Paf1 Paf1, RNA polymerase II complex component [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Paf1provided by MGI
Official Full Name: Paf1, RNA polymerase II complex componentprovided by MGI
Primary source: MGI:MGI:1923988
See related: Ensembl:ENSMUSG00000003437 AllianceGenome:MGI:1923988
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: 5730511K23Rik
Summary: Enables chromatin binding activity. Involved in several processes, including cellular response to lipopolysaccharide; endodermal cell fate commitment; and negative regulation of transcription by RNA polymerase II. Part of Cdc73/Paf1 complex. Is expressed in several structures, including central nervous system; early conceptus; and genitourinary system. Orthologous to human PAF1 (PAF1 homolog, Paf1/RNA polymerase II complex component). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in adrenal adult (RPKM 57.2), ovary adult (RPKM 38.1) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 A3; 7 16.73 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (28074998..28098813)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (28392996..28399383)

Chromosome 7 - NC_000073.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma.
Title: PAF1c links S-phase progression to immune evasion and MYC function in pancreatic carcinoma.
The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells.
Title: The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells.
Study shows that the Paf1 complex (Paf1C) modulates Pol II elongation rate, and loss of Paf1 results in accumulation of Ser5P in the first 20 to 30 kb of gene bodies, coinciding with reduction of histone H2B ubiquitylation specifically within this region. Moreover, reduced elongation rates provoked by Paf1 depletion resulted in defects in Pol II processivity and premature termination of transcription.
Title: Paf1C regulates RNA polymerase II progression by modulating elongation rate.
ENL overcomes polycomb silencing through recruitment of PAF1 via the conserved YEATS domain, which recognizes acetylated histone H3.
Title: The interaction of ENL with PAF1 mitigates polycomb silencing and facilitates murine leukemogenesis.
link Paf1C with PolII elongation and RNA processing indicates that Paf1C subunits could play roles in controlling transcript length through suppression of PolII accumulation at transcription start site (TSS)-proximal pA sites
Title: PAF Complex Plays Novel Subunit-Specific Roles in Alternative Cleavage and Polyadenylation.
The PAF1 complex is required for mammalian development, likely through regulation of H3K36me3, indicating a functional conservation of the PAF1 complex from yeast to mammals in vivo.
Title: CTR9/PAF1c regulates molecular lineage identity, histone H3K36 trimethylation and genomic imprinting during preimplantation development.
As part of a cell-intrinsic transcriptional pathway, Paf1 regulates neuronal migration in the brain.
Title: The X-linked intellectual disability protein PHF6 associates with the PAF1 complex and regulates neuronal migration in the mammalian brain.
MLL interacts directly with the polymerase associated factor complex (PAFc) via Paf1 and CTR9. PAFc augments MLL and MLL-AF9 mediated transcriptional activation of Hoxa9 and their interaction is essential for leukemogenesis.
Title: The PAF complex synergizes with MLL fusion proteins at HOX loci to promote leukemogenesis.
show that Paf1/PD2 is overexpressed in mouse embryonic stem cells (ESCs) and is involved in the maintenance of mouse ESCs.
Title: RNA polymerase II associated factor 1/PD2 maintains self-renewal by its interaction with Oct3/4 in mouse embryonic stem cells.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9Mit34.1 (e-PCR), detects polymorphism
- UniSTS:131903

RH124350 (e-PCR)
- UniSTS:161172

AU048852 (e-PCR)
- UniSTS:145302

RH143879 (e-PCR)
- UniSTS:233125

Gene Ontology Provided by MGI

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	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II complex binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to protein binding	IPI Inferred from Physical Interaction more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
involved_in endodermal cell fate commitment	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA 3'-end processing	ISO Inferred from Sequence Orthology more info
involved_in mRNA 3'-end processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of myeloid cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myeloid cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell cycle G1/S phase transition	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell cycle G1/S phase transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein localization to nucleus	IEA Inferred from Electronic Annotation more info
involved_in protein localization to nucleus	ISO Inferred from Sequence Orthology more info
involved_in stem cell population maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription elongation by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of Cdc73/Paf1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Cdc73/Paf1 complex	IPI Inferred from Physical Interaction more info	PubMed
part_of Cdc73/Paf1 complex	ISO Inferred from Sequence Orthology more info
part_of Cdc73/Paf1 complex	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in fibrillar center	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology 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

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_019458.3 → NP_062331.2 RNA polymerase II-associated factor 1 homolog

See identical proteins and their annotated locations for NP_062331.2

Status: PROVISIONAL

Source sequence(s)

AC149606

Consensus CDS

CCDS21043.1

UniProtKB/Swiss-Prot

Q3UY97, Q8K2T8, Q9CS63, Q9JJ99

Related

ENSMUSP00000003529.9, ENSMUST00000003529.9

Conserved Domains (1) summary

pfam03985
Location:30 → 443

Paf1

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000073.7 Reference GRCm39 C57BL/6J

Range

28074998..28098813

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036153258.1 → XP_036009151.1 RNA polymerase II-associated factor 1 homolog isoform X1

UniProtKB/Swiss-Prot

Q3UY97, Q8K2T8, Q9CS63, Q9JJ99

Conserved Domains (1) summary

pfam03985
Location:30 → 443

Paf1