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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_Os01g13770.2
intron # 4
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|29616222|gb|CB621234.1|CB621234
EST:     GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCG                         CCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
genomic: GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCGgtaatttcta ... ctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
EST: gi|66928470|gb|CX115318.1|CX115318
EST:     GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCG                         CCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
genomic: GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCGgtaatttcta ... ctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
EST: gi|29661884|gb|CB658159.1|CB658159
EST:     GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCG                         CCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
genomic: GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCGgtaatttcta ... ctttttgtagCCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
EST: gi|29657881|gb|CB654156.1|CB654156
EST:     GTGTCGTGTACTGCCTCGTGAGCTGGACCGTCGGGCTCCCAAAGCGTGCG                         CCTATCAATTCGACACTCTTGAAGCTGCTCTTTCCAGTTGCGTTGTGCCAT
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