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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataccttgtttgtttttccaatatataggtctttcaccttttctgatatcaaatattgtttgggtagaatgttgactgatatcatgttacttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATCAACAAGGCACTTGAACTGATGCTAGAAAACAAGTGTTTGCGATGTGTGA

Basic information

species Oryza sativa
transcript LOC_Os02g42520.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g42520.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G149272_T02 (Zea mays), 3'ss of exon 9
ataccttgtttgtttttccaatatataggtctttcaccttttctgatatc----aaatattg-tttgggtagaatgttgactgatatcatgttacttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATCAACAAGGCACTTGAACTGATGCTAGAAAACAAGTGTTTGCGATGTGTGA
    ||| ||||   |     | |  | |  ||| | |||       ||     ||  ||    | |  | || |  ||  |  | |  | ||     || ||||||||||||||| |||| ||| || || |||||| |  ||||| || | |||||||| || |||||  ||||||||||||||||||| ||| |||||||||
----cttatttgacgtattggt-tgaatgcttttaagcttaaaaaggatttagaaagcataaactcgcattgactaatgtatcttgtattcttgtcatttatcagGAAATCCAAGTTGATGGCCTAGTCACGCATGATATACCATTCAATGAAATCAACAAAGCGCTTGAGTTGATGCTAGAAAACAAGTGCTTGAGATGTGTGA
















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|86840908|gb|CI335080.1|CI335080
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|89195803|gb|CI007222.1|CI007222
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|86500952|gb|CI143585.1|CI143585
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|29643822|gb|CB648829.1|CB648829
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|88227619|gb|CI227099.1|CI227099
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|86505804|gb|CI148437.1|CI148437
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|29618347|gb|CB623359.1|CB623359
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATGACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|86257487|gb|CI004304.1|CI004304
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|88964247|gb|CI045440.1|CI045440
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|117244917|gb|CT849641.1|CT849641
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATGACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|32948088|gb|BP184660.1|BP184660
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|88965373|gb|CI011624.1|CI011624
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
EST: gi|58684609|gb|CK073296.1|CK073296
EST:     GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTC
genomic: GGAGACCTAAATCTGATCTACCTTTGTTAGTGGACAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTC
EST: gi|88906992|gb|CI376064.1|CI376064
EST:     CAAGTATGCAAACAAG                         GAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC
genomic: CAAGTATGCAAACAAGgtacggagac ... ttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcaaatattgtttgggtagaatgttgactgatatcatgttacttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATCAACAAGGCACTTGAACTGATGCTAGAAAACAAGTGTTTGCGATGTGTGA
                            gactgat  putative branch site (score: 3)
                                       tgttacttcttctc  putative PPT
     aaatattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataccttgtttgtttttccaatatataggtctttcaccttttctgatatcaaatattgtttgggtagaatgttgactgatatcatgttacttcttctcagGAAATCCAAGTCGATGACCTTGTTACACATGATTTGTCATTCGATTACATCAACAAGGCACTTGAACTGATGCTAGAAAACAAGTGTTTGCGATGTGTGA

- - -ttgtttg
- - - tgtttgt
- - - - - - - - - - - - - - - - - - - - ttctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcatgt