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0  structures 607  species 0  interactions 661  sequences 15  architectures

Family: RRP14 (PF15459)

Summary: 60S ribosome biogenesis protein Rrp14

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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.

60S ribosome biogenesis protein Rrp14 Provide feedback

RRP14 is a family of nucleolar 60S ribosomal biogenesis proteins from eukaryotes. RRP14 functions in ribosome synthesis as it is required for the maturation of both small and large subunit rRNAs and it helps to prevent premature cleavage of the pre-rRNA at site C2 [1]. It also plays a role in cell polarity and/or spindle positioning 2],

Literature references

  1. Oeffinger M, Fatica A, Rout MP, Tollervey D;, Nucleic Acids Res. 2007;35:1354-1366.: Yeast Rrp14p is required for ribosomal subunit synthesis and for correct positioning of the mitotic spindle during mitosis. PUBMED:17272295 EPMC:17272295

  2. Yamada H, Horigome C, Okada T, Shirai C, Mizuta K;, RNA. 2007;13:1977-1987.: Yeast Rrp14p is a nucleolar protein involved in both ribosome biogenesis and cell polarity. PUBMED:17804645 EPMC:17804645


This tab holds annotation information from the InterPro database.

InterPro entry IPR029188

This entry represents the N-terminal domain of the Rrp14 (ribosomal RNA-processing protein 14) protein.

Saccharomyces cerevisiae Rrp14 interacts with proteins involved in ribosomal biogenesis and cell polarity [PUBMED:15629442]. It is required for the synthesis of both 40S and 60S ribosomal subunits and may also play some direct role in correct positioning of the mitotic spindle during mitosis [PUBMED:17272295, PUBMED:17804645].

Domain organisation

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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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(55)
Full
(661)
Representative proteomes UniProt
(901)
NCBI
(1023)
Meta
(0)
RP15
(183)
RP35
(395)
RP55
(533)
RP75
(667)
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PP/heatmap 1 View               

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

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

Format an alignment

  Seed
(55)
Full
(661)
Representative proteomes UniProt
(901)
NCBI
(1023)
Meta
(0)
RP15
(183)
RP35
(395)
RP55
(533)
RP75
(667)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(55)
Full
(661)
Representative proteomes UniProt
(901)
NCBI
(1023)
Meta
(0)
RP15
(183)
RP35
(395)
RP55
(533)
RP75
(667)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   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: Pfam-B_10508 (release 26.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Wood V , Coggill P
Number in seed: 55
Number in full: 661
Average length of the domain: 56.70 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 12.02 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.5 22.5
Noise cut-off 22.1 22.0
Model length: 62
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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