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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacacatcacacataattaagctaattaaattaagctgataattagttaatttggtgatcgatcgatctgtggttgtgcgtgcgtcagCAATGGCGGTGATAGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACCGCAAGTACCGGAACGGCGACCGGCCGAACCGGGTGACGGCGTCGGGGTA

Basic information

species Oryza sativa
transcript LOC_Os05g34600.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34600.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G134687_T01 (Zea mays), 3'ss of exon 1
------gtacacacatcacacataattaagctaattaaattaagctgataattagttaatttggtgatcgatcgatctgtggttgtgcgtgcgtca---gCAATGGCGGTGATAGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACCGCAAGTACCGGAACGGCGACCGGCCGAACCGGGTGACGGCGTCGGGGTA
       |    | || |  |     ||   |  ||       || |  |  | | |   | | |   ||  ||  |   |     |   ||| ||   |||||||||||||| || | ||||||||||||||||||||||||| ||||||| |||||||||||||| |||||||||||||||||||||||||| |||||
tcttggctgattaaattaatccgctgtacaattgtttgcgcgcgcggtgatctggattgctcgctccccggccggacgacgacgacgacggcgccaccagCAATGGCGGTGATGGGCGGGAAGGAGTGGTTCTTCTACGTGCCGAGGGACCGTAAGTACCGGAACGGAGACCGGCCGAACCGGGTGACGGCGTCCGGGTA

upper sequence: LOC_Os05g34600.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G147867_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------gtacacacatcacacataattaagctaa--ttaaattaagctgataattagttaatttggtgatcgatcgatctgtggttgtgcgtgcgt-cagCAATGGCGGTGATAGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACCGCAAGTACCGGAACGGCGACCGGCCGAACCGGGTGACGGCGTCGGGGTA
                                                   |   ||  |  |    |||| | || |   |  ||  | ||  |   || |||||| | ||      | ||   |||  |  ||   |  |||||||||||||||| || | ||||||||||||||||||||||||| ||||||| |||||||||||||| ||||| || |||||||||||||||||||||||
gtaaccatcaattaatggtagcgcatgcatctggaagcttcgttctctgcttgatcagctagcctcgaattgaactgagtctcgatcgatct--tggctaattaattcgttg--tatacaattgctggacggacggcggcgcagCAATGGCGGTGATGGGCGGGAAGGAGTGGTTCTTCTACGTGCCGAGGGACCGTAAGTACCGGAACGGAGACCGCCCAAACCGGGTGACGGCGTCGGGGTA
















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|58687901|gb|CK076588.1|CK076588
EST:     GCTCATCACCTTCCTCGACCTCTACCGCTTCGACCCATGGGAGCTCCCCG                         CAATGGCGGTGATTGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACC
genomic: GCTCATCACCTTCCTCGACCTCTACCGCTTCGACCCATGGGAGCTCCCCGgtacacacat ... cgtgcgtcagCAATGGCGGTGATAGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACC
EST: gi|58593793|gb|CF992101.1|CF992101
EST:     CCCATGGGAGCTCCCCG                         CAATGGCGGTGATTGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACC
genomic: CCCATGGGAGCTCCCCGgtacacacat ... cgtgcgtcagCAATGGCGGTGATAGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACC
EST: gi|29644355|gb|CB649362.1|CB649362
EST:     GCTCATCACCTTCCTCGACCTCTACCGCTTCGACCCATGGGAGCTCCCCG                         CAATGGCGGTGATAGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACC
genomic: GCTCATCACCTTCCTCGACCTCTACCGCTTCGACCCATGGGAGCTCCCCGgtacacacat ... cgtgcgtcagCAATGGCGGTGATAGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgataattagttaatttggtgatcgatcgatctgtggttgtgcgtgcgtcagCAATGGCGGTGATAGGGGAGAAGGAGTGGTTCTTCTACGTGCCGCGGGACCGCAAGTACCGGAACGGCGACCGGCCGAACCGGGTGACGGCGTCGGGGTA
           agttaat  putative branch site (score: 4)
     ataattagttaattt  TA-rich tract