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8  structures 309  species 0  interactions 1689  sequences 52  architectures

Family: Surp (PF01805)

Summary: Surp module

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "SWAP protein domain". More...

SWAP protein domain Edit Wikipedia article

Surp
PDB 1ug0 EBI.jpg
Solution structure of SURP domain in BAB30904.
Identifiers
Symbol Surp
Pfam PF01805
InterPro IPR000061

In molecular biology, the protein domain SWAP is derived from the term Suppressor-of-White-APricot, a splicing regulator from the model organism Drosophila melanogaster. The protein domain is found in regulators that control splicing. It is found in splicing regulatory proteins.[1] When a gene is expressed the DNA must be transcribed into messenger RNA (mRNA). However, it sometimes contains intervening or interrupting sequences named introns. mRNA splicing helps to remove these sequences, leaving a more favourable sequence. mRNA splicing is an essential event in the posttranscriptional process of gene expression.[2] SWAP helps to control this process in all cells except gametes.

Function[edit]

The role of the protein domain SWAP is to control sex-independent pre-mRNA processing in somatic cells, that is, in every cell except the sex cells This includes autoregulation, whereby it regulates the splicing of its own pre-mRNA.[3] The mammalian homologue of SWAP acts as a thyroid hormone regulated gene. This mean it is controlled by the thyroid.[4][5]

Structure[edit]

SWAP proteins share a colinearly arrayed series of novel sequence motifs.[3] This means that they have been conserved over time. The SWAP protein in different organisms share some similarity in terms of sequence and may have been related at some point in evolutionary history.

References[edit]

  1. ^ Denhez F, Lafyatis R (June 1994). "Conservation of regulated alternative splicing and identification of functional domains in vertebrate homologs to the Drosophila splicing regulator, suppressor-of-white-apricot". J. Biol. Chem. 269 (23): 16170–9. PMID 8206918. 
  2. ^ Clancy, Suzanne (2008). "RNA Splicing: Introns, Exons and Spliceosome". Nature Education 1 (1). Retrieved 31 March 2011. 
  3. ^ a b Spikes DA, Kramer J, Bingham PM, Van Doren K (1994). "SWAP pre-mRNA splicing regulators are a novel, ancient protein family sharing a highly conserved sequence motif with the prp21 family of constitutive splicing proteins.". Nucleic Acids Res 22 (21): 4510–9. doi:10.1093/nar/22.21.4510. PMC 308487. PMID 7971282. 
  4. ^ Cuadrado A, Bernal J, Muñoz A (1999). "Identification of the mammalian homolog of the splicing regulator Suppressor-of-white-apricot as a thyroid hormone regulated gene.". Brain Res Mol Brain Res 71 (2): 332–40. PMID 10521587. 
  5. ^ Khan A, Sulkowski ZL, Chen T, Zavacki AM, Sajdel-Sulkowska EM (2012). "Sex-dependent changes in cerebellar thyroid hormone-dependent gene expression following perinatal exposure to thimerosal in rats.". J Physiol Pharmacol 63 (3): 277–83. PMID 22791642. 

This article incorporates text from the public domain Pfam and InterPro IPR000061

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

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This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding [1].

Literature references

  1. Denhez F, Lafyatis R; , J Biol Chem. 1994;269:16170-16179.: Conservation of regulated alternative splicing and identification of functional domains in vertebrate homologs to the Drosophila splicing regulator, suppressor-of-white-apricot. PUBMED:8206918 EPMC:8206918


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000061

SWAP is derived from the Suppressor-of-White-APricot splicing regulator from Drosophila melanogaster. The domain is found in regulators responsible for pervasive, nonsex-specific alternative pre-mRNA splicing characteristics and has been found in splicing regulatory proteins [PUBMED:8206918]. These ancient, conserved SWAP proteins share a colinearly arrayed series of novel sequence motifs [PUBMED:7971282].

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
(64)
Full
(1689)
Representative proteomes NCBI
(1679)
Meta
(12)
RP15
(351)
RP35
(557)
RP55
(826)
RP75
(1115)
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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
(64)
Full
(1689)
Representative proteomes NCBI
(1679)
Meta
(12)
RP15
(351)
RP35
(557)
RP55
(826)
RP75
(1115)
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
(64)
Full
(1689)
Representative proteomes NCBI
(1679)
Meta
(12)
RP15
(351)
RP35
(557)
RP55
(826)
RP75
(1115)
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: Bateman A
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 64
Number in full: 1689
Average length of the domain: 53.40 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 10.94 %

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 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 20.9 21.0
Model length: 55
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Surp domain has been found. There are 8 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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