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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatactgtatgcattctgtaggcttggtgttattgtattgtataatgctactatttttttccaatgattaatttaattttactatgtgtaaagtgtggtaacatatgtttttacagGAACCGATATCTACCAACAATATCTGGTTAAGGCACTTGCAAAACACTTTGGTGCTAGGTTGCTCACCATAGACTCTTCCATGCTATTTGGT

Basic information

species Oryza sativa
transcript LOC_Os03g22420.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22420.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 3
gtacatactgtatgcattctgtaggcttggtgttattgtattgtataatgctactatttttttccaatgattaatttaattttactatgtgtaaagtgtggtaacatatgtttttacagGAACCGATATCTACCAACAATATCTGGTTAAGGCACTTGCAAAACACTTTGGTGCTAGGTTGCTCACCATAGACTCTTCCATGCTATTTGGT
        | |||||||    ||| | ||    || | ||||   ||    || |      || || | |||  ||   ||||  ||    | |||| || |||| |||  |||||||||||| || ||||| ||| |||||||||| ||||||||||||||  | ||||||||||| ||||||||  |||| ||||||||||| ||||||
-------gtatatgcatgtgttagacatg----tactttatt---tagctttatttgaaacttgcatt-attgtttctgttttttta----ttaagtatgctaacttat-cttttacagGAACTGACATCTATCAAGAATATCTGGTGAAGGCACTTGCAAAGAATTTTGGTGCTAGATTGCTCACTGTAGATTCTTCCATGCTGTTTGGT
















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|58662518|gb|CK051204.1|CK051204
EST:     AAAAGATATTTCTTCTCTTAGTCAGCGAGTACTGCTGTCTGGTCCGGCAG                         GAACCGATATCTACCAACAATA
genomic: AAAAGATATTTCTTCTCTTAGTCAGCGAGTACTGCTGTCTGGTCCGGCAGgtacatactg ... gtttttacagGAACCGATATCTACCAACAATA
EST: gi|58670569|gb|CK059255.1|CK059255
EST:     AAAAGATATTTCTTCTCTTAGTCAGCGAGTACTGCTGTCTGGTCCGGCAG                         GAACCGATATCTACCAACAATATCTGG
genomic: AAAAGATATTTCTTCTCTTAGTCAGCGAGTACTGCTGTCTGGTCCGGCAGgtacatactg ... gtttttacagGAACCGATATCTACCAACAATATCTGG
EST: gi|88311581|gb|CI574798.1|CI574798
EST:     AAAAGATATTTCTTCTCTTAGTCAGCGAGTACTGCTGTCTGGTCCGGCAG                         GAACCGATATCTAGCAACAATATCTGGTTAAGGCACTTGCAAAACACTTTG
genomic: AAAAGATATTTCTTCTCTTAGTCAGCGAGTACTGCTGTCTGGTCCGGCAGgtacatactg ... gtttttacagGAACCGATATCTACCAACAATATCTGGTTAAGGCACTTGCAAAACACTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgattaatttaattttactatgtgtaaagtgtggtaacatatgtttttacagGAACCGATATCTACCAACAATATCTGGTTAAGGCACTTGCAAAACACTTTGGTGCTAGGTTGCTCACCATAGACTCTTCCATGCTATTTGGT
                                  tggtaac  putative branch site (score: 2)
                                            tgttttt  putative PPT
     attaatttaattttac  TA-rich tract