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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acattttttcttgaattatcagtttctactcatccaagacaatgcatctaatgtggaaattaccaacaaattgacaaaaaagaaccttgtctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCATGCTCTTGGTCATGTCACTAGCAATGTATCGTTTGCTACTGTTGCAGTTT

Basic information

species Oryza sativa
transcript LOC_Os01g13770.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13770.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 4
---acattttttcttgaattatcagtttctactcatccaagacaatgcatctaatgtggaaattaccaacaaattgacaaaaaagaaccttgtctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCATGCTCTTGGTCATGTCACTAGCAATGTATCGTTTGCTACTGTTGCAGTTT
    |   |   | || ||  |   | |   || ||  | |||     | ||| |      ||| ||  |    | |   |  || |  |  |  |||||||||||||||||   || ||| ||||||| ||||||||||| ||  ||||||||| | |||||||  ||||||||||||| || || ||| |||||||||| |
gtagcccatccccatgcatcgtttatctaatctaatgaaggacggactagctagt------atttccggc---ctcatctagcagtatttctttgttttgtagCCTATCAATGGCACGCTCCTGAAGCTTCTCTTTCCAGTCGCCCTGTGCCATGGTATTGGTCACATCACTAGCAATGTGTCCTTCGCTGCTGTTGCAGTCT
















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|313084102|gb|HO213885.1|HO213885
EST:     CCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCG                         CCTATCAATTCGACACTCTTGAAGCTGTTCTTTCCAGTTGCGTTGTGTCAT
genomic: CCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCGgtaatttcta ... ctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
EST: gi|29643944|gb|CB648951.1|CB648951
EST:     GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCG                         CCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
genomic: GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCGgtaatttcta ... ctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
EST: gi|29661884|gb|CB658159.1|CB658159
EST:     GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCG                         CCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
genomic: GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCGgtaatttcta ... ctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
EST: gi|25797136|gb|CA753097.1|CA753097
EST:     GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCG                         CCTATCAATGCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTGGTGCCAT
genomic: GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCGgtaatttcta ... ctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctaatgtggaaattaccaacaaattgacaaaaaagaaccttgtctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCATGCTCTTGGTCATGTCACTAGCAATGTATCGTTTGCTACTGTTGCAGTTT
                       aattgac  putative branch site (score: 3)
                                       ccttgtctttttgt  putative PPT
                      aaattgacaaaaaa  TA-rich tract