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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatattttcaaatgaattttgactgttcattgattttgttgtccattggtttatttttcttatgaactttattttagGAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACTTTGCATTCCGGACAGTCTGTAACATGAGAAAGTGCAATACACCAAGACC

Basic information

species Oryza sativa
transcript LOC_Os08g41010.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G868981_T01 (Zea mays), 3'ss of exon 4
gtatatattttcaaatga--attttgactgttc---attgattttgttgtccattggtt---tattt-----ttcttatgaacttt-attttagGAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACTTTGCATTCCGGACAGTCTGTAACATGAGAAAGTGCAATACACCAAGACC
|||| | |  |  |||    |||||||||  |    ||| || | |||  |  ||| ||   |||||     ||||  ||||||||   |  ||||||||| ||||||||||||||| | || || |||||| | ||||| |||||||  || || ||||||||||| |||||||||||||| ||||| |||||
gtatgtctcattgaatttttattttgacttatttatattaatgtggttagcacttgattaattatttgcctattctcctgaacttttgatgaagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCATAACATCAACTTTGGCTTTCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACC

upper sequence: LOC_Os08g41010.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G134770_T04 (Zea mays), 3'ss of exon 6
gtatatattttcaaat--gaattttgactgttc---attgattttgttgtccattggtttattttt--------cttatgaactt-tattttagGAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACTTTGCATTCCGGACAGTCTGTAACATGAGAAAGTGCAATACACCAAGACC
|||||| || |  |||  | |||||||||  |    ||| || | |||| |   || |  ||| ||        | | ||||||| |  |  ||||||||| ||||||||||||||| | || || |||||| ||||||| |||||||  ||||| ||||||||||| |||||||||||||| ||||| |||||
gtatatcttattgaatttgtattttgacttatttatattaatgtggttggcacgtgatgaattctttgcctatccctctgaacttctgatgcagGAGCTGGCCGTGATAATGATTGGGAGTGTCCAAATTGCCACAACATCAACTTTGGCTTCCGCACAGTCTGTAATATGAGAAAGTGCAACACACCTAGACC
















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|88671645|gb|CI725443.1|CI725443
EST:     CGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAG                         GAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT
genomic: CGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAGgtatatattt ... tttattttagGAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT
EST: gi|29680937|gb|CB677212.1|CB677212
EST:     CGAGGAAGGATCCCAGAAGAAGCCTGCAG                         GAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT
genomic: CGAGGAAGGATCCCAGAAGAAGCCTGCAGgtatatattt ... tttattttagGAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT
EST: gi|88677245|gb|CI729903.1|CI729903
EST:     CGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAG                         GAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT
genomic: CGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAGgtatatattt ... tttattttagGAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT
EST: gi|88904764|gb|CI712063.1|CI712063
EST:     CGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAG                         GAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT
genomic: CGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAGgtatatattt ... tttattttagGAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT
EST: gi|58673635|gb|CK062321.1|CK062321
EST:     CGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAG                         GAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT
genomic: CGCGAGGGCTGGTTCATATTCCGAGGAAGGATCCCAGAAGAAGCCTGCAGgtatatattt ... tttattttagGAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttcattgattttgttgtccattggtttatttttcttatgaactttattttagGAGCTGGGCGTGATAATGATTGGAAATGCCCTAATTGCAACAACATTAACTTTGCATTCCGGACAGTCTGTAACATGAGAAAGTGCAATACACCAAGACC
     cattgat  putative branch site (score: 4)
                                            ctttatttt  putative PPT
                           tttatttttcttatga  TA-rich tract