ||  ||  || || | |||||||||||||||| |||||||| ||||| ||||||||||| ||||||||||||||||||||||||||| |  | ||||||||| | |||||||| || |
ggactatacttattcaat---aaatgtgcatgatgtgtaacattgttgtatatgttttctatttactgtgacatcaagaataattcttgtaccattttttcagGTTGTCCATTTCAAAGGTTCAAGAAAGCGATTGATGCTTGAGGCATGGAATTTCTACAACTCAACCTCTAAGATGTCTGATATGCTATGCCTAATCTTGA
















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|29671601|gb|CB667876.1|CB667876
EST:     CACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAG                         GTTGTCCATTTCAAGGGTTCAAGGAAGCGTTTGATGCTTGAAGCATGGAAT
genomic: CACCACCTGAAGGTGCTGGACAGTTCCATGGTATGCCATTGGATGTAAAGgtacaccatt ... atgttgttagGTTGTCCATTTCAAGGGTTCAAGGAAGCGTTTGATGCTTGAAGCATGGAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatttatttcccatcaactgatgcacaggataatcctgatatatgttgttagGTTGTCCATTTCAAGGGTTCAAGGAAGCGTTTGATGCTTGAAGCATGGAATTTCTACAACTCAACCTCTGAATTATCTGATATGTTGTGCCTAATTTTAA
                                    tcctgat  putative branch site (score: 3)
                                         atatatgtt  TA-rich tract