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POLR1E RNA polymerase I subunit E [ Homo sapiens (human) ]

Gene ID: 64425, updated on 13-Apr-2024

Summary

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Official Symbol
POLR1Eprovided by HGNC
Official Full Name
RNA polymerase I subunit Eprovided by HGNC
Primary source
HGNC:HGNC:17631
See related
Ensembl:ENSG00000137054 AllianceGenome:HGNC:17631
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
A49; PAF53; PRAF1; RPA49
Summary
Predicted to enable DNA binding activity; DNA-directed 5'-3' RNA polymerase activity; and RNA polymerase I general transcription initiation factor binding activity. Involved in nucleolar large rRNA transcription by RNA polymerase I. Located in fibrillar center and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 15.6), endometrium (RPKM 8.0) and 25 other tissues See more
Orthologs
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Genomic context

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See POLR1E in Genome Data Viewer
Location:
9p13.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (37485948..37503697)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (37509662..37527361)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (37485945..37503694)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene glyoxylate and hydroxypyruvate reductase Neighboring gene zinc finger and BTB domain containing 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:37464369-37465054 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:37465055-37465740 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37465741-37466426 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37466427-37467112 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37468922-37469753 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:37477128-37478327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37485410-37486001 Neighboring gene potassium channel tetramerization domain containing 9 pseudogene 3 Neighboring gene ribosomal protein L21 pseudogene 83 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37511563-37512119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37515395-37515896 Neighboring gene F-box protein 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28399 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28400 Neighboring gene MPRA-validated peak7234 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28401 Neighboring gene translocase of outer mitochondrial membrane 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Regulation of ribosomal RNA synthesis during the final phases of porcine oocyte growth. Bjerregaard B, et al. Biol Reprod, 2004 Apr. PMID 14627545
  2. Immunolocalization of upstream binding factor and pocket protein p130 during final stages of bovine oocyte growth. Baran V, et al. Biol Reprod, 2004 Apr. PMID 14613906
  3. Expression of nucleolar-related proteins in porcine preimplantation embryos produced in vivo and in vitro. Bjerregaard B, et al. Biol Reprod, 2004 Apr. PMID 14585813
  4. Constitutive and strong association of PAF53 with RNA polymerase I. Seither P, et al. Chromosoma, 1997 Sep. PMID 9254723
  5. RNA polymerase I associated factor 53 binds to the nucleolar transcription factor UBF and functions in specific rDNA transcription. Hanada K, et al. EMBO J, 1996 May 1. PMID 8641287, Free PMC Article

See all (66) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PAF49: An RNA Polymerase I subunit essential for rDNA transcription and stabilization of PAF53.
    Title: PAF49: An RNA Polymerase I subunit essential for rDNA transcription and stabilization of PAF53.
  2. Nucleolar detention requires binding of SIRT7 to nascent pre-rRNA, linking the spatial distribution of SIRT7 and deacetylation of PAF53 to ongoing transcription.
    Title: Repression of RNA polymerase I upon stress is caused by inhibition of RNA-dependent deacetylation of PAF53 by SIRT7.
  3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

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)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of polymerase (RNA) I polypeptide E (POLR1E, 53kDa) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ13390, FLJ13970, FLJ43482

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase I general transcription initiation factor binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA polymerase I preinitiation complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nucleolar large rRNA transcription by RNA polymerase I 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
  
involved_in transcription initiation at RNA polymerase I promoter 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 
located_in fibrillar center IDA
Inferred from Direct Assay
more info
  
located_in nucleolus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
DNA-directed RNA polymerase I subunit RPA49
Names
DNA-directed RNA polymerase I subunit E
RNA polymerase I subunit A49
RNA polymerase I-associated factor 53
polymerase (RNA) I associated factor 1
polymerase (RNA) I polypeptide E, 53kDa
polymerase (RNA) I subunit E

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_001282766.2 → NP_001269695.1  DNA-directed RNA polymerase I subunit RPA49 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate exon the coding region which results in the use of downstream start codon compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AL158156
    UniProtKB/TrEMBL
    B4E005
    Conserved Domains (1) summary
    pfam06870
    Location:47 → 341
    RNA_pol_I_A49; A49-like RNA polymerase I associated factor

  2. NM_022490.4 → NP_071935.1  DNA-directed RNA polymerase I subunit RPA49 isoform 1

    See identical proteins and their annotated locations for NP_071935.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL158156
    Consensus CDS
    CCDS6611.1
    UniProtKB/Swiss-Prot
    Q5VZT3, Q8NBA9, Q96L20, Q9GZS1
    UniProtKB/TrEMBL
    B4E005
    Related
    ENSP00000367029.4, ENST00000377798.9
    Conserved Domains (1) summary
    pfam06870
    Location:36 → 411
    RNA_pol_I_A49; A49-like RNA polymerase I associated factor

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    37485948..37503697
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423729.1 → XP_047279685.1  DNA-directed RNA polymerase I subunit RPA49 isoform X1

    Related
    ENSP00000367023.3, ENST00000377792.3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    37509662..37527361
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363550.1 → XP_054219525.1  DNA-directed RNA polymerase I subunit RPA49 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9GZS1.3 GenPept UniProtKB/Swiss-Prot:Q9GZS1

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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