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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagggtcatgtttcttgcattatcaaattcgtggaggttttcccccacataatgtcaattgatcctgtttcgtaaaaaaaaatagtaagcaattctttgtggctttttatatgcacttcttgtttgattttccgcaagaatacagtatgtctataatatgacctagtatttgtattgcagGATATTGTTTGATGATCTGCACAAGACAGGGATCTTTACATGGGATTACTTGCACCACCTAGGTTCTAACAAGTTTGGTCTGATGCGAAGCTATATCACA

Basic information

species Oryza sativa
transcript LOC_Os02g10430.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10430.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G006277_T01 (Zea mays), 3'ss of exon 3
gtgagggtcatgtttcttgcattatcaaattcgtggaggttttccc-ccacataatgtcaattgatcctgtttcgtaaaaaaaaatagtaagcaattctttgtggc-tttttatatgcacttcttgtttgattttccgcaagaatacagtatgtctataatatgacctagtatttgtattgcagGATATTGTTTGATGATCTGCACAAGACAGGGATCTTTACATGGGATTACTTGCACCACCTAGGTTCTAACAAGTTTGGTCTGATGCGAAGCTATATCACA
                                |||  |||| |||     ||||   |   ||  ||    |||  |   | |  | | |   | |    |||| | ||| ||| |   |   |      | | |  ||| |          ||  || || ||  ||| | ||||  | | |||||| | ||||||||  ||||||||||||||||||| |||||||||||||||||||| || ||||| ||||| ||  |||||||| |||  || |||| |
--------------------------------gtgagggttgtcctgtttcatagcat--gtttttctcagttctcagtcata--ttgcaga-agtcagctgtgacatttctatctat-caaataaaaaaaatatttgcatgt------cgggttcatgatctg--ctattgtttgcgt-gtagGATACTCTTTGATGACTTGCACAAGACAGGGATCTTCACATGGGATTACTTGCACCATCTCGGTTCAAACAAATTCAGTCTGATGAGAAATTACATCAGA
















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|66913206|gb|CX100054.1|CX100054
EST:     TGTTGGAATAATGTCAGCTGAATCAGTAGGAAATTACGGAGTACG                         GATATTGTTTGATGATCTGCACAAGACAGGGATCTTTACATGGGATTACTT
genomic: TGTTGGAATAATGTCAGCTGAATCAGTAGGAAATTACGGAGTACGgtgagggtca ... tgtattgcagGATATTGTTTGATGATCTGCACAAGACAGGGATCTTTACATGGGATTACTT
EST: gi|29665750|gb|CB662025.1|CB662025
EST:     CGACATGTTGGAATAATGTCAGCTGAATCAGTAGGAAATTACGGAGTACG                         GATATTGTTTGATGATCTGCACAAGACAGGGATCTTTACATGGGATTACTT
genomic: CGACATGTTGGAATAATGTCAGCTGAATCAGTAGGAAATTACGGAGTACGgtgagggtca ... tgtattgcagGATATTGTTTGATGATCTGCACAAGACAGGGATCTTTACATGGGATTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttccgcaagaatacagtatgtctataatatgacctagtatttgtattgcagGATATTGTTTGATGATCTGCACAAGACAGGGATCTTTACATGGGATTACTTGCACCACCTAGGTTCTAACAAGTTTGGTCTGATGCGAAGCTATATCACA
 gtttgat  putative branch site (score: 5)
                    tatgtctataatat  TA-rich tract