Summary: RNA binding domain
RNA binding domain Provide feedback
This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN).
Internal database links
|SCOOP:||RRM_3 DUF2414 SET_assoc RRM_5 Nup35_RRM_2 PHM7_cyt RRM_7|
|Similarity to PfamA using HHSearch:||RRM_1|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR014789
This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN). PARN is a 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails [PUBMED:9736620].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||nucleus (GO:0005634)|
|Molecular function||poly(A)-specific ribonuclease activity (GO:0004535)|
|metal ion binding (GO:0046872)|
|RNA binding (GO:0003723)|
|Biological process||mRNA catabolic process (GO:0006402)|
- 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
- the number of residues in the sequence
- the Pfam graphic itself.
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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 18 members:BRAP2 Calcipressin DUF1866 GUCT Limkain-b1 Nup35_RRM Nup35_RRM_2 PHM7_cyt RNA_bind RRM_1 RRM_2 RRM_3 RRM_5 RRM_7 RRM_occluded Smg4_UPF3 Tap-RNA_bind 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:
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||11|
|Number in full:||100|
|Average length of the domain:||76.00 aa|
|Average identity of full alignment:||60 %|
|Average coverage of the sequence by the domain:||13.01 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|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 is 1 interaction 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 RNA_bind domain has been found. There are 5 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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