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0  structures 313  species 0  interactions 865  sequences 6  architectures

Family: Sas10_Utp3 (PF04000)

Summary: Sas10/Utp3/C1D family

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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.

Sas10/Utp3/C1D family Provide feedback

This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex [2]. It also includes the human C1D protein and Saccharomyces cerevisiae YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs [3] and Sas10 which has been identified as a regulator of chromatin silencing [1]. This family also includes the human protein Neuroguidin an initiation factor 4E (eIF4E) binding protein [6].

Literature references

  1. Kamakaka RT, Rine J; , Genetics 1998;149:903-914.: Sir- and silencer-independent disruption of silencing in Saccharomyces by Sas10p. PUBMED:9611201 EPMC:9611201

  2. 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

  3. Mitchell P, Petfalski E, Houalla R, Podtelejnikov A, Mann M, Tollervey D; , Mol Cell Biol 2003;23:6982-6992.: Rrp47p is an exosome-associated protein required for the 3' processing of stable RNAs. PUBMED:12972615 EPMC:12972615

  4. Venema J, Tollervey D; , Annu Rev Genet 1999;33:261-311.: Ribosome synthesis in Saccharomyces cerevisiae. PUBMED:10690410 EPMC:10690410

  5. Wiederkehr T, Pretot RF, Minvielle-Sebastia L; , RNA. 1998;4:1357-1372.: Synthetic lethal interactions with conditional poly(A) polymerase alleles identify LCP5, a gene involved in 18S rRNA maturation. PUBMED:9814757 EPMC:9814757

  6. Jung MY, Lorenz L, Richter JD; , Mol Cell Biol. 2006;26:4277-4287.: Translational control by neuroguidin, a eukaryotic initiation factor 4E and CPEB binding protein. PUBMED:16705177 EPMC:16705177


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007146

This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex [PUBMED:12068309]. It also includes the Homo sapiens (Human) C1D protein and Saccharomyces cerevisiae (Baker's yeast) YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs [PUBMED:9611201] and Sas10 which has been identified as a regulator of chromatin silencing [PUBMED:12972615]. This entry also includes the human protein Neuroguidin, an initiation factor 4E (eIF4E)-binding protein [PUBMED:9611201].

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
(122)
Full
(865)
Representative proteomes NCBI
(854)
Meta
(4)
RP15
(186)
RP35
(316)
RP55
(487)
RP75
(604)
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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
(122)
Full
(865)
Representative proteomes NCBI
(854)
Meta
(4)
RP15
(186)
RP35
(316)
RP55
(487)
RP75
(604)
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
(122)
Full
(865)
Representative proteomes NCBI
(854)
Meta
(4)
RP15
(186)
RP35
(316)
RP55
(487)
RP75
(604)
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_6555 (release 7.3)
Previous IDs: none
Type: Family
Author: Bateman A, Wood V
Number in seed: 122
Number in full: 865
Average length of the domain: 85.50 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 23.39 %

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 20.5 20.5
Trusted cut-off 20.6 20.6
Noise cut-off 20.1 19.9
Model length: 85
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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