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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGGACGCTGGTTCATATCAGGGATCCCCTGTTTACAATGTGAACTCGATGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAAgtatgacaaaattgagtagttagcatccaattttatccacattgtttgggcattgtttatctttatctggtatttttggtcacagtatcataatttgtgtatgccatcttattgcag

Basic information

species Oryza sativa
transcript LOC_Os03g18080.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g18080.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G047894_T04 (Zea mays), 5'ss of exon 3
AAGGGACGCTGGTTCATATCAGGGATCCCCTGTTTACAATGTGAACTCGATGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAAgtatgacaaaattgagtagttagcatccaattttatccacattgtttgg----------gcattgtttatctttatctggtatttttggtcacagtatcataatttgtgtatgccatcttattgcag
 |  || ||||| || |||| ||| |||||||| ||| | |||||||| ||||||||||||||||||||||||||||| ||||| || ||| |||| |||||| |  || ||| |  |   ||  | |||||| |||||||||| ||||          ||| || ||   ||| ||||||  ||  |||| | | ||   | |||     | | || |  ||||||
GAAAGATGCTGGCTCTTATCTGGGCTCCCCTGTGTACCAAGTGAACTCAATGAAATTCTTATGCTGCAACGAGGCTATCAAGCACTTGACTCCACAGGAAgtaagtaaacatt-atca--cagtgtgcaatttaatccacattgcttggtcacaactaagcactgattgcatttctctggtgctt--ggtcgctgcatttaagttttctacttctatgtgcttgcag
















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|33675005|gb|CF303244.1|CF303244
EST:     TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAA                         AAAAGGGATGAGGCATATTTCATGTCTCTCCTGAAAATCGCAGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAAgtatgacaaa ... cttattgcagAAAAGGGATGAGGCATATTTCATGTCTCTCCTGAAAATCGCAGAAACTACT
EST: gi|88298501|gb|CI563496.1|CI563496
EST:     TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAA                         AAAAGGGATGAGGCATATTTCATGTCTCTCCTGAAAATCGCAGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAAgtatgacaaa ... cttattgcagAAAAGGGATGAGGCATATTTCATGTCTCTCCTGAAAATCGCAGAAACTACT
EST: gi|117222519|gb|CT845898.1|CT845898
EST:     TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAA                         AAAAGGGATGAGGCATATTTCATGTCTCTCCTGAAAATCGCAGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAAgtatgacaaa ... cttattgcagAAAAGGGATGAGGCATATTTCATGTCTCTCCTGAAAATCGCAGAAACTACT
EST: gi|29624693|gb|CB629704.1|CB629704
EST:     TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAA                         AAAAGGGATGAGGCATATTTCATGTCTCTCCTGAAAATTGCAGAAACTACT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAAgtatgacaaa ... cttattgcagAAAAGGGATGAGGCATATTTCATGTCTCTCCTGAAAATCGCAGAAACTACT
EST: gi|86883987|gb|CI309935.1|CI309935
EST:     TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAA                         AAAAGGGATGAGGCATAT
genomic: TGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAAgtatgacaaa ... cttattgcagAAAAGGGATGAGGCATAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGGACGCTGGTTCATATCAGGGATCCCCTGTTTACAATGTGAACTCGATGAAATTCTTATGCTGCAACGAGGCTATAAAGCATTTAACTGCACAAGAAgtatgacaaaattgagtagttagcatccaattttatccacattgtttgggcattgtttatctttatctggtatttttggtcacagtatcataatttgtgtatgccatcttattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC