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0  structures 284  species 0  interactions 330  sequences 21  architectures

Family: Utp21 (PF04192)

Summary: Utp21 specific WD40 associated putative domain

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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.

Utp21 specific WD40 associated putative domain Provide feedback

Utp21 is a subunit of U3 snoRNP, which is essential for synthesis of 18S rRNA.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007319

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.

Utp21 is a component of the SSU processome, which is required for pre-18S rRNA processing. It interacts with Utp18 [PUBMED:15590835].

Gene Ontology

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

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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...

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
(28)
Full
(330)
Representative proteomes NCBI
(331)
Meta
(2)
RP15
(84)
RP35
(137)
RP55
(203)
RP75
(242)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(28)
Full
(330)
Representative proteomes NCBI
(331)
Meta
(2)
RP15
(84)
RP35
(137)
RP55
(203)
RP75
(242)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(28)
Full
(330)
Representative proteomes NCBI
(331)
Meta
(2)
RP15
(84)
RP35
(137)
RP55
(203)
RP75
(242)
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_16350 (release 7.3);
Previous IDs: none
Type: Domain
Author: Wood V, Finn RD
Number in seed: 28
Number in full: 330
Average length of the domain: 226.30 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 24.85 %

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 22.1 22.1
Trusted cut-off 23.1 23.1
Noise cut-off 20.2 19.2
Model length: 237
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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