POLR2F RNA polymerase II, I and III subunit F [Homo sapiens (human)] - Gene

Summary

Official Symbol: POLR2Fprovided by HGNC
Official Full Name: RNA polymerase II, I and III subunit Fprovided by HGNC
Primary source: HGNC:HGNC:9193
See related: Ensembl:ENSG00000100142 MIM:604414; AllianceGenome:HGNC:9193
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: RPB6; POLRF; RPC15; RPABC2; RPB14.4; HRBP14.4; RPABC14.4
Summary: This gene encodes the sixth largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. In yeast, this polymerase subunit, in combination with at least two other subunits, forms a structure that stabilizes the transcribing polymerase on the DNA template. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression: Ubiquitous expression in brain (RPKM 8.9), kidney (RPKM 5.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q13.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (37953663..38041915)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (38415270..38503533)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (38349670..38437922)

Chromosome 22 - NC_000022.11 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 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?

Three human RNA polymerases interact with TFIIH via a common RPB6 subunit.
Title: Three human RNA polymerases interact with TFIIH via a common RPB6 subunit.
These results suggest that RPAP2 controls Pol II activity through a direct interaction with Rpb6
Title: Human RNA polymerase II-associated protein 2 (RPAP2) interacts directly with the RNA polymerase II subunit Rpb6 and participates in pre-mRNA 3'-end formation.
Observational study of gene-disease association, gene-gene interaction, and gene-environment interaction. (HuGE Navigator)
Title: Genetic polymorphisms in 85 DNA repair genes and bladder cancer risk.
POLR2F and PRNP exhibited elevated levels in carcinomas compared to normal tissue samples suggesting a possible role for these molecules in colorectal cancer.
Title: POLR2F, ATP6V0A1 and PRNP expression in colorectal cancer: new molecules with prognostic significance?
Solution structure of the hRPABC14.4 subunit of human RNA polymerases.(RPABC14.4 ?)
Title: Solution structure of the hRPABC14.4 subunit of human RNA polymerases.

Submit: New GeneRIF Correction

Phenotypes

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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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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	The transcription factors and kinases c-Jun, JNK, MEK, p38 MAPK, STAT-3, JAK-1, TFII D, TFII F, eIF-4E, and RNA polymerase II are induced by HIV-1 gp120	PubMed
Tat	tat	The interaction of Tip110 with HIV-1 Tat leads to a higher efficiency of elongation for RNAPII complexes formed on the LTR promoter	PubMed
	tat	Expression of both Tip110 and Tat enhances phosphorylation of RNAPII at both serine 2 and serine 5, which account for Tip110 function in transcription activation	PubMed
	tat	The interaction of Tip110 with HIV-1 Tat and the RNAPII C-terminal domain leads to the recruitment of increased CDK9/CycT1 to the transcription complex	PubMed
	tat	HIV-1 Tat complexes with RNA polymerase II and cellular transcription factors as part of the HIV-1 transcription preinitiation and elongation complexes and stimulates RNA polymerase II processivity by inducing the phosphorylation of its C-terminal Domain	PubMed
	tat	A small molecule compound C3 inhibits HIV-1 replication by suppressing HIV-1 Tat-mediated HIV-1 LTR-driven gene expression and phosphorylation of RNAPII through inhibition of Tat binding to CycT1	PubMed
	tat	JQ1, a small molecule inhibitor of Brd4, directly dissociates Brd4 from HIV-1 promoter and promotes subsequently HIV-1 Tat binding to HIV-1 promoter, resulting in increased phosphorylation of RNA polymerase II and viral transcription	PubMed
	tat	HIV-1 Tat 41/44 peptide TAALS from the core domain of Tat inhibits Tat-mediated HIV-1 gene expression and replication by binding the Cdk2/Cyclin E complex and inhibiting the phosphorylation of serine 5 of RNAPII	PubMed
Vpr	vpr	HIV-1 Vpr interacts with basal transcription complexes such as P-TEFb, TFIIH, TFIID (TBP) and TFIIB which activate RNA polymerase II gene transcription	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

RH71313 (e-PCR)
- UniSTS:43093

D11S942E (e-PCR)
- UniSTS:147388

Clone Names

FLJ22674, FLJ25861, FLJ36715, DKFZp547H2218

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
contributes_to RNA polymerase I activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to RNA polymerase II activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to RNA polymerase III activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in tRNA transcription by RNA polymerase III	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription by RNA polymerase I	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of RNA polymerase I complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase I complex	IDA Inferred from Direct Assay more info	PubMed
part_of RNA polymerase II, core complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase II, core complex	IDA Inferred from Direct Assay more info	PubMed
part_of RNA polymerase III complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase III complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in fibrillar center	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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: DNA-directed RNA polymerases I, II, and III subunit RPABC2

Names: DNA-directed RNA polymerase II subunit F; DNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptide; RNA Polymerase II subunit 14.4 kD; RNA polymerase II subunit F; RNA polymerases I, II, and III subunit ABC2; polymerase (RNA) II (DNA directed) polypeptide F; polymerase (RNA) II subunit F

NP_001288058.1

EC 2.7.7.6

NP_001288059.1

EC 2.7.7.6

NP_001288060.1

EC 2.7.7.6

NP_001350754.1

EC 2.7.7.6

NP_068809.1

EC 2.7.7.6

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_001301129.2 → NP_001288058.1 DNA-directed RNA polymerases I, II, and III subunit RPABC2 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate exon in the 5' region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AL031587, DA083933

UniProtKB/TrEMBL

U3KPY1

Related

ENSP00000475343.1, ENST00000492213.5

Conserved Domains (1) summary

PLN00152
Location:21 → 118

PLN00152; DNA-directed RNA polymerase; Provisional
NM_001301130.2 → NP_001288059.1 DNA-directed RNA polymerases I, II, and III subunit RPABC2 isoform 3

See identical proteins and their annotated locations for NP_001288059.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 3' exon structure, resulting in a different 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has a distinct C-terminus and is longer than isoform 1.

Source sequence(s)

AK026327, BP195499

Consensus CDS

CCDS77673.1

UniProtKB/TrEMBL

B0QYL9

Related

ENSP00000385725.1, ENST00000407936.5

Conserved Domains (1) summary

cl14651
Location:26 → 100

RNA_pol_Rpb6; RNA polymerase Rpb6
NM_001301131.2 → NP_001288060.1 DNA-directed RNA polymerases I, II, and III subunit RPABC2 isoform 4

See identical proteins and their annotated locations for NP_001288060.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate 3' exon structure, resulting in a different 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AK026327, DN989996

UniProtKB/TrEMBL

U3KQS8

Related

ENSP00000476187.1, ENST00000606538.5

Conserved Domains (1) summary

cl14651
Location:26 → 102

RNA_pol_Rpb6; RNA polymerase Rpb6
NM_001363825.1 → NP_001350754.1 DNA-directed RNA polymerases I, II, and III subunit RPABC2 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (6) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (5) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AL031587

Consensus CDS

CCDS87025.1

UniProtKB/TrEMBL

F8WC47, U3KQS8

Related

ENSP00000406826.1, ENST00000443002.5

Conserved Domains (1) summary

cl14651
Location:26 → 97

RNA_pol_Rpb6; RNA polymerase Rpb6
NM_021974.5 → NP_068809.1 DNA-directed RNA polymerases I, II, and III subunit RPABC2 isoform 1

See identical proteins and their annotated locations for NP_068809.1

Status: REVIEWED

Description

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

Source sequence(s)

AL031587, DA372532

Consensus CDS

CCDS13963.1

UniProtKB/Swiss-Prot

P41584, P61218, Q6IAY3

UniProtKB/TrEMBL

B2R4H6

Related

ENSP00000403852.2, ENST00000442738.7

Conserved Domains (1) summary

PLN00152
Location:26 → 127

PLN00152; DNA-directed RNA polymerase; Provisional

RNA

NR_125371.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate splice site at an 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)

AL031587, DA203006