Summary: Zc3h12a-like Ribonuclease NYN domain
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Zc3h12a-like Ribonuclease NYN domain Provide feedback
This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes [1]. It has been suggested that this domain belongs to the PIN domain superfamily [1]. This domain has also been identified as part of the NYN domain family [2].
Literature references
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Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, Miyake T, Satoh T, Kato H, Tsujimura T, Nakamura H, Akira S;, Nature;458:1185-1190.: Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. PUBMED:19322177 EPMC:19322177
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Anantharaman V, Aravind L; , RNA Biol. 2006; [Epub ahead of print]: The NYN Domains: Novel Predicted RNAses with a PIN Domain-Like Fold. PUBMED:17114934 EPMC:17114934
Internal database links
SCOOP: | PRORP RNase_Zc3h12a_2 |
Similarity to PfamA using HHSearch: | PRORP |
This tab holds annotation information from the InterPro database.
InterPro entry IPR021869
This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes [PUBMED:19322177]. It has been suggested that this domain belongs to the PIN domain superfamily [PUBMED:19322177]. This domain has also been identified as part of the NYN domain family [PUBMED:17114934].
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 PIN (CL0280), which has the following description:
This superfamily contains a variety of nuclease enzymes, including PIN domains and the FLAP exonucleases.
The clan contains the following 27 members:
5_3_exonuc_N DUF1308 DUF188 DUF4411 DUF5615 DUF5616 Fcf1 Mut7-C NYN NYN_YacP PIN PIN7 PIN_10 PIN_11 PIN_12 PIN_2 PIN_3 PIN_4 PIN_5 PIN_6 PIN_8 PIN_9 PRORP RNase_Zc3h12a RNase_Zc3h12a_2 XPG_N XRN_NAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (20) |
Full (1991) |
Representative proteomes | UniProt (3557) |
NCBI (5584) |
Meta (17) |
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RP15 (264) |
RP35 (614) |
RP55 (1380) |
RP75 (2105) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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.
Seed (20) |
Full (1991) |
Representative proteomes | UniProt (3557) |
NCBI (5584) |
Meta (17) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (264) |
RP35 (614) |
RP55 (1380) |
RP75 (2105) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | [1] |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 20 |
Number in full: | 1991 |
Average length of the domain: | 145.50 aa |
Average identity of full alignment: | 47 % |
Average coverage of the sequence by the domain: | 22.04 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 156 | ||||||||||||
Family (HMM) version: | 9 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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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Interactions
There is 1 interaction for this family. More...
RNase_Zc3h12aStructures
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 RNase_Zc3h12a domain has been found. There are 12 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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