RMVar-Database of functional variants involved in RNA modification

RMVar! Database of functional variants involved in RNA modifications

Search by RMVar_ID, Rs_ID, Gene, Region or Disease:

What are RNA Modification associated variants

According to different levels of RNA modifications sites confidence, we extracted the corresponding RNA modifications associated variants as follows:
1． For RNA modifications sites with high confidence level, we retained the variants that located nearby the RNA modifications sites and then looked for the variants that destroy modification motif of the modification sites.
2． For RNA modifications sites with medium confidence level, the RNA modification associated variants were derived from the intersection between the variants and RNA modification sites generated from MeRIP-Seq experiments and m⁶A-Seal-Seq experiments. Then, we applied our prediction models to find the variants nearby the RNA modification sites that change the sequence features essential for RNA modification.
3． For RNA modification sites low confidence level, a genome-wide prediction based on deep convolutional neural network was performed for the sequences around all the collected variants from dbSNP, HGVD, TCGA, ICGC and COSMIC to find the variants that cause potential gain or loss of RNA modification sites.

What's in RMVar

In RMVar, you can search or browse:

1) RNA modification associated genetic mutations (dbSNP, HGVD)

2) RNA modification associated cancer somatic mutations (TCGA, ICGC, COSMIC)

3) Disease related RNA modification associated variants (GWAS and ClinVar)

4) Splicing sites affected by RNA modification associated variants

5) RNA binding protein affected by RNA modification associated variants

6) miRNA targeting and processing affected by RNA modification associated variants

7) circRNA affected by RNA modification associated variants.

8) UCSC genome browser tracks for RNA modification associated variants of human and mouse are available.

Data overview

We collected millions of variants, as well as thousands of RNA modification sites from 28 miCLIP experiments, 2 PA-m⁶A-Seq experiments, 2 m6ACE-Seq experiments, 3 DART-Seq experiments, 7 m⁶A-REF-Seq experiments, 4 MAZTER-seq experiments, 2 m¹A-quant-seq experiments, 2 m¹A-IP-Seq experiments, 2 m¹A-MAP experiments, 5 m⁷G-seq, 10 BS-Seq experiments, 2 Nm-Seq experiments, 14 RiboMeth-Seq experiments, 2 ψ-Seq experiments, 1 DM-ψ-Seq experiment, 3 Ceu-Seq experiments, 3 RBS-Seq experiments, 2 m⁶A-Seal-Seq experiments and 507 MeRIP-Seq experiments, together with a large number of predicted RNA modification sites are involved. At present, RMVar contains 941,955 RNA modification sites and 1,678,126 RNA modification associated variants, which are composed of 1,457,898 RNA modification associated germline mutations from dbSNP and HGVD, and 220,228 RNA modification associated somatic mutations from TCGA, ICGC and COSMIC.