Text search

RNAcentral text search supports advanced queries using the following syntax:

Exact matching

Use double quotes ("") to search for exact matches.

Example: "hsa-mir-21" will find only hsa-mir-21 and not hsa-mir-212


A wildcard character (*) can match any number of characters. Wildcards are added automatically to all search terms that are not enclosed in double quotes.

Example: a search for HOTAIR (no double quotes) will find both HOTAIR and HOTAIRM1 genes and a search for "HOTAIR" (with double quotes) will find only HOTAIR.

Field-specific search

Search can be restricted to specific fields using the field_name:"field value" syntax. Please note that "field value" must be enclosed in double quotes.

Field Examples
expert database expert_db:"tmrna website", expert_db:"mirbase", search for RNA and look at the "Expert databases" facet
NCBI taxonomic identifier taxonomy:"9606" where 9606 is the NCBI taxonomy id for Homo sapiens
taxonomy string tax_string:"primates" - allows to search for taxonomic group
scientific species name species:"Mus musculus"
common species name common_name:"mouse"
RNA type rna_type:"pirna", search for RNA and look at the "RNA types" facet.
gene gene:"hotair"
organelle organelle:"mitochondrion", organelle:"plastid"
description description:"16S"
length length:"1500", length:[9000 to 10000] (supports range queries)
publication title pub_title:"Danish population"
author author:"Girard A."
PubMed id pubmed:"17881443"
Digital Object Identifier doi:"10.1093/nar/19.22.6328"
MD5 md5:"020711a90d35bb197e29e085595dd52e" MD5 hash value of uppercase DNA corresponding to RNAcentral sequence.
interacting proteins interacting_protein:"ENSG00000277791"
secondary structure has_secondary_structure:"True"

Logic operators

  • and (default)

    Multiple search terms separated by white spaces are combined using AND, so a query like Homo sapiens is treated as Homo AND sapiens and only entries having both terms will be found.

  • or (to indicate equivalence)

    *Example: rna_type:"pirna" or rna_type:"mirna"

  • not (to indicate exclusion)

    *Example: expert_db:"lncrnadb" not expert_db:"rfam".


Use parentheses to group and nest logical terms.

Example: (expert_db:"mirbase" OR expert_db:"lncrnadb") NOT expert_db:"rfam"

Search tips

  • Make sure your spelling is correct.

    Example: misspelled terms like Esherichia (missing "c") won't find any results.

  • Use full species names.

    Example: use Escherichia coli and not E. coli as your search terms.

Download search results

The RNAcentral text search can only export up to 1,000,000 search results. If you need to export more sequences, you can use the public Postgres database

RNAcentral CPB protocol

Our latest article describes different ways of accessing the data.

See the text search section

About RNAcentral search

RNAcentral is powered by the EBI search, which provides a publicly available REST interface for querying the data.

Improve this page