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PAAF1 proteasomal ATPase associated factor 1 [ Homo sapiens (human) ]

Gene ID: 80227, updated on 2-Nov-2024

Summary

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Official Symbol
PAAF1provided by HGNC
Official Full Name
proteasomal ATPase associated factor 1provided by HGNC
Primary source
HGNC:HGNC:25687
See related
Ensembl:ENSG00000175575 MIM:619772; AllianceGenome:HGNC:25687
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PAAF; Rpn14; WDR71
Summary
This gene encodes a WD repeat-containing protein involved in regulation of association of proteasome components. During HIV infection, the encoded protein is thought to promote provirus transcription through recruitment of the 19S regulatory complex. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jun 2012]
Expression
Ubiquitous expression in brain (RPKM 8.9), testis (RPKM 8.5) and 25 other tissues See more
Orthologs
all
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Genomic context

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See PAAF1 in Genome Data Viewer
Location:
11q13.4
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (73876699..73931114)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (73805848..73860264)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (73587744..73642159)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L48 Neighboring gene RN7SK pseudogene 243 Neighboring gene MIX23 pseudogene 5 Neighboring gene Sharpr-MPRA regulatory region 5745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5244 Neighboring gene cytochrome c oxidase assembly factor 4 homolog Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:73608007-73608786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5245 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:73631557-73631769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:73637447-73637946 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:73643667-73643917 Neighboring gene actin related protein 2/3 complex subunit 3 pseudogene 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:73647840-73648474 Neighboring gene DnaJ heat shock protein family (Hsp40) member B13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5247 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3751 Neighboring gene uncoupling protein 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Reduction in inflammatory gene expression in skeletal muscle from Roux-en-Y gastric bypass patients randomized to omentectomy. Tamboli RA, et al. PLoS One, 2011. PMID 22194858, Free PMC Article
  2. The proteasome regulates HIV-1 transcription by both proteolytic and nonproteolytic mechanisms. Lassot I, et al. Mol Cell, 2007 Feb 9. PMID 17289585
  3. Lower expression of catalytic and structural subunits of the proteasome contributes to decreased proteolysis in peripheral blood T lymphocytes during aging. Ponnappan S, et al. Int J Biochem Cell Biol, 2007. PMID 17317272
  4. Spt6 levels are modulated by PAAF1 and proteasome to regulate the HIV-1 LTR. Nakamura M, et al. Retrovirology, 2012 Feb 8. PMID 22316138, Free PMC Article
  5. New crystal structure of the proteasome-dedicated chaperone Rpn14 at 1.6 Å resolution. Kim S, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2012 May 1. PMID 22691779, Free PMC Article

See all (48) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification of a quality-control factor that monitors failures during proteasome assembly.
    Title: Identification of a quality-control factor that monitors failures during proteasome assembly.
  2. These results show that intracellular levels of Spt6 are fine-tuned by PAAF1 and proteasome, which is required for HIV-1 transcription and extends to cellular genes implicated in cancer.
    Title: Spt6 levels are modulated by PAAF1 and proteasome to regulate the HIV-1 LTR.
  3. Proteasomal ATPase-associated factor 1 (PAAF1) functions as a negative regulator of the proteasome by controlling the assembly/disassembly of the proteasome.
    Title: Proteasomal ATPase-associated factor 1 negatively regulates proteasome activity by interacting with proteasomal ATPases.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11848

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to RNA polymerase II general transcription initiation factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in transcription initiation at RNA polymerase II promoter IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of SAGA complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of proteasome complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription factor TFIID complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
proteasomal ATPase-associated factor 1
Names
WD repeat domain 71
WD repeat-containing protein 71

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001267803.2 → NP_001254732.1  proteasomal ATPase-associated factor 1 isoform 1

    See identical proteins and their annotated locations for NP_001254732.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes longest protein (isoform 1). Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AF087895, AP002770, BC028628, DC354686
    Consensus CDS
    CCDS58157.1
    Related
    ENSP00000438124.1, ENST00000536003.5
    Conserved Domains (3) summary
    COG2319
    Location:40 → 375
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:78 → 115
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:72 → 321
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  2. NM_001267804.2 → NP_001254733.1  proteasomal ATPase-associated factor 1 isoform 1

    See identical proteins and their annotated locations for NP_001254733.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate splicing structure in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AF087895, AP002770, CD243380, DC354686
    Consensus CDS
    CCDS58157.1
    Conserved Domains (3) summary
    COG2319
    Location:40 → 375
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:78 → 115
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:72 → 321
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  3. NM_001267805.2 → NP_001254734.1  proteasomal ATPase-associated factor 1 isoform 1

    See identical proteins and their annotated locations for NP_001254734.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate splicing structure in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AF087895, AK021910, AP002770
    Consensus CDS
    CCDS58157.1
    Related
    ENSP00000441494.1, ENST00000544552.5
    Conserved Domains (3) summary
    COG2319
    Location:40 → 375
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:78 → 115
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:72 → 321
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  4. NM_001267806.2 → NP_001254735.1  proteasomal ATPase-associated factor 1 isoform 3

    See identical proteins and their annotated locations for NP_001254735.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks an internal exon, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AF087895, AK298258, AP002770
    Consensus CDS
    CCDS58158.1
    UniProtKB/Swiss-Prot
    Q9BRP4
    Related
    ENSP00000441333.1, ENST00000541951.5
    Conserved Domains (3) summary
    COG2319
    Location:2 → 277
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:23 → 59
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:1 → 223
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  5. NM_001363556.2 → NP_001350485.1  proteasomal ATPase-associated factor 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AK309133, AP002770
    Consensus CDS
    CCDS86227.1
    UniProtKB/TrEMBL
    F5H0C4
    Related
    ENSP00000438071.1, ENST00000544909.5
    Conserved Domains (2) summary
    sd00039
    Location:96 → 133
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:90 → 339
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  6. NM_025155.3 → NP_079431.1  proteasomal ATPase-associated factor 1 isoform 2

    See identical proteins and their annotated locations for NP_079431.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an exon in the 5' region, and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is longer than isoform 1.
    Source sequence(s)
    AF087895, AK021910, AP002770
    Consensus CDS
    CCDS8226.1
    UniProtKB/Swiss-Prot
    A6NDR5, B4DPB0, B7ZAS9, Q4G165, Q53HS9, Q7Z500, Q8TBU6, Q9BRP4, Q9HAB6
    Related
    ENSP00000311665.4, ENST00000310571.8
    Conserved Domains (3) summary
    COG2319
    Location:57 → 392
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:95 → 132
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:89 → 338
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    73876699..73931114
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427639.1 → XP_047283595.1  proteasomal ATPase-associated factor 1 isoform X1

RNA

  1. XR_007062508.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    73805848..73860264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370044.1 → XP_054226019.1  proteasomal ATPase-associated factor 1 isoform X1

RNA

  1. XR_008488461.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BRP4.2 GenPept UniProtKB/Swiss-Prot:Q9BRP4

Gene LinkOut

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