a comprehensive database of putative human microRNA target site (MTS) SNVs and their functional predictions


​dbMTS collects all potential SNVs microRNA target seed regions in human 3’UTRs and provides their functional predictions and annotations to facilitate the steps of filtering and prioritizing SNVs from a huge list of all SNVs discovered in a whole exome sequencing (WES) study. The core functional annotations in the database are the targeting efficacy scores for the reference and mutant loci based on three microRNA target prediction algorithms, TargetScan v7.0, RNAhybrid, and miRanda. Based on their predictions, we further classify the effect of each SNV into three categories, substitution, target loss and target gain. The maximum difference between the reference score and variant-induced score was calculated to estimate how the microRNA targeting efficacy was changed after introducing the variant. Additional functional annotations of the SNVs were also collected in dbMTS including variant consequences by SnpEff, VEP and ANNOVAR, dbSNP variant IDs, GWAS Catalog entries, allele frequencies from various populations, clinical consequences from ClinVar, expression quantitative trait loci (eQTLs) from GTEx, mappability scores etc.


dbMTS v1.0 is available, you could compose your query at the next section below. A description of the columns can be found here.

Attachment to dbNSFP

dbMTS can be queried as an attached database for dbNSFP. More information can be found on the dbNSFP website.


Please define the your output:

Please select range:
HG38 HG19
Please select output resources:
1. Basic information 2. VEP_ensembl 3. rs_dbSNP150 4. GWAS_catalog
5. GRASP 6. clinvar 7. GTEx_V6p 8. 1000G_strict_masked
9. RepeatMasker_masked 10. Ancestral_allele 11. phyloP46way 12. phyloP20way
13. phyloP100way 14. phastCons46way_primate 15. phastCons20way 16. phastCons100way
17. GERP 18. SiPhy_29way 19. integrated 20. GM12878
21. H1-hESC 22. HUVEC 23. GenoCanyon 24. 1000Gp3
25. UK10K 26. TWINSUK 27. ALSPAC 28. RegulomeDB
29. Motif_breaking 30. network_hub 31. ENCODE_annotated 32. sensitive
33. target_gene 34. funseq 35. CADD 36. DANN
37. fathmm-MKL 38. Eigen 39. miRanda 40. TargetScan
41. RNAhybrid

Selected range:

Selected output resources:

Single Query

Please enter the query parameters:
chr: *
pos: *
ref: *
alt: *
* indicates required

Multiple Queries:

Please enter your queries line-by-line at the box below:

You could sumbit multiple queries by one input file:

(1). Specify your query parameters line by line, each line represents one query;

(2). Put them into one file, name the file as query.txt (.vcf format is also supported);

txt sample file

vcf sample file: hg38 hg19

(3). Upload and sumbit it at the box below.



​Please cite:
Chang Li, Michael D. Swartz, Bing Yu, Yongsheng Bai, Xiaoming Liu. dbMTS: a comprehensive database of putative human microRNA target site SNVs and their functional predictions. bioRxiv 554485; doi: https://doi.org/10.1101/554485

Contact Me

         Xiaoming Liu, Ph.D.

         Associate Professor,

         USF Genomics,

Phone: 813-974-9865

Email: xiaomingliu@health.usf.edu

Lab Page: http://liulab.science

University of South Florida,
         3720 Spectrum Boulevard,
         Suite 304,
         Tampa, FL 33612