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2  structures 95  species 0  interactions 129  sequences 3  architectures

Family: PAF (PF15715)

Summary: PCNA-associated factor histone like domain

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 "KIAA0101". More...

KIAA0101 Edit Wikipedia article

PCLAF
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases PCLAF, L5, NS5ATP9, OEATC, OEATC-1, OEATC1, PAF, PAF15, p15(PAF), p15/PAF, p15PAF, KIAA0101, PCNA clamp associated factor
External IDs MGI: 1915276 HomoloGene: 8829 GeneCards: PCLAF
Gene location (Human)
Chromosome 15 (human)
Chr. Chromosome 15 (human)[1]
Chromosome 15 (human)
Genomic location for PCLAF
Genomic location for PCLAF
Band 15q22.31 Start 64,364,311 bp[1]
End 64,387,687 bp[1]
RNA expression pattern
PBB GE KIAA0101 202503 s at fs.png

PBB GE KIAA0101 211713 x at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001029989
NM_014736

NM_026515

RefSeq (protein)

NP_001025160
NP_055551

NP_080791

Location (UCSC) Chr 15: 64.36 – 64.39 Mb Chr 15: 65.89 – 65.9 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

PCNA-associated factor is a protein that in humans is encoded by the KIAA0101 gene.[5][6][7]

Interactions

KIAA0101 has been shown to interact with PCNA.[5]

Model organisms

Model organisms have been used in the study of KIAA0101 function. A conditional knockout mouse line called 2810417H13Riktm1a (EUCOMM)Wtsi was generated at the Wellcome Trust Sanger Institute.[8] Male and female animals underwent a standardized phenotypic screen[9] to determine the effects of deletion.[10][11][12][13] Additional screens performed: - In-depth immunological phenotyping[14] - in-depth bone and cartilage phenotyping[15]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000166803 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000040204 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ a b Yu P, Huang B, Shen M, Lau C, Chan E, Michel J, Xiong Y, Payan DG, Luo Y (Jan 2001). "p15(PAF), a novel PCNA associated factor with increased expression in tumor tissues". Oncogene. 20 (4): 484–9. PMID 11313979. doi:10.1038/sj.onc.1204113. 
  6. ^ Simpson F, Lammerts van Bueren K, Butterfield N, Bennetts JS, Bowles J, Adolphe C, Simms LA, Young J, Walsh MD, Leggett B, Fowles LF, Wicking C (Jan 2006). "The PCNA-associated factor KIAA0101/p15(PAF) binds the potential tumor suppressor product p33ING1b". Experimental Cell Research. 312 (1): 73–85. PMID 16288740. doi:10.1016/j.yexcr.2005.09.020. 
  7. ^ "Entrez Gene: KIAA0101 KIAA0101". 
  8. ^ 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. 
  9. ^ a b "International Mouse Phenotyping Consortium". 
  10. ^ 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. 
  11. ^ Dolgin E (Jun 2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. PMID 21677718. doi:10.1038/474262a. 
  12. ^ 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. 
  13. ^ 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. 
  14. ^ a b "Infection and Immunity Immunophenotyping (3i) Consortium". 
  15. ^ a b "OBCD 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.

PCNA-associated factor histone like domain Provide feedback

This domain corresponds to a histone like fold in p15(PAF).

Literature references

  1. Yu P, Huang B, Shen M, Lau C, Chan E, Michel J, Xiong Y, Payan DG, Luo Y;, Oncogene. 2001;20:484-489.: p15(PAF), a novel PCNA associated factor with increased expression in tumor tissues. PUBMED:11313979 EPMC:11313979


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR031444

PCNA-associated factor or p15PAF is a nuclear protein first identified as a proliferating-cell-nuclear-antigen (PCNA)-binding protein [PUBMED:11313979]. As a direct transcriptional target of activating transcription factor 3 (ATF3) it is involved in maintaining genomic integrity after UV exposure [PUBMED:19219066]. It is also a direct transcriptional target of the Rb/E2F pathway, playing an essential role in DNA synthesis and cell cycle progression [PUBMED:23593430]. p15PAF/KIAA0101 is overexpressed in multiple types of human cancer [PUBMED:21689861, PUBMED:22576474, PUBMED:24197986].

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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Pfam Clan

This family is a member of clan Histone (CL0012), which has the following description:

Members of this clan all possess a histone fold. Generally proteins in this clan are DNA binding.

The clan contains the following 17 members:

Bromo_TP Bromo_TP_like CBFD_NFYB_HMF CENP-S CENP-T_C CENP-W CENP-X DUF1931 Histone PAF TAF TAF4 TAFII28 TFIID-18kDa TFIID-31kDa TFIID_20kDa TFIID_30kDa

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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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
(16)
Full
(129)
Representative proteomes UniProt
(212)
NCBI
(595)
Meta
(1)
RP15
(35)
RP35
(65)
RP55
(96)
RP75
(136)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(16)
Full
(129)
Representative proteomes UniProt
(212)
NCBI
(595)
Meta
(1)
RP15
(35)
RP35
(65)
RP55
(96)
RP75
(136)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(16)
Full
(129)
Representative proteomes UniProt
(212)
NCBI
(595)
Meta
(1)
RP15
(35)
RP35
(65)
RP55
(96)
RP75
(136)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Jackhmmer:Q15004
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Eberhardt R , Coggill P , Hetherington K
Number in seed: 16
Number in full: 129
Average length of the domain: 107.80 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 92.61 %

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 23.4 23.4
Trusted cut-off 23.4 23.4
Noise cut-off 23.3 23.3
Model length: 135
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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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 PAF domain has been found. There are 2 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 sequence.

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