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

Gene ID: 5434, updated on 17-Jun-2024

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
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Genomic context

See POLR2E in Genome Data Viewer
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_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9652 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1028384-1028559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1038259-1038760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1038761-1039260 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1041153-1041950 Neighboring gene calponin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9655 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1051115-1051279 Neighboring gene MPRA-validated peak3219 silencer Neighboring gene ATP binding cassette subfamily A member 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1056183-1056682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1061566-1062329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1063170-1064022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1066609-1067115 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13580 Neighboring gene Rho GTPase activating protein 45 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9661 Neighboring gene Sharpr-MPRA regulatory region 10458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1081390-1082265 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1085889-1086388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1094025-1094560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13585 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1100293-1100430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1101543-1102077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13586 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13587 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13588 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1106419-1107295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1110839-1111758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1111759-1112678 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1112679-1113598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1116907-1117420 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1117421-1117933 Neighboring gene glutathione peroxidase 4 Neighboring gene strawberry notch homolog 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1122338-1122841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1131030-1131694 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1133023-1133686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1133705-1134206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1134207-1134706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1147791-1148629 Neighboring gene uncharacterized LOC102723798

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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
NP_001303253.1
NP_002686.3
XP_011526372.1
XP_016882372.1
XP_054177215.1
XP_054177216.1

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)

  1. NM_001316323.2NP_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:1116
    PTZ00061; DNA-directed RNA polymerase; Provisional
  2. NM_001316324.2NP_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:1116
    PTZ00061; DNA-directed RNA polymerase; Provisional
  3. NM_002695.5NP_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:1209
    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

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    1086574..1095375 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

    UniProtKB/TrEMBL
    A0A087WVZ9
    Conserved Domains (3) summary
    PLN03111
    Location:1210
    PLN03111; DNA-directed RNA polymerase II subunit family protein; Provisional
    pfam01191
    Location:138210
    RNA_pol_Rpb5_C; RNA polymerase Rpb5, C-terminal domain
    pfam03871
    Location:492
    RNA_pol_Rpb5_N; RNA polymerase Rpb5, N-terminal domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    1051240..1060040 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A087WWX0
  2. XM_054321240.1XP_054177215.1  DNA-directed RNA polymerases I, II, and III subunit RPABC1 isoform X1

    UniProtKB/TrEMBL
    A0A087WVZ9