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0  structures 291  species 0  interactions 482  sequences 7  architectures

Family: Utp14 (PF04615)

Summary: Utp14 protein

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Utp14 protein Provide feedback

This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA [1]. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome [1].

Literature references

  1. Dragon F, Gallagher JE, Compagnone-Post PA, Mitchell BM, Porwancher KA, Wehner KA, Wormsley S, Settlage RE, Shabanowitz J, Osheim Y, Beyer AL, Hunt DF, Baserga SJ; , Nature 2002;0:0-0.: A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. PUBMED:12068309 EPMC:12068309


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006709

A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [PUBMED:12068309, PUBMED:15590835]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties:

  • They are nucleolar.
  • They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome).
  • They are required for 18S rRNA biogenesis.

There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble [PUBMED:15489292]. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA.

This entry contains Utp14, a large ribonuclear protein associated with snoRNA U3 [PUBMED:12068309].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(39)
Full
(482)
Representative proteomes NCBI
(487)
Meta
(11)
RP15
(127)
RP35
(183)
RP55
(260)
RP75
(309)
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Format an alignment

  Seed
(39)
Full
(482)
Representative proteomes NCBI
(487)
Meta
(11)
RP15
(127)
RP35
(183)
RP55
(260)
RP75
(309)
Alignment:
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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
(39)
Full
(482)
Representative proteomes NCBI
(487)
Meta
(11)
RP15
(127)
RP35
(183)
RP55
(260)
RP75
(309)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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_5404 (release 7.4)
Previous IDs: none
Type: Family
Author: Bateman A, Wood V
Number in seed: 39
Number in full: 482
Average length of the domain: 532.10 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 84.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 21.2
Trusted cut-off 23.8 21.6
Noise cut-off 19.7 19.7
Model length: 735
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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