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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagtcttttgcgtattttttttttgcacatcaagcattactacctcagtattcttatttgcaaatttgctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCTCTCCAGGTTAGACAGTAAGCTACTCTAGGAGAAGCAGAGCAACTAGCTA

Basic information

species Oryza sativa
transcript LOC_Os12g07880.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07880.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G005848_T01 (Zea mays), 3'ss of exon 16
----------------gtactagtcttttgcgtattttttttttgcacatcaagcat--tactacc-tcagtattcttatttgcaaatttgctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCTCTCCAGGTTAGACAGTAAGCTACTCTAGGAGAAGCAGAGCAACTAGCTA
                | | | | |   ||  || |    ||||     |  | |||  ||  |   |  | | |  |  ||     || ||||| |||||||||| ||||||||||| || || | ||||||||| |||||||| |||||||| |||||||| ||||| || |  ||   |       || | || | ||
taactactgtagcaaagca-tgggcaactgactactgcagttttaagtgtttaccatgttaagattgttgggaataattattattgtttcgctgggttcagATCAAGCGCTTAAAGGAAAAGTTTGGAGAGATAAATAAGAAGCTCAATTCTCTTCAGGTTAGGCAGTAGGCCAGGCTCAAAATTTAGCAGTAGCTTGGTA
















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|88661327|gb|CI452383.1|CI452383
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTNAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|88487246|gb|CI424517.1|CI424517
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|88283314|gb|CI404760.1|CI404760
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|88664116|gb|CI490801.1|CI490801
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|88547254|gb|CI477536.1|CI477536
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|86834266|gb|CI344026.1|CI344026
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|88513751|gb|CI441257.1|CI441257
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATGTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|29629953|gb|CB634962.1|CB634962
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|88511000|gb|CI438506.1|CI438506
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|33798114|gb|CF324917.1|CF324917
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|89185796|gb|CI047665.1|CI047665
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
EST: gi|89173643|gb|CI041536.1|CI041536
EST:     GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGG                         ATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT
genomic: GCCATTCACTTGGGCAGAGGAAGAGAGATCTGGAGATCGAATTGAAGCGGgtactagtct ... ctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcacatcaagcattactacctcagtattcttatttgcaaatttgctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCTCTCCAGGTTAGACAGTAAGCTACTCTAGGAGAAGCAGAGCAACTAGCTA
                              ttatttgcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactagtcttttgcgtattttttttttgcacatcaagcattactacctcagtattcttatttgcaaatttgctggtttcagATCAAACGCTTAAAGGAGAAATTCGCAGAGATAAACAAGAAGCTGAATTCTCTCCAGGTTAGACAGTAAGCTACTCTAGGAGAAGCAGAGCAACTAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA