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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtgccacaagaactataattatcttttacttcaaacattctctggtctgatcctcatattttgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT

Basic information

species Oryza sativa
transcript LOC_Os12g13130.2
intron # 9
splice site 3'
intron type U2

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|88690274|gb|CI734353.1|CI734353
EST:     ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG                         GGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
genomic: ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAGgtctgtgcca ... tgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
EST: gi|86841250|gb|CI342973.1|CI342973
EST:     CACTGTTCTATCTCATAGTATTCTTGCACCAGAG                         GGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
genomic: CACTGTTCTATCTCATAGTATTCTTGCACCAGAGgtctgtgcca ... tgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
EST: gi|88849353|gb|CI087875.1|CI087875
EST:     ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG                         GGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
genomic: ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAGgtctgtgcca ... tgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
EST: gi|88688437|gb|CI732013.1|CI732013
EST:     ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG                         GGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
genomic: ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAGgtctgtgcca ... tgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
EST: gi|29645805|gb|CB650812.1|CB650812
EST:     ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG                         GGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
genomic: ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAGgtctgtgcca ... tgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
EST: gi|29645769|gb|CB650776.1|CB650776
EST:     ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG                         GGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
genomic: ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAGgtctgtgcca ... tgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
EST: gi|88260579|gb|CI362872.1|CI362872
EST:     ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG                         GGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
genomic: ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAGgtctgtgcca ... tgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
EST: gi|88222581|gb|CI222537.1|CI222537
EST:     ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAG                         GGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA
genomic: ACAATAGTACTTTTGCCACTGTTCTATCTCATAGTATTCTTGCACCAGAGgtctgtgcca ... tgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatcttttacttcaaacattctctggtctgatcctcatattttgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT
                            gtctgat  putative branch site (score: 4)
                                     tcatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtgccacaagaactataattatcttttacttcaaacattctctggtctgatcctcatattttgtggttcagGGAAATGAAGAAAGGCGGTCAAAATTTAAGACGAATTTCGAAAGTTGTCCAAAAGAAAAAACCATCTTAGGTACCTAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA