Transcriptome-wide microRNA target prediction including lncRNAs
miRcode 11 (June 2012) based on: UCSC GRCh37/hg19, GENCODE 11 transcripts, Multiz 46 species, TargetScan6 families
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Tab-delimited text files format and other frequent questions:

  • Predictions are based on GENCODE transripts/genes (see info page. For easy-of-use, we classify these into several categories, such as intergenic lncRNAs.
  • Site predictions are done on individual transcripts, and later aggregated into non-redundant sets for individual genes. This allows splice junction-spanning sites to be identified.
  • The Region column indicates if the site is in the 3'UTR, CDS or 5'UTR of a gene. Situations can arise where region assignment is ambigous (different region in different transcript isoforms). In this case, several regions are indicated (e.g. '3pUTR,ncRNA'). Sites in non-coding RNAs, or in non-coding spliceforms of coding genes, show 'ncRNA' in this column.
  • MicroRNA family names follows the TargetScan nomenclature, as these are widely used.
  • Dito for seed match types: 7-mer-A1 is a 6-mer match flanked by an adenosine in the target sequence, at the positions complementary to the 5'-most base of the microRNA.
  • 7-mer-m8 is simply a 7-mer complementary seed match, but for consistency with TargetScan we use this name.
  • 8-mer is a 7-mer match flanked by an adenosine (see 7-mer-A1 above).
  • All site positions refer to the 5' end of the microRNA.
  • The repeat column indicates that the seed overlaps with a RepeatMasker-defined repeat region (e.g. Alu).
  • Conservation scores are given, that indicate conservation (%) in primates (9), non-primate mammals (23), and more distant vertebrates (13).
  • In the downloadable files, these columns are preceeded by a total conservation column (%) (45 species excluding human).

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