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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Source data information

The current miRcode release is based on the hg19 genome assembly and relies on data sources listed below.

GENCODE transcripts/genes

Transcripts in the GENCODE 11 annotation were analyzed in all regions, and results aggregated on a per-gene basis. For easy-of-use, we classify genes into a few broad categories, but all of GENCODE is included and searchable.

Total transcripts1179,905
Total genes153,520
LncRNA genes2All10,419
Coding genes419,999
1Ambigously mapped transcripts are excluded, leading to subtle differences compared to official counts.
2Having no coding spliceforms, and mature transcripts >200 nt.
3Not overlapping with any transcript of a coding gene.
4Genes producing at least one coding, non-NMD, isoform, although several non-coding transcripts may also be produced.
5GENCODE pseudogenes are also included in this miRcode release.
6Remaining genes (e.g. tRNAs, snoRNAs, all-NMD coding genes).

Multiz alignments

The Multiz 46-way vertebrate alignment was used for evaluating site conservation.

Placental mammals23
Non-mammal vertebrates13

TargetScan microRNA family definitions

Analyses are based on microRNA seed families as defined by TargetScan 6, as these are widely adopted.

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