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

Summary

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

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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
Elevated PAF1-RAD52 axis confers chemoresistance to human cancers.
Title: Elevated PAF1-RAD52 axis confers chemoresistance to human cancers.
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.
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.
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.
PAF1 cooperates with YAP1 in metaplastic ducts to promote pancreatic cancer.
Title: PAF1 cooperates with YAP1 in metaplastic ducts to promote pancreatic cancer.
Crystal Structure of the Core Module of the Yeast Paf1 Complex.
Title: Crystal Structure of the Core Module of the Yeast Paf1 Complex.
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.
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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH36195 (e-PCR)
- UniSTS:76295

RH91454 (e-PCR)
- UniSTS:85028

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)

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
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

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

39385629..39391106 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

42189906..42213952 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054321275.1 → XP_054177250.1 RNA polymerase II-associated factor 1 homolog isoform X1
XM_054321276.1 → XP_054177251.1 RNA polymerase II-associated factor 1 homolog isoform X1