PCF11 PCF11 cleavage and polyadenylation factor subunit [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCF11provided by HGNC
Official Full Name: PCF11 cleavage and polyadenylation factor subunitprovided by HGNC
Primary source: HGNC:HGNC:30097
See related: Ensembl:ENSG00000165494 MIM:608876; AllianceGenome:HGNC:30097
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
Summary: The protein encoded by this gene binds to CLP1 to form pre-mRNA cleavage factor IIm. The encoded protein is necessary for efficient Pol II transcription termination and may be involved in degradation of the 3' product of polyA site cleavage. [provided by RefSeq, Oct 2016]
Expression: Ubiquitous expression in lymph node (RPKM 13.1), spleen (RPKM 12.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q14.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (83157131..83187451)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (83093603..83123924)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (82868173..82898493)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PCF11 is autoregulated through a conserved IPA site, the removal of which leads to global activation of PASs close to gene promotors. Therefore, PCF11 uses distinct mechanisms to regulate genes of different sizes, and its autoregulation maintains homeostasis of PAS usage in the cell.
Title: Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA Expression of Long Genes.
PCF11 selectively attenuates the expression of other transcriptional regulators by premature cleavage/polyadenylation and termination.
Title: Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination.
Utilising extensive RNAi-screening authors reveal the landscape and drivers of transcriptome 3'end-diversification, discovering PCF11 as critical regulator, directing alternative polyadenylation (APA) of hundreds of transcripts including a differentiation RNA-operon.
Title: Transcriptome 3'end organization by PCF11 links alternative polyadenylation to formation and neuronal differentiation of neuroblastoma.
We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactions, whereas hClp1 by itself is not. Pcf11 moderately stimulates the RNA 5' kinase activity of hClp1; the kinase activity is dispensable for RNA cleavage
Title: Reconstitution of mammalian cleavage factor II involved in 3' processing of mRNA precursors.
WNK1 and the associated phosphorylation of the PCF11 CID act to promote transcript release from chromatin-associated Pol II, which in turn facilitates mRNA export to the cytoplasm
Title: WNK1 kinase and the termination factor PCF11 connect nuclear mRNA export with transcription.
Pcf11 is required for the efficient degradation of the 3' product of poly(A) site cleavage.
Title: Human Pcf11 enhances degradation of RNA polymerase II-associated nascent RNA and transcriptional termination.
Pcf11 can act as a negative elongation factor to repress RNA Pol II gene expression in eukaryotic cells.
Title: Transcription termination factor Pcf11 limits the processivity of Pol II on an HIV provirus to repress gene expression.
Human PCf11 is a pre-mRNA processing factor.
Title: Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors.

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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

EBI GWAS Catalog

Description
Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wide association study meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH11546 (e-PCR)
- UniSTS:71442

RH46173 (e-PCR)
- UniSTS:80443

WI-11852 (e-PCR)
- UniSTS:69732

RH46125 (e-PCR)
- UniSTS:27759

RH78058 (e-PCR)
- UniSTS:22150

A007H35 (e-PCR)
- UniSTS:46302

MARC_14809-14810:1017254905:1 (e-PCR)
- UniSTS:267744

MARC_14809-14810:1027964802:1 (e-PCR)
- UniSTS:267744

ksks262 (e-PCR)
- UniSTS:514300

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 mRNA 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 co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in termination of RNA polymerase II transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in termination of RNA polymerase II transcription	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
part_of mRNA cleavage factor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of mRNA cleavage factor complex	NAS Non-traceable Author Statement more info	PubMed
located_in mitochondrion	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: pre-mRNA cleavage complex 2 protein Pcf11

Names: PCF11, cleavage and polyadenylation factor subunit, homolog; PCF11p homolog; pre-mRNA cleavage complex II protein Pcf11

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.

Genomic

NG_051805.1 RefSeqGene

Range

5037..33700

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001346413.3 → NP_001333342.1 pre-mRNA cleavage complex 2 protein Pcf11 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AP000873

Consensus CDS

CCDS91554.1

UniProtKB/TrEMBL

A0A8I5KX04

Related

ENSP00000508500.1, ENST00000690938.1
NM_001346414.2 → NP_001333343.1 pre-mRNA cleavage complex 2 protein Pcf11 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.

Source sequence(s)

AP000873
NM_001346415.2 → NP_001333344.1 pre-mRNA cleavage complex 2 protein Pcf11 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses two alternate in-frame splice junctions compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to variant 1.

Source sequence(s)

AP000873
NM_015885.4 → NP_056969.2 pre-mRNA cleavage complex 2 protein Pcf11 isoform 3

See identical proteins and their annotated locations for NP_056969.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AP000873, BC146778, DB053362

Consensus CDS

CCDS44689.1

UniProtKB/Swiss-Prot

A6H8W7, O43671, O94913, Q6P0X8

Related

ENSP00000298281.4, ENST00000298281.8

Conserved Domains (1) summary

cd03562
Location:19 → 130

CID; CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA ...