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 transcripts1 | 179,905 |
| Total genes1 | 53,520 |
| LncRNA genes2 | All | 10,419 |
| Intergenic3 | 5,680 |
| Overlapping | 4,739 |
| Coding genes4 | 19,999 |
| Pseudogenes5 | 12,549 |
| Other6 | 10,553 |
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.
| Primates | 9 |
| Placental mammals | 23 |
| Non-mammal vertebrates | 13 |
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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