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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacctggaaaaaaaaccaatcccttatctgcagtaatttgctcttaggatttccagcaagaaggtattgagaatttgagatcatggctttctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAAGCAAGTCCAGCAGAAGGACACTAATGATCCACCATTGTTCTCAGTCACT

Basic information

species Oryza sativa
transcript LOC_Os12g02420.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g02420.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G063216_T01 (Zea mays), 3'ss of exon 2
tacctggaaaaaaaaccaatcccttatctgcagtaatttgctcttaggatttccagcaagaaggtattgaga---atttgagatcatggctttctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAAGCAAGTCCAGCAGAAGGACACTAATGATCCACCATTGTTCTCAGTCACT
    |  ||  |    ||  |  | || |        | | |   || |||| ||            | |      |||  |  |||| | |  ||| | ||||||||| ||||||||||| |||||||| |||||||||||||| || ||||||||||| |||||||||||||  |  || || ||| ||||||| ||||||
---gtaaaagtatttacatgcggtcattttgtacttgtcggttaaagcatttacactgcattttctcttacccttgttttggtacatgccatcttatctccagGTTCTACTACAGATGCACATACAAGAACGACATGAAGTGCCCCGCGACGAAGCAAGTGCAGCAGAAGGACAGCAGCGACCCGCCACTGTTCTCCGTCACT
















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|58602862|gb|CK013390.1|CK013390
EST:     CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAG                         GTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
genomic: CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAGgtaccttccg ... ctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
EST: gi|33822052|gb|CF336835.1|CF336835
EST:     CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAG                         GTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
genomic: CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAGgtaccttccg ... ctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
EST: gi|88327524|gb|CI646713.1|CI646713
EST:     CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAG                         GTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
genomic: CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAGgtaccttccg ... ctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
EST: gi|33803500|gb|CF327625.1|CF327625
EST:     CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAG                         GTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
genomic: CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAGgtaccttccg ... ctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
EST: gi|33691269|gb|CF319508.1|CF319508
EST:     CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAG                         GTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
genomic: CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAGgtaccttccg ... ctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
EST: gi|58600345|gb|CK010873.1|CK010873
EST:     CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAG                         GTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
genomic: CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAGgtaccttccg ... ctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
EST: gi|33693069|gb|CF321308.1|CF321308
EST:     CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAG                         GTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA
genomic: CAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTCCCAAGgtaccttccg ... ctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatttccagcaagaaggtattgagaatttgagatcatggctttctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAAGCAAGTCCAGCAGAAGGACACTAATGATCCACCATTGTTCTCAGTCACT
                                         ctttctattt  CT-rich tract
                                          tttctattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacctggaaaaaaaaccaatcccttatctgcagtaatttgctcttaggatttccagcaagaaggtattgagaatttgagatcatggctttctatttgcagGTTCTATTACAGATGCACCTACAAGAATGACATGAAGTGCCCTGCTACGAAGCAAGTCCAGCAGAAGGACACTAATGATCCACCATTGTTCTCAGTCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
tacctgg
- - - -aaaaaaa
- - - - - - - - - - - - -atctgca
- - - - - - - - - - - - - - - - - - - - - - - - - -tccagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggct