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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgatatgtggatgcacagtttccagtggacaattgaggagtcagccctattatttatcttgtatacatttgcatgatgtttttttttctcaaaacagGCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATCAAACTTATGATCCAAAGTAATATGTTCAAGTACCTTGGGATCCTTCTTG

Basic information

species Oryza sativa
transcript LOC_Os06g02130.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02130.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G429113_T01 (Zea mays), 3'ss of exon 4
ttctgatatgtggatgcacagtttccagtggacaattgaggagtcagccc----tattatttatcttgtatacatttgcatgatgtttttttttctcaaaacagGCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATCAAACTTATGATCCAAAGTAATATGTTCAAGTACCTTGGGATCCTTCTTG
  |   |  ||  ||   | ||| ||  |      || |   | ||| |     ||| |||||||||| ||||||||||||||  |||  ||| |  | ||||||| ||||| ||||||| || ||| |||||  | || |||||||| | ||||||||| ||||||||||| || ||||| |||||||| ||||| || ||||
--catttgagttcatatcctgttacccttatttggtttacatgacaggctaagttatcatttatcttgcatacatttgcatgacatttggtttac--ataacagGCTAAGTTGTTATACGGCAATAGATTTACTGATGAGGAACTTGAGAATATCAAACTAATGATCCAAAGCAACATGTTTAAGTACCTGGGGATTCTGCTTG
















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|58693598|gb|CK082285.1|CK082285
EST:     TTCTTATTCTTGGATCGCCTGGAGCTGGTACAAGCACCATATTCAAGCAG                         GCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATC
genomic: TTCTTATTCTTGGATCGCCTGGAGCTGGTACAAGCACCATATTCAAGCAGgtacgaccaa ... ctcaaaacagGCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATC
EST: gi|29622064|gb|CB627075.1|CB627075
EST:     TTCTTATTCTTGGATCGCCTGGAGCTGGTACAAGCACCATATTCAAGCAG                         GCAAAGTTATTATACGACACTANGTTTAC
genomic: TTCTTATTCTTGGATCGCCTGGAGCTGGTACAAGCACCATATTCAAGCAGgtacgaccaa ... ctcaaaacagGCAAAGTTATTATACGACACTAGGTTTAC
EST: gi|29667807|gb|CB664082.1|CB664082
EST:     CTGGTACAAGCACCATATTCAAGCAG                         GCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATC
genomic: CTGGTACAAGCACCATATTCAAGCAGgtacgaccaa ... ctcaaaacagGCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATC
EST: gi|58592696|gb|CF991004.1|CF991004
EST:     TTCTTATTCTTGGATCGCCTGGAGCTGGTACAAGCACCATATTCAAGCAG                         GCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATC
genomic: TTCTTATTCTTGGATCGCCTGGAGCTGGTACAAGCACCATATTCAAGCAGgtacgaccaa ... ctcaaaacagGCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATC
EST: gi|29667761|gb|CB664036.1|CB664036
EST:     CTGGTACAAGCACCATATTCTAGCAG                         GCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATC
genomic: CTGGTACAAGCACCATATTCAAGCAGgtacgaccaa ... ctcaaaacagGCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATC
EST: gi|58661665|gb|CK050345.1|CK050345
EST:     TGCTTATTCTTGGATCGCCTGGAGCTGGTACAAGCACCATATTCAAGCAG                         GCAAAGTTATTATACGACACTAGGTTTACCCGAGAAGAACTTGATAGTATC
genomic: TTCTTATTCTTGGATCGCCTGGAGCTGGTACAAGCACCATATTCAAGCAGgtacgaccaa ... ctcaaaacagGCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccctattatttatcttgtatacatttgcatgatgtttttttttctcaaaacagGCAAAGTTATTATACGACACTAGGTTTACCCAAGAAGAACTTGATAGTATCAAACTTATGATCCAAAGTAATATGTTCAAGTACCTTGGGATCCTTCTTG
                                  tgtttttttttctc  CT-rich tract
     tattatttatcttgta  TA-rich tract