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38  structures 691  species 0  interactions 6089  sequences 111  architectures

Family: RRM_5 (PF13893)

Summary: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

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 recognition motif. (a.k.a. RRM, RBD, or RNP domain) Provide feedback

The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins.

Literature references

  1. Birney E., Kumar S., Krainer A.R. , Nucleic Acid Res 1993;21:5803-5816.: Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. PUBMED:8290338 EPMC:8290338


Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

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

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Pfam Clan

This family is a member of clan RRM (CL0221), which has the following description:

This clan contains families that are related to the RNA recognition motif domains. However, not all these families are RNA binding.

The clan contains the following 32 members:

BRAP2 Calcipressin DbpA DUF1743 DUF1866 DUF4523 GlcNAc-1_reg GUCT Limkain-b1 Nup35_RRM Nup35_RRM_2 PHM7_cyt RL RNA_bind RRM_1 RRM_2 RRM_3 RRM_5 RRM_7 RRM_8 RRM_9 RRM_occluded RRM_Rrp7 SET_assoc Smg4_UPF3 Spo7_2_N Tap-RNA_bind Transposase_22 U1snRNP70_N xRRM XS YlmH_RBD

Alignments

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...

View options

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.

  Seed
(6)
Full
(6089)
Representative proteomes UniProt
(10684)
RP15
(829)
RP35
(2214)
RP55
(5007)
RP75
(6927)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(6)
Full
(6089)
Representative proteomes UniProt
(10684)
RP15
(829)
RP35
(2214)
RP55
(5007)
RP75
(6927)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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.

  Seed
(6)
Full
(6089)
Representative proteomes UniProt
(10684)
RP15
(829)
RP35
(2214)
RP55
(5007)
RP75
(6927)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

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...

Trees

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: JCSG:Target_421317_RF20609A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 6
Number in full: 6089
Average length of the domain: 112.30 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 28.09 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 10.0
Trusted cut-off 27.0 10.0
Noise cut-off 26.9 9.9
Model length: 125
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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

Selections

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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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Tree controls

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Structures

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 RRM_5 domain has been found. There are 38 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
A0A0B4K6W9 View 3D Structure Click here
A0A0B4K6W9 View 3D Structure Click here
A0A0B4K7I2 View 3D Structure Click here
A0A0R0G0X8 View 3D Structure Click here
A0A0R0HXC9 View 3D Structure Click here
A0A0R0KL81 View 3D Structure Click here
A0A0R4IZG6 View 3D Structure Click here
A0A1D6FPL6 View 3D Structure Click here
A0A1D6KP33 View 3D Structure Click here
A0A1D6M5G3 View 3D Structure Click here
A0A1D6M5G3 View 3D Structure Click here
A0A1D6NJH5 View 3D Structure Click here
A0A1D6Q1I5 View 3D Structure Click here
A0A1D6Q1I5 View 3D Structure Click here
A0A2R8RN29 View 3D Structure Click here
A4HUI2 View 3D Structure Click here
A5PM68 View 3D Structure Click here
A8KC22 View 3D Structure Click here
C6KSR3 View 3D Structure Click here
D4A3E1 View 3D Structure Click here
E7FB37 View 3D Structure Click here
E7FB37 View 3D Structure Click here
F1LQ48 View 3D Structure Click here
F1M040 View 3D Structure Click here
F1QKG2 View 3D Structure Click here
F1QKG2 View 3D Structure Click here
I1JDD2 View 3D Structure Click here
I1LX73 View 3D Structure Click here
I1MAI0 View 3D Structure Click here
I1N4F1 View 3D Structure Click here
I1NH38 View 3D Structure Click here
K7KUR7 View 3D Structure Click here
K7LFQ1 View 3D Structure Click here
O95758 View 3D Structure Click here
O95758 View 3D Structure Click here
P14866 View 3D Structure Click here
P17225 View 3D Structure Click here
P17225 View 3D Structure Click here
P26599 View 3D Structure Click here
P26599 View 3D Structure Click here
P40567 View 3D Structure Click here
Q00438 View 3D Structure Click here
Q00438 View 3D Structure Click here
Q0DHV7 View 3D Structure Click here
Q0DHV7 View 3D Structure Click here
Q0JHE8 View 3D Structure Click here
Q10KN8 View 3D Structure Click here
Q18999 View 3D Structure Click here
Q4DY41 View 3D Structure Click here
Q4DY42 View 3D Structure Click here
Q503D3 View 3D Structure Click here
Q503D3 View 3D Structure Click here
Q54NR9 View 3D Structure Click here
Q54PW8 View 3D Structure Click here
Q54PW8 View 3D Structure Click here
Q54YS7 View 3D Structure Click here
Q553T2 View 3D Structure Click here
Q553T2 View 3D Structure Click here
Q553T2 View 3D Structure Click here
Q5ZBG2 View 3D Structure Click here
Q66H20 View 3D Structure Click here
Q6ICX4 View 3D Structure Click here
Q6YWJ5 View 3D Structure Click here
Q80XZ1 View 3D Structure Click here
Q8BHD7 View 3D Structure Click here
Q8R081 View 3D Structure Click here
Q8WVV9 View 3D Structure Click here
Q91Z31 View 3D Structure Click here
Q921F4 View 3D Structure Click here
Q95QR5 View 3D Structure Click here
Q9FGL9 View 3D Structure Click here
Q9MAC5 View 3D Structure Click here
Q9UKA9 View 3D Structure Click here
Q9Z118 View 3D Structure Click here