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

    Gene ID: 80227, updated on 27-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
    • 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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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