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0  structures 66  species 0  interactions 90  sequences 2  architectures

Family: SR-25 (PF10500)

Summary: Nuclear RNA-splicing-associated protein

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Nuclear RNA-splicing-associated protein Provide feedback

SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissues. At the N-terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing [1]. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1) signalling pathway [2].

Literature references

  1. Sasahara K, Yamaoka T, Moritani M, Tanaka M, Iwahana H, Yoshimoto K, Miyagawa J, Kuroda Y, Itakura M; , Biochem Biophys Res Commun. 2000;269:444-450.: Molecular cloning and expression analysis of a putative nuclear protein, SR-25. PUBMED:10708573 EPMC:10708573

  2. Lee SC, Sim N, Clement MV, Yadav SK, Pervaiz S; , Proteomics. 2007;7:4112-4122.: Dominant negative Rac1 attenuates paclitaxel-induced apoptosis in human melanoma cells through upregulation of heat shock protein 27: a functional proteomic analysis. PUBMED:17952876 EPMC:17952876


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019532

SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing [PUBMED:10708573]. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see INTERPRO) signalling pathway [PUBMED:17952876].

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
(6)
Full
(90)
Representative proteomes NCBI
(97)
Meta
(1)
RP15
(15)
RP35
(20)
RP55
(36)
RP75
(53)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(6)
Full
(90)
Representative proteomes NCBI
(97)
Meta
(1)
RP15
(15)
RP35
(20)
RP55
(36)
RP75
(53)
Alignment:
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Sequence:
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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
(6)
Full
(90)
Representative proteomes NCBI
(97)
Meta
(1)
RP15
(15)
RP35
(20)
RP55
(36)
RP75
(53)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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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: TreeFam_TF105478
Previous IDs: none
Type: Family
Author: Buljan M, Coggill P
Number in seed: 6
Number in full: 90
Average length of the domain: 186.70 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 80.28 %

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 55.0 55.0
Trusted cut-off 55.5 55.4
Noise cut-off 44.1 50.7
Model length: 225
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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