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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatagaagctgtagcgtctcacttaagattgctcgatgttcatgttttgtacttttgtgttagtcctacaaattaaggcaaatcatttgatgatttcagATATCTGGCGATTGGCACAACAGGTGAAAGTTAGACAAAG

Basic information

species Oryza sativa
transcript LOC_Os09g32680.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G408242_T05 (Zea mays), 3'ss of exon 2
ttatagaagctgtagcgtctcac---ttaagattgctcgatgttcatgttttgt----acttttgtgttagtcctacaa-----attaaggcaaatcatttgatgatttcagATATCTGGCGATTGGCACAACAGGTGAAAGTTAGACAAAG------------------------------------------------------------
             ||  ||||||   || | |||  | ||||| ||| ||   |    ||   ||   || |  |  |      || ||  |||  |||||||||||||||||||||||| |  | ||||| ||||| |||||||| |||||                                                            
----------cacagtatctcacattttcacatta-ttgatgtccattttgcattaggacacctggtgtatttttgaatgccttatcaatacaag-catttgatgatttcagATATCTGGAGGCTAGCACAGCAGGTTAAAGTTAGGCAAAGGTTAGGCCTTGTTTGCATAACCTGATTTATTTGCTTCTTTTGTGATGCTAAAAGGAACGT

upper sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G408242_T04 (Zea mays), 3'ss of exon 2
ttatagaagctgtagcgtctcac---ttaagattgctcgatgttcatgttttgt----acttttgtgttagtcctacaa-----attaaggcaaatcatttgatgatttcagATATCTGGCGATTGGCACAACAGGTGAAAGTTAGACAAAG
             ||  ||||||   || | |||  | ||||| ||| ||   |    ||   ||   || |  |  |      || ||  |||  |||||||||||||||||||||||| |  | ||||| ||||| |||||||| |||||
----------cacagtatctcacattttcacatta-ttgatgtccattttgcattaggacacctggtgtatttttgaatgccttatcaatacaag-catttgatgatttcagATATCTGGAGGCTAGCACAGCAGGTTAAAGTTAGGCAAAG
















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|88306627|gb|CI671386.1|CI671386
EST:     GCCTCCGCCCTGCCCACGATGGCCGCCAACTTCTGGACGTCGTCGCACTG                         ATATCTGGCGATTGGCACAACAGGTGAAAGTTAGACAAAG
genomic: GCCTCCGCCCTGCCCACGATGGCCGCCAACTTCTGGACGTCGTCGCACTGgtaagcgtcc ... atgatttcagATATCTGGCGATTGGCACAACAGGTGAAAGTTAGACAAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtacttttgtgttagtcctacaaattaaggcaaatcatttgatgatttcagATATCTGGCGATTGGCACAACAGGTGAAAGTTAGACAAAG
                                        atttgat  putative branch site (score: 5)
                      tacaaattaa  TA-rich tract