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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaacatgtacactgtgccagtattaaaaaatgcatctgcattccatttgtctagtcgcatgcacttgcatctaacgcttttgttttggtttctttcagCGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGACAGAAGAGTTGGCACCTAACTTGCTAGAGAATGATATGGATTTGCATTT

Basic information

species Oryza sativa
transcript LOC_Os01g56820.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56820.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G085602_T02 (Zea mays), 3'ss of exon 2
atgaacatgtacact-gtgccagtat-taaaaaatgcatctgcattccatttgtctagtcgcatgcacttgcatctaacgcttttgttttggtttctttcagCGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGACAGAAGAGTTGGCACCTAACTTGCTAGAGAATGATATGGATTTGCATTT
 |||     || | |      ||| | ||||    | |  |  |||||| || |||  |   | ||| ||   | || |   |    ||   ||||||||||| ||||||| ||||||| | ||||| |||||||| || || ||||| |||||||||||  |||||||||||||||||||||||||||||||| | |||||
-tgagtgcataaaatcacaaaagtttgtaaattgagtaattatattccagttatctgatgata-gcaattttttgtatctaatagccttgactttctttcagCAATTTTTAATTTTGTGCTAGAAGGGAATGCCCTTAAAGCCATAGAGCTGACAGAAGAAATGGCACCTAACTTGCTAGAGAATGATATGGATCTACATTT
















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|88396710|gb|CI620043.1|CI620043
EST:     TGGTTTGGAACTGGCTGTTGATTACACTGTAGATGTAGATAAGCGTAAAG                         CGATTTTTAGTTTTGTGTTGGAAGGCCATGCACTGAAGGCTATAGACCTGA
genomic: TGGTTTGGAACTGCCTGTTGATTACACTGTAGATGTAGATAAGCGTAAAGgtatttattc ... tttctttcagCGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGA
EST: gi|40486859|gb|BX898175.1|BX898175
EST:     TGGTTTGGAACTGCCTGTTGATTACACTGTGGATGTAGATAAGCGTAAAG                         CGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGA
genomic: TGGTTTGGAACTGCCTGTTGATTACACTGTAGATGTAGATAAGCGTAAAGgtatttattc ... tttctttcagCGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGA
EST: gi|88428634|gb|CI599350.1|CI599350
EST:     TGGTTTGGAACTGCCTGTTGATTACACTGTAGATGTAGATAAGCGTAAAG                         CGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGA
genomic: TGGTTTGGAACTGCCTGTTGATTACACTGTAGATGTAGATAAGCGTAAAGgtatttattc ... tttctttcagCGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGA
EST: gi|117234957|gb|CT847981.1|CT847981
EST:     TGGTTTGGAACTGCCTGTTGATTACACTGTGGATGTAGATAAGCGTAAAG                         CGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGA
genomic: TGGTTTGGAACTGCCTGTTGATTACACTGTAGATGTAGATAAGCGTAAAGgtatttattc ... tttctttcagCGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgtctagtcgcatgcacttgcatctaacgcttttgttttggtttctttcagCGATTTTTAGTTTTGTGTTGGAAGGCAATGCCCTGAAGGCTATAGACCTGACAGAAGAGTTGGCACCTAACTTGCTAGAGAATGATATGGATTTGCATTT
                         atctaac  putative branch site (score: 2)
                                       ttttggtttctttc  putative PPT
                                  ttttgtttt  TA-rich tract