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    PAF1 PAF1 homolog, Paf1/RNA polymerase II complex component [ Homo sapiens (human) ]

    Gene ID: 54623, updated on 3-Nov-2024

    Summary

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    Official Symbol
    PAF1provided by HGNC
    Official Full Name
    PAF1 homolog, Paf1/RNA polymerase II complex componentprovided by HGNC
    Primary source
    HGNC:HGNC:25459
    See related
    Ensembl:ENSG00000006712 MIM:610506; AllianceGenome:HGNC:25459
    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
    PD2; F23149_1
    Summary
    This gene encodes a subunit of the polymerase associated factor (PAF1) complex. The PAF1 complex interacts with RNA polymerase II and plays a role in transcription elongation as well as histone modifications including ubiquitylation and methylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]
    Expression
    Ubiquitous expression in testis (RPKM 32.1), ovary (RPKM 17.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PAF1 in Genome Data Viewer
    Location:
    19q13.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39385629..39391106, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (42189906..42213952, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (39876269..39881746, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene glia maturation factor gamma Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10597 Neighboring gene sterile alpha motif domain containing 4B Neighboring gene RNA, 7SL, cytoplasmic 566, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr19:39880404-39880535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14614 Neighboring gene mediator complex subunit 29 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14615 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39893943-39894450 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39897901-39898538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39898539-39899177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39899178-39899815 Neighboring gene ZFP36 ring finger protein

    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. Novel role of pancreatic differentiation 2 in facilitating self-renewal and drug resistance of pancreatic cancer stem cells. Vaz AP, et al. Br J Cancer, 2014 Jul 29. PMID 25003666, Free PMC Article
    2. Emerging Insights into the Roles of the Paf1 Complex in Gene Regulation. Van Oss SB, et al. Trends Biochem Sci, 2017 Oct. PMID 28870425, Free PMC Article
    3. Transcription recycling assays identify PAF1 as a driver for RNA Pol II recycling. Chen Z, et al. Nat Commun, 2021 Nov 3. PMID 34732721, Free PMC Article
    4. RNA Polymerase II-Associated Factor 1 Regulates Stem Cell Features of Pancreatic Cancer Cells, Independently of the PAF1 Complex, via Interactions With PHF5A and DDX3. Karmakar S, et al. Gastroenterology, 2020 Nov. PMID 32781084, Free PMC Article
    5. PAF1 regulation of promoter-proximal pause release via enhancer activation. Chen FX, et al. Science, 2017 Sep 22. PMID 28860207, Free PMC Article

    See all (169) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NELF and PAF1C complexes are core transcriptional machineries controlling colon cancer stemness.
      Title: NELF and PAF1C complexes are core transcriptional machineries controlling colon cancer stemness.
    2. RFX2 promotes tumor cell stemness through epigenetic regulation of PAF1 in spinal ependymoma.
      Title: RFX2 promotes tumor cell stemness through epigenetic regulation of PAF1 in spinal ependymoma.
    3. Elevated PAF1-RAD52 axis confers chemoresistance to human cancers.
      Title: Elevated PAF1-RAD52 axis confers chemoresistance to human cancers.
    4. Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression.
      Title: Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression.
    5. CNOT4 suppresses nonsmall cell lung cancer progression by promoting the degradation of PAF1.
      Title: CNOT4 suppresses nonsmall cell lung cancer progression by promoting the degradation of PAF1.
    6. Role of the Paf1 complex in the maintenance of stem cell pluripotency and development.
      Title: Role of the Paf1 complex in the maintenance of stem cell pluripotency and development.
    7. PAF1 cooperates with YAP1 in metaplastic ducts to promote pancreatic cancer.
      Title: PAF1 cooperates with YAP1 in metaplastic ducts to promote pancreatic cancer.
    8. Crystal Structure of the Core Module of the Yeast Paf1 Complex.
      Title: Crystal Structure of the Core Module of the Yeast Paf1 Complex.
    9. SUMO Modification of PAF1/PD2 Enables PML Interaction and Promotes Radiation Resistance in Pancreatic Ductal Adenocarcinoma.
      Title: SUMO Modification of PAF1/PD2 Enables PML Interaction and Promotes Radiation Resistance in Pancreatic Ductal Adenocarcinoma.
    10. Transcription recycling assays identify PAF1 as a driver for RNA Pol II recycling.
      Title: Transcription recycling assays identify PAF1 as a driver for RNA Pol II recycling.
    Submit: New GeneRIF Correction See all GeneRIFs (39)

    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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat forms at least two distinct P-TEFb-containing complexes. Tatcom1 is composed of P-TEFb, AF9, ENL, ELL, AFF1, AFF4, and PAF1, presenting strong CTD-kinase activity, while Tatcom2 consists of 7SK, LARP7, and MEPCE with two molecules of Tat/P-TEFb PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11123

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding 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 Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to lipopolysaccharide ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in endodermal cell fate commitment ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in mRNA 3'-end processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of myeloid cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of cell cycle G1/S phase transition IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein localization to nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription elongation by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Cdc73/Paf1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Cdc73/Paf1 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    RNA polymerase II-associated factor 1 homolog
    Names
    Paf1, RNA polymerase II associated factor, homolog
    pancreatic differentiation protein 2

    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_001256826.2 → NP_001243755.1  RNA polymerase II-associated factor 1 homolog isoform 2

      See identical proteins and their annotated locations for NP_001243755.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region and uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK098423, BC000017, BC013402, DA821359
      Consensus CDS
      CCDS59387.1
      UniProtKB/Swiss-Prot
      Q8N7H5
      Related
      ENSP00000468874.1, ENST00000595564.5
      Conserved Domains (1) summary
      pfam03985
      Location:20 → 361
      Paf1; Paf1

    2. NM_019088.4 → NP_061961.2  RNA polymerase II-associated factor 1 homolog isoform 1

      See identical proteins and their annotated locations for NP_061961.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC000017, DA821359
      Consensus CDS
      CCDS12533.1
      UniProtKB/Swiss-Prot
      M0QX35, O75239, Q8N7H5, Q9H166, Q9NUU9
      Related
      ENSP00000221265.2, ENST00000221265.8
      Conserved Domains (1) summary
      pfam03985
      Location:30 → 443
      Paf1

    RNA

    1. NR_046384.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an internal exon and includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK294625, BC000017

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      39385629..39391106 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      42189906..42213952 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321275.1 → XP_054177250.1  RNA polymerase II-associated factor 1 homolog isoform X1

    2. XM_054321276.1 → XP_054177251.1  RNA polymerase II-associated factor 1 homolog isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N7H5.2 GenPept UniProtKB/Swiss-Prot:Q8N7H5

    Gene LinkOut

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

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