Summary: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
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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.
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
|SCOOP:||Dscam_C Limkain-b1 Nup35_RRM_2 RRM_1 RRM_3 RRM_7 RRM_occluded|
|Similarity to PfamA using HHSearch:||RRM_1|
This tab holds annotation information from the InterPro database.
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- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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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 25 members:BRAP2 Calcipressin DbpA DUF1743 DUF1866 DUF4523 GUCT Limkain-b1 Nup35_RRM Nup35_RRM_2 PHM7_cyt RNA_bind RRM_1 RRM_2 RRM_3 RRM_5 RRM_7 RRM_occluded SET_assoc Smg4_UPF3 Spo7_2_N Tap-RNA_bind Transposase_22 U1snRNP70_N XS
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Number in seed:||7|
|Number in full:||2350|
|Average length of the domain:||115.00 aa|
|Average identity of full alignment:||24 %|
|Average coverage of the sequence by the domain:||31.03 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There are 4 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 26 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 seqence.
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