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7  structures 1014  species 0  interactions 5206  sequences 136  architectures

Family: RdRP (PF05183)

Summary: RNA dependent RNA polymerase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

RNA dependent RNA polymerase Provide feedback

This family of proteins are eukaryotic RNA dependent RNA polymerases. These proteins are involved in post transcriptional gene silencing where they are thought to amplify dsRNA templates.

Literature references

  1. Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, Timmons L, Plasterk RH, Fire A; , Cell 2001;107:465-476.: On the role of RNA amplification in dsRNA-triggered gene silencing. PUBMED:11719187 EPMC:11719187

  2. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC; , Cell 2000;101:543-553.: An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. PUBMED:10850496 EPMC:10850496

  3. Iyer LM, Koonin EV, Aravind L;, BMC Struct Biol. 2003;3:1.: Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. PUBMED:12553882 EPMC:12553882

This tab holds annotation information from the InterPro database.

InterPro entry IPR007855

This entry represents various eukaryotic RNA-dependent RNA polymerases (RDRP; EC ), such as RCRP-1, RDRP-2 and RDRP-6. These enzymes are involved in the amplification of regulatory microRNAs during post-transcriptional gene silencing [ PUBMED:12553882 ]; they are also required for transcriptional gene silencing. Double-stranded RNA has been shown to induce gene silencing in diverse eukaryotes and by a variety of pathways [ PUBMED:16691418 ]. These enzymes also play a role in the RNA interference (RNAi) pathway, which is important for heterochromatin formation, accurate chromosome segregation, centromere cohesion and telomere function during mitosis and meiosis. RDRP enzymes are highly conserved in most eukaryotes, but are missing in archaea and bacteria. The core catalytic domain of RDRP enzymes is structurally similar to the beta' subunit of DNA-dependent RNA polymerases (DDRP), however the other domains of DDRP show no similarity to those of RDRP.

This entry also includes QDE-1 from the filamentous fungus Neurospora. QDE-1 is both an RdRP and a DNA-dependent RNA polymerase (DdRP). It is able to synthesize RNA from both ssRNA and single-stranded DNA (ssDNA) [ PUBMED:20957187 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Representative proteomes UniProt

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_2226 (release 7.7)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Bateman A
Number in seed: 256
Number in full: 5206
Average length of the domain: 481.30 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 48.09 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.8 23.8
Trusted cut-off 24.4 23.8
Noise cut-off 23.7 23.7
Model length: 586
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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The tree shows the occurrence of this domain across different species. More...


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RdRP domain has been found. There are 7 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R0JN45 View 3D Structure Click here
A0A0R0JXX8 View 3D Structure Click here
A0A1D6E8W9 View 3D Structure Click here
A0A1D6EFA2 View 3D Structure Click here
A0A1D6EFA3 View 3D Structure Click here
A0A1D6EFB2 View 3D Structure Click here
A0A1D6HJL8 View 3D Structure Click here
A0A1D6MTP6 View 3D Structure Click here
A0A1D6MTP7 View 3D Structure Click here
A0A1D6P5B6 View 3D Structure Click here
A0A1D6P5I1 View 3D Structure Click here
G5EBQ3 View 3D Structure Click here
G5ECM1 View 3D Structure Click here
G5EE53 View 3D Structure Click here
G5EFA8 View 3D Structure Click here
I1KKW7 View 3D Structure Click here
I1MTJ2 View 3D Structure Click here
K7K152 View 3D Structure Click here
K7K760 View 3D Structure Click here
K7KIJ3 View 3D Structure Click here
K7VBP9 View 3D Structure Click here
O14227 View 3D Structure Click here
O82188 View 3D Structure Click here
O82189 View 3D Structure Click here
O82190 View 3D Structure Click here
O82504 View 3D Structure Click here
Q0DXS3 View 3D Structure Click here
Q0JPV9 View 3D Structure Click here
Q54EH7 View 3D Structure Click here
Q54H25 View 3D Structure Click here
Q54UI6 View 3D Structure Click here
Q5QMN4 View 3D Structure Click here
Q5QMN5 View 3D Structure Click here
Q7XM31 View 3D Structure Click here
Q8LHH9 View 3D Structure Click here
Q9LQV2 View 3D Structure Click here
Q9SG02 View 3D Structure Click here