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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggcgccccgccgtacgtcgccgcgtgcgcgacaagagctcggtcgcgttggggtttggggatcgattgatttataggcttttttgtttttgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGAGTCCGGCACGGGTGGAGGAGTACGGCGACCCGCTTTTTTCTTAGCGATT

Basic information

species Oryza sativa
transcript LOC_Os03g17570.1
intron # 1
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|88330650|gb|CI635280.1|CI635280
EST:     TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACG                         GGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
genomic: TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACGgtgcggcgcc ... tgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
EST: gi|88573494|gb|CI665065.1|CI665065
EST:     TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACG                         GGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
genomic: TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACGgtgcggcgcc ... tgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
EST: gi|88695536|gb|CI737574.1|CI737574
EST:     TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACG                         GGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
genomic: TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACGgtgcggcgcc ... tgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
EST: gi|29661058|gb|CB657333.1|CB657333
EST:     TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACG                         GGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
genomic: TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACGgtgcggcgcc ... tgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
EST: gi|88359680|gb|CI622370.1|CI622370
EST:     TCACGGTTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACG                         GGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
genomic: TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACGgtgcggcgcc ... tgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
EST: gi|88391633|gb|CI600822.1|CI600822
EST:     TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACG                         GGGGTGAGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
genomic: TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACGgtgcggcgcc ... tgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
EST: gi|88288553|gb|CI663342.1|CI663342
EST:     TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACG                         GGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA
genomic: TCACGGCTCCTCGCCGCCGGCTTGTGCCTCCGATACGTGAGCTCCCCACGgtgcggcgcc ... tgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgttggggtttggggatcgattgatttataggcttttttgtttttgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGAGTCCGGCACGGGTGGAGGAGTACGGCGACCCGCTTTTTTCTTAGCGATT
                   gattgat  putative branch site (score: 4)
                                 cttttttgtttttgt  putative PPT
                                  ttttttgtttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcggcgccccgccgtacgtcgccgcgtgcgcgacaagagctcggtcgcgttggggtttggggatcgattgatttataggcttttttgtttttgtgcggcagGGGGTGCGAGGGGGTCTGGAAACCGGCGGATCTCGGCCGCTCGCCGCCGGAGTCCGGCACGGGTGGAGGAGTACGGCGACCCGCTTTTTTCTTAGCGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG