POLR2E RNA polymerase II, I and III subunit E [Homo sapiens (human)] - Gene

Summary

Official Symbol: POLR2Eprovided by HGNC
Official Full Name: RNA polymerase II, I and III subunit Eprovided by HGNC
Primary source: HGNC:HGNC:9192
See related: Ensembl:ENSG00000099817 MIM:180664; AllianceGenome:HGNC:9192
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: RPB5; XAP4; RPABC1; hRPB25; hsRPB5
Summary: This gene encodes the fifth largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. This subunit is shared by the other two DNA-directed RNA polymerases and is present in two-fold molar excess over the other polymerase subunits. An interaction between this subunit and a hepatitis virus transactivating protein has been demonstrated, suggesting that interaction between transcriptional activators and the polymerase can occur through this subunit. A pseudogene is located on chromosome 11. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
Expression: Ubiquitous expression in fat (RPKM 46.7), kidney (RPKM 21.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (1086574..1095375, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (1051240..1060040, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (1086573..1095374, complement)

Chromosome 19 - NC_000019.10 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
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?

Our results indicated that the rs3787016 polymorphism in polymerase II polypeptide E was associated with the risk of both breast cancer and cervical cancer
Title: The POLR2E rs3787016 polymorphism is strongly associated with the risk of female breast and cervical cancer.
we here conducted a case-control study to investigate the association of POLR2E rs3787016 polymorphism with risk of liver and lung cancer..Although no significant association was found for rs3787016 with risk of liver or lung cancer, the further stratified analysis identified that rs3787016 contributed to liver cancer risk particularly for over than 60 years individuals who drink
Title: The association of POLR2E rs3787016 polymorphism and cancer risk: a Chinese case-control study and meta-analysis.
rs3787016 T/rs1046040 C significantly increased the risk of prostate cancer compared to C/C (p = 0.037
Title: Long non-coding RNA POLR2E gene polymorphisms increased the risk of prostate cancer in a sample of the Iranian population.
POLR2E rs3787016T allele was associated with an increased cancer risk in Chinese population
Title: Long non-coding RNA POLR2E rs3787016 is associated with the risk of papillary thyroid carcinoma in Chinese population.
POLR2E rs3787016 C/T and HULC rs7763881 were associated with a significantly decreased risk for ESCC 0.005). ANRIL rs2151280 T/C SNP was not associated with risk of ESCC.
Title: Long noncoding RNAs POLR2E rs3787016 C/T and HULC rs7763881 A/C polymorphisms are associated with decreased risk of esophageal cancer.
ELL has an early and essential role during rapid high-amplitude gene expression that is required for both Pol II pause site entry and release
Title: ELL facilitates RNA polymerase II pause site entry and release.
crystal of RPB5 diffracted to 2.8 A resolution and belonged to space group P4(3)2(1)2.
Title: Crystallization and preliminary X-ray analysis of the RPB5 subunit of human RNA polymerase II.
RPB5-mediating protein is required for the proliferation of hepatocellular carcinoma cells.
Title: RPB5-mediating protein is required for the proliferation of hepatocellular carcinoma cells.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity.
Is part of an RNA polymerase II-associated complex with possible chaperone activity.
Title: High-resolution mapping of the protein interaction network for the human transcription machinery and affinity purification of RNA polymerase II-associated complexes.

Submit: New GeneRIF Correction See all GeneRIFs (12)

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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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

D19S692E (e-PCR)
- UniSTS:150591

RH25429 (e-PCR)
- UniSTS:16966

D15S1477 (e-PCR)
- UniSTS:474482

MARC_21329-21330:1023910044:1 (e-PCR)
- UniSTS:268531

RH80177 (e-PCR)
- UniSTS:83962

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-directed 5'-3' RNA polymerase activity	TAS Traceable Author Statement more info	PubMed
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
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in protein stabilization	NAS Non-traceable Author Statement more info	PubMed
involved_in tRNA transcription by RNA polymerase III	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
involved_in transcription elongation by RNA polymerase I	IBA Inferred from Biological aspect of Ancestor more info

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
part_of RPAP3/R2TP/prefoldin-like complex	IPI Inferred from Physical Interaction more info	PubMed
located_in cytosol	TAS Traceable Author Statement 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 RPABC1

Names: DNA directed RNA polymerase II 23 kda polypeptide; DNA-directed RNA polymerase II 23 kDa polypeptide; DNA-directed RNA polymerase II subunit E; DNA-directed RNA polymerase subunit RPABC1; RNA polymerase II subunit E; RNA polymerases I, II, and III subunit ABC1; RPB5 homolog; polymerase (RNA) II (DNA directed) polypeptide E, 25kDa; polymerase (RNA) II subunit E

NP_001303252.1

EC 2.7.7.6

NP_001303253.1

EC 2.7.7.6

NP_002686.3

EC 2.7.7.6

XP_011526372.1

EC 2.7.7.6

XP_016882372.1

EC 2.7.7.6

XP_054177215.1

EC 2.7.7.6

XP_054177216.1

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_001316323.2 → NP_001303252.1 DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate 5' exon compared to variant 1. This difference causes translation initiation at a downstream AUG and results in an isoform (b) with a shorter N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).

Source sequence(s)

AC004151, DC351659, DC414435

UniProtKB/TrEMBL

A0A087WWX0, B4DJ89

Related

ENSP00000480562.1, ENST00000585838.2

Conserved Domains (1) summary

PTZ00061
Location:1 → 116

PTZ00061; DNA-directed RNA polymerase; Provisional
NM_001316324.2 → NP_001303253.1 DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate 5' exon and contains another alternate 5' exon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (b) with a shorter N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).

Source sequence(s)

AC004151, AK295975, DC414435

UniProtKB/TrEMBL

A0A087WWX0, B4DJ89

Conserved Domains (1) summary

PTZ00061
Location:1 → 116

PTZ00061; DNA-directed RNA polymerase; Provisional
NM_002695.5 → NP_002686.3 DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).

Source sequence(s)

AC004151

Consensus CDS

CCDS12056.1

UniProtKB/Swiss-Prot

B2R6L4, D6W5Y1, O43380, P19388, Q6PIH5, Q9BT06

UniProtKB/TrEMBL

A0A087WVZ9, E5KT65

Related

ENSP00000478303.1, ENST00000615234.5

Conserved Domains (1) summary

PLN03111
Location:1 → 209

PLN03111; DNA-directed RNA polymerase II subunit family protein; Provisional

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

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

1086574..1095375 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017026883.3 → XP_016882372.1 DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform X2

UniProtKB/TrEMBL

A0A087WWX0
XM_011528070.4 → XP_011526372.1 DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform X1

UniProtKB/TrEMBL

A0A087WVZ9

Conserved Domains (3) summary

PLN03111
Location:1 → 210

PLN03111; DNA-directed RNA polymerase II subunit family protein; Provisional

pfam01191
Location:138 → 210

RNA_pol_Rpb5_C; RNA polymerase Rpb5, C-terminal domain

pfam03871
Location:4 → 92

RNA_pol_Rpb5_N; RNA polymerase Rpb5, N-terminal domain

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

1051240..1060040 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054321241.1 → XP_054177216.1 DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform X2
XM_054321240.1 → XP_054177215.1 DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform X1