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fRNAdb specifications


Unique identifier OMICS_02783
Name fRNAdb
Alternative name Functional RNA Database
Restrictions to use None
Maintained Yes

Publications for Functional RNA Database

fRNAdb citations


Genome wide gene expression analysis in the amphioxus, Branchiostoma belcheri after poly (I: C) challenge using strand specific RNA seq

PMCID: 5752451
PMID: 29312538
DOI: 10.18632/oncotarget.21553

[…] nces, invalid reads with unknown bases, or low-quality sequences (>50% bases with Q value ≤ 10). Filtered cleans reads were mapped to public rRNA databases ( using SOAP2 (version 2.2.1,, and these mapped reads were removed. Next, all high-quality, clean reads were mapped to the B. belcheri reference genome ( […]


An integrated analysis revealed different microRNA mRNA profiles during skeletal muscle development between Landrace and Lantang pigs

Sci Rep
PMCID: 5451474
PMID: 28566753
DOI: 10.1038/s41598-017-02558-7

[…] uality reads and trimming the adaptor sequences, clean reads were obtained. We used the genomic position information of small RNAs and repeats in the annotation files from the UCSC Genome Browser and fRNAdb ( to assign the mapped reads to RNA classes. For known miRNAs (miRBase ver. 18), the number of raw, clean tags in each sample was normalized to Tags per Million (TPM […]


Genome wide identification of conserved intronic non coding sequences using a Bayesian segmentation approach

BMC Genomics
PMCID: 5369223
PMID: 28347272
DOI: 10.1186/s12864-017-3645-2

[…] We analysed the pathway-focussed PFEs using the same methods used in the genome-wide analysis (EvoFold, RNAz, DNase I footprints, and fRNAdb entries). An example WIG profile of a 169 nt long PFE identified in the 3-way alignment of eya1 is shown in Fig. . Three possible translation phases (top) indicate a lack of open reading frame […]


Identification and characterization of L1 specific endo siRNAs essential for early embryonic development in pig

PMCID: 5410294
PMID: 28423565
DOI: 10.18632/oncotarget.15517

[…] ttp:// The other known noncoding RNAs, including transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA),were identified by using the fRNAdb database ( The 18–24nt sncRNAs that were not annotated as known noncoding RNAs were considered as putative endo-siRNAs. We further identified endo-siRNAs associate […]


Induced Packaging of Cellular MicroRNAs into HIV 1 Virions Can Inhibit Infectivity

PMCID: 5241401
PMID: 28096489
DOI: 10.1128/mBio.02125-16
call_split See protocol

[…] l Bowtie alignment parameters): (i) 3′ and 5′ adapters, -v 0 –noRC; (ii) HIV genome, -v 1; (iii) miRBase version 20 Homo sapiens, -v 1 –noRC (), (iv) Ensembl ncRNAv70 Homo sapiens, -v 1 –noRC (); (v) fRNAdb version 3.4 Homo sapiens, -v 1 –noRC (); (vi) human genome 19, -v 2. miRNA sequences were given a -5p or -3p designation if they aligned with the 5′ or 3′ stem region, respectively, of the miRN […]


The non coding RNA composition of the mitotic chromosome by 5′ tag sequencing

Nucleic Acids Res
PMCID: 4889943
PMID: 27016738
DOI: 10.1093/nar/gkw195

[…] :// Visualizations were performed using Circos (). Enriched clusters were similarly compared to appropriate ncRNA data sets: lncRNA database: NONCODE (V3.0); snoRNA, snRNA database: fRNAdb (V3.4); uRNA (). These databases were also used to tabulate the number of annotated ncRNA in mice.A track of conserved genomic regions based on a phastCons analysis of an alignment of 60 verteb […]


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fRNAdb institution(s)
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan

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