Summary: Zc3h12a-like Ribonuclease NYN domain
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Zc3h12a-like Ribonuclease NYN domain Provide feedback
This family is found to be a divergent form of the NYN-domain- containing RNAse family.
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
Internal database links
|Similarity to PfamA using HHSearch:||RNase_Zc3h12a|
- the number of sequences which exhibit this architecture
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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 superfamily contains a variety of nuclease enzymes, including PIN domains and the FLAP exonucleases.
The clan contains the following 18 members:5_3_exonuc_N DUF188 DUF4411 Fcf1 Mut7-C NYN NYN_YacP PIN PIN_2 PIN_3 PIN_4 PIN_5 PIN_6 PRORP RNase_Zc3h12a RNase_Zc3h12a_2 XPG_N XRN_N
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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Curation and family details
|Number in seed:||4|
|Number in full:||35|
|Average length of the domain:||115.20 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||22.46 %|
|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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