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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagacatatatagctgctgatgtattaagttcatttatctgcatactttgtcctctgaagtcaaaactgtaaaatcacctaaagtctgcaatatttttgttgatagGCACCGACTACTTCCCATCAAGAAGCTTGCCGCTTTGTTGTAACAGACCTTACGGCACAGTTATGTCTACGGATTGTACTTTGGCTTGAGGGTCTTGCTT

Basic information

species Oryza sativa
transcript LOC_Os11g42420.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g42420.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G348675_T02 (Zea mays), 3'ss of exon 5
gtaagagacata----tatagctgctgatgtattaagttcatttatctgcatactttgtcctctgaagtcaaaactgtaaaatcacctaaagtctgcaatatttttgttgatagGCACCGACTACTTCCCATCAAGAAGCTTGCCGCTTTGTTGTAACAGACCTTACGGCACAGTTATGTCTACGGATTGTACTTTGGCTTGAGGGTCTTGCTT
|||||| | ||     ||||||| |  ||| ||| |  || ||| |     ||  || |  ||     ||  |  |||| | ||||||||  | ||  ||||  ||||  | || | || | ||| || ||||| || |||||||||||||||| | ||||| |||| |||||  | ||||| |||||  ||||||||||||| ||||||||||
gtaagacatattaagttatagctaccaatggattcaagtccttttttcctttaaattattgtcc----tctgatatgtatattcacctaagttttgtgatatgcttgtaaacagCCGCCAATTACATCTCATCAGGAGGCTTGCCGCTTTGTTGCAGCAGACATTACAGCACAACTGTGTCTGCGGATCATACTTTGGCTTGAAGGTCTTGCTT
















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|29622702|gb|CB627713.1|CB627713
EST:     GAAATGACGAGCTTCCTGGAGAGCTATTTGTG                         GCACCGACTACTTCCCATCAAGAAGCTTGCCGCTTTGTTGTAACAGACCTT
genomic: GAAATGAGGAGCTTCCTGGAGAGCTATTTGTGgtaagagaca ... ttgttgatagGCACCGACTACTTCCCATCAAGAAGCTTGCCGCTTTGTTGTAACAGACCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctgaagtcaaaactgtaaaatcacctaaagtctgcaatatttttgttgatagGCACCGACTACTTCCCATCAAGAAGCTTGCCGCTTTGTTGTAACAGACCTTACGGCACAGTTATGTCTACGGATTGTACTTTGGCTTGAGGGTCTTGCTT
                         acctaaa  putative branch site (score: 3)
                                          tttttgtt  putative PPT
                                      aatatttttgttgata  TA-rich tract