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

Gene ID: 54623, updated on 7-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39385629..39391106, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (42189906..42213952, complement)
105.20220307 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
  • 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. 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
  2. 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
  3. 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
  4. PAF1 regulation of promoter-proximal pause release via enhancer activation. Chen FX, et al. Science, 2017 Sep 22. PMID 28860207, Free PMC Article
  5. Overexpression of PD2 leads to increased tumorigenicity and metastasis in pancreatic ductal adenocarcinoma. Vaz AP, et al. Oncotarget, 2016 Jan 19. PMID 26689992, Free PMC Article

See all (147) 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_2023_10

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.

Chemical Information
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