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0  structures 176  species 0  interactions 270  sequences 6  architectures

Family: SAP130_C (PF16014)

Summary: Histone deacetylase complex subunit SAP130 C-terminus

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 "SAP130". More...

SAP130 Edit Wikipedia article

SAP130
Identifiers
Aliases SAP130, Sin3A associated protein 130
External IDs MGI: 1919782 HomoloGene: 11577 GeneCards: SAP130
Gene location (Human)
Chromosome 2 (human)
Chr. Chromosome 2 (human)[1]
Chromosome 2 (human)
Genomic location for SAP130
Genomic location for SAP130
Band n/a Start 127,941,217 bp[1]
End 128,028,120 bp[1]
RNA expression pattern
PBB GE SAP130 220367 s at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_172965

RefSeq (protein)

NP_766553

Location (UCSC) Chr 2: 127.94 – 128.03 Mb Chr 2: 31.63 – 31.72 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Histone deacetylase complex subunit SAP130 is an enzyme that in humans is encoded by the SAP130 gene.[5][6][7]

Function

SAP130 is a subunit of the histone deacetylase (see HDAC1; MIM 601241)-dependent SIN3A (MIM 607776) corepressor complex (Fleischer et al., 2003).[supplied by OMIM][7]

Interactions

SAP130 has been shown to interact with:

Model organisms

Model organisms have been used in the study of SAP130 function. A conditional knockout mouse line called Sap130tm1a(KOMP)Mbp was generated at the Wellcome Trust Sanger Institute.[10] Male and female animals underwent a standardized phenotypic screen[11] to determine the effects of deletion.[12][13][14][15] Additional screens performed: - In-depth immunological phenotyping[16]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000136715 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000024260 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ Wiemann S, Weil B, Wellenreuther R, Gassenhuber J, Glassl S, Ansorge W, Böcher M, Blöcker H, Bauersachs S, Blum H, Lauber J, Düsterhöft A, Beyer A, Köhrer K, Strack N, Mewes HW, Ottenwälder B, Obermaier B, Tampe J, Heubner D, Wambutt R, Korn B, Klein M, Poustka A (Mar 2001). "Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs". Genome Research. 11 (3): 422–35. PMC 311072Freely accessible. PMID 11230166. doi:10.1101/gr.GR1547R. 
  6. ^ a b Fleischer TC, Yun UJ, Ayer DE (May 2003). "Identification and characterization of three new components of the mSin3A corepressor complex". Molecular and Cellular Biology. 23 (10): 3456–67. PMC 164750Freely accessible. PMID 12724404. doi:10.1128/MCB.23.10.3456-3467.2003. 
  7. ^ a b "Entrez Gene: SAP130 Sin3A-associated protein, 130kDa". 
  8. ^ a b c Menon S, Tsuge T, Dohmae N, Takio K, Wei N. "Association of SAP130/SF3b-3 with Cullin-RING ubiquitin ligase complexes and its regulation by the COP9 signalosome". BMC Biochemistry. 9: 1. PMC 2265268Freely accessible. PMID 18173839. doi:10.1186/1471-2091-9-1. 
  9. ^ Liu X, Tesfai J, Evrard YA, Dent SY, Martinez E (May 2003). "c-Myc transformation domain recruits the human STAGA complex and requires TRRAP and GCN5 acetylase activity for transcription activation". The Journal of Biological Chemistry. 278 (22): 20405–12. PMC 4031917Freely accessible. PMID 12660246. doi:10.1074/jbc.M211795200. 
  10. ^ Gerdin AK (2010). "The Sanger Mouse Genetics Programme: high throughput characterisation of knockout mice". Acta Ophthalmologica. 88: 925–7. doi:10.1111/j.1755-3768.2010.4142.x. 
  11. ^ a b "International Mouse Phenotyping Consortium". 
  12. ^ Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W, Iyer V, Mujica AO, Thomas M, Harrow J, Cox T, Jackson D, Severin J, Biggs P, Fu J, Nefedov M, de Jong PJ, Stewart AF, Bradley A (Jun 2011). "A conditional knockout resource for the genome-wide study of mouse gene function". Nature. 474 (7351): 337–42. PMC 3572410Freely accessible. PMID 21677750. doi:10.1038/nature10163. 
  13. ^ Dolgin E (Jun 2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. PMID 21677718. doi:10.1038/474262a. 
  14. ^ Collins FS, Rossant J, Wurst W (Jan 2007). "A mouse for all reasons". Cell. 128 (1): 9–13. PMID 17218247. doi:10.1016/j.cell.2006.12.018. 
  15. ^ White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP (Jul 2013). "Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes". Cell. 154 (2): 452–64. PMC 3717207Freely accessible. PMID 23870131. doi:10.1016/j.cell.2013.06.022. 
  16. ^ a b "Infection and Immunity Immunophenotyping (3i) Consortium". 

Further reading

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.

Histone deacetylase complex subunit SAP130 C-terminus Provide feedback

No Pfam abstract.

Literature references

  1. Fleischer TC, Yun UJ, Ayer DE;, Mol Cell Biol. 2003;23:3456-3467.: Identification and characterization of three new components of the mSin3A corepressor complex. PUBMED:12724404 EPMC:12724404


This tab holds annotation information from the InterPro database.

InterPro entry IPR031963

SAP130 (Sin3-associated protein 130) is a component of the histone deacetylase-dependent co-repressor complex mSin3A that acts as a transcriptional repressor. It may function in the assembly and/or enzymatic activity of mSin3A or in mediating interactions between the complex and other regulatory complexes [PUBMED:12724404].

This entry represents the C-terminal domain of SAP130.

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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  Seed
(7)
Full
(270)
Representative proteomes UniProt
(444)
NCBI
(1245)
Meta
(0)
RP15
(55)
RP35
(114)
RP55
(182)
RP75
(217)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(7)
Full
(270)
Representative proteomes UniProt
(444)
NCBI
(1245)
Meta
(0)
RP15
(55)
RP35
(114)
RP55
(182)
RP75
(217)
Alignment:
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  Seed
(7)
Full
(270)
Representative proteomes UniProt
(444)
NCBI
(1245)
Meta
(0)
RP15
(55)
RP35
(114)
RP55
(182)
RP75
(217)
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.

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.

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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: Jackhmmer:Q8IQH9
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R
Number in seed: 7
Number in full: 270
Average length of the domain: 286.80 aa
Average identity of full alignment: 43 %
Average coverage of the sequence by the domain: 28.85 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 28.1 27.1
Noise cut-off 25.0 26.8
Model length: 406
Family (HMM) version: 5
Download: download the raw HMM for this family

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