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POLR1A RNA polymerase I subunit A [ Homo sapiens (human) ]

Gene ID: 25885, updated on 14-Nov-2024

Summary

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Official Symbol
POLR1Aprovided by HGNC
Official Full Name
RNA polymerase I subunit Aprovided by HGNC
Primary source
HGNC:HGNC:17264
See related
Ensembl:ENSG00000068654 MIM:616404; AllianceGenome:HGNC:17264
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
A190; RPA1; HLD27; RPO14; AFDCIN; RPA190; RPA194; RPO1-4
Summary
The protein encoded by this gene is the largest subunit of the RNA polymerase I complex. The encoded protein represents the catalytic subunit of the complex, which transcribes DNA into ribosomal RNA precursors. Defects in this gene are a cause of the Cincinnati type of acrofacial dysostosis. [provided by RefSeq, May 2016]
Expression
Ubiquitous expression in testis (RPKM 5.9), endometrium (RPKM 5.1) and 25 other tissues See more
Orthologs
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Genomic context

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See POLR1A in Genome Data Viewer
Location:
2p11.2
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86020216..86105886, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86022315..86107956, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86247339..86333009, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906031 Neighboring gene uncharacterized LOC105374843 Neighboring gene CRISPRi-validated cis-regulatory element chr2.3134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86239243-86239743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16150 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:86260844-86261047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11710 Neighboring gene conserved acetylation island sequence 34 enhancer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:86272354-86273553 Neighboring gene MPRA-validated peak3776 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:86296595-86297794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86301664-86302164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86302165-86302665 Neighboring gene uncharacterized LOC124907852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16154 Neighboring gene pentatricopeptide repeat domain 3 Neighboring gene Sharpr-MPRA regulatory region 1812 Neighboring gene MPRA-validated peak3777 silencer Neighboring gene small nucleolar RNA, C/D box 94 Neighboring gene inner membrane mitochondrial protein Neighboring gene microRNA 4779

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 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. Severe neurodegenerative disease in brothers with homozygous mutation in POLR1A. Kara B, et al. Eur J Hum Genet, 2017 Feb. PMID 28051070, Free PMC Article
  2. Upregulated long non-coding RNA LOC90784 promotes cell proliferation and invasion and is associated with poor clinical features in HCC. Xu JH, et al. Biochem Biophys Res Commun, 2017 Aug 26. PMID 28651931
  3. Human Nopp140, which interacts with RNA polymerase I: implications for rRNA gene transcription and nucleolar structural organization. Chen HK, et al. Mol Cell Biol, 1999 Dec. PMID 10567578, Free PMC Article
  4. Cryo-EM structures of human RNA polymerase I. Misiaszek AD, et al. Nat Struct Mol Biol, 2021 Dec. PMID 34887565, Free PMC Article
  5. Identification of an E3 ligase that targets the catalytic subunit of RNA Polymerase I upon transcription stress. Pitts S, et al. J Biol Chem, 2022 Dec. PMID 36372232, Free PMC Article

See all (119) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Expression of RNA polymerase I catalytic core is influenced by RPA12.
    Title: Expression of RNA polymerase I catalytic core is influenced by RPA12.
  2. POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies.
    Title: POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies.
  3. Data show that BRCA1 interacts directly with the basal RNA polymerase I (Pol-I) transcription factors as well as interacting with RNA Pol-I itself.
    Title: The identification of a novel role for BRCA1 in regulating RNA polymerase I transcription.
  4. Homozygous c.2801C>T (p.(Ser934Leu)) in POLR1A was identified in two brothers with unusual neurological disease that manifested with ataxia, psychomotor retardation, cerebellar and cerebral atrophy, and leukodystrophy.
    Title: Severe neurodegenerative disease in brothers with homozygous mutation in POLR1A.
  5. Consistent with this observation, we discovered that polr1a mutant zebrafish exhibited cranioskeletal anomalies mimicking the human phenotype. polr1a loss of function led to perturbed ribosome biogenesis and p53-dependent cell death
    Title: Acrofacial Dysostosis, Cincinnati Type, a Mandibulofacial Dysostosis Syndrome with Limb Anomalies, Is Caused by POLR1A Dysfunction.
  6. SIRT7 knockdown leads to reduced levels of RNA Pol I protein, but not messenger RNA
    Title: Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription.
  7. findings demonstrate that Bloom's syndrome helicase (BLM)interacts with RPA194; studies suggest that nucleolar BLM modulates rDNA structures in association with RNA polymerase I to facilitate RNA polymerase I-mediated rRNA transcription
    Title: BLM helicase facilitates RNA polymerase I-mediated ribosomal RNA transcription.
  8. Interference of POLR1A inhibited the synthesis of rRNA and hindered cell cycle progression in cells with inactivated p53, as a consequence of downregulation of the transcription factor E2F-1.
    Title: Selective inhibition of rRNA transcription downregulates E2F-1: a new p53-independent mechanism linking cell growth to cell proliferation.
  9. 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.
  10. analyzed the kinetics of assembly and elongation of the RNA polymerase I complex on endogenous ribosomal genes in the nuclei of living cells with the use of in vivo microscopy [RPA43]
    Title: A kinetic framework for a mammalian RNA polymerase in vivo.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Acrofacial dysostosis Cincinnati type
MedGen: C4225317 OMIM: 616462 GeneReviews: Not available
not available
Leukodystrophy, hypomyelinating, 27
MedGen: C5882743 OMIM: 620675 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

  • FLJ10750, FLJ21915, MGC87965, DKFZp586M0122

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
contributes_to DNA-directed 5'-3' RNA polymerase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-directed 5'-3' RNA polymerase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA/RNA hybrid binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase I activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables RNA polymerase II activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase III activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase IV activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase V activity IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables magnesium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables mitochondrial single subunit type RNA polymerase activity IEA
Inferred from Electronic Annotation
more info
  
enables plastid single subunit type RNA polymerase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in mitochondrial transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of protein localization to nucleolus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in plastid transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription by RNA polymerase I IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription by RNA polymerase III IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription by RNA polymerase IV IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription by RNA polymerase V IEA
Inferred from Electronic Annotation
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 
located_in chromosome ISS
Inferred from Sequence or Structural Similarity
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 RPA1
Names
DNA-directed RNA polymerase I largest subunit
DNA-directed RNA polymerase I subunit A
DNA-directed RNA polymerase I subunit A1
RNA polymerase I 194 kDa subunit
polymerase (RNA) I polypeptide A, 194kDa
polymerase (RNA) I subunit A
NP_056240.2

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

  1. NG_050742.2 RefSeqGene

    Range
    5270..90940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_015425.6 → NP_056240.2  DNA-directed RNA polymerase I subunit RPA1

    See identical proteins and their annotated locations for NP_056240.2

    Status: REVIEWED

    Source sequence(s)
    AC012511, AK302458, AK307490, BC073824, BP363163
    Consensus CDS
    CCDS42706.1
    UniProtKB/Swiss-Prot
    B7Z7T0, D6W5M0, O95602, Q0VG05, Q9UEH0, Q9UFT9
    UniProtKB/TrEMBL
    B7ZKR9
    Related
    ENSP00000263857.6, ENST00000263857.11
    Conserved Domains (4) summary
    cd02735
    Location:1199 → 1716
    RNAP_I_Rpa1_C; Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain
    PRK08566
    Location:4 → 1025
    PRK08566; DNA-directed RNA polymerase subunit A'; Validated
    cd01435
    Location:16 → 1004
    RNAP_I_RPA1_N; Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain
    pfam04998
    Location:958 → 1671
    RNA_pol_Rpb1_5; RNA polymerase Rpb1, domain 5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    86020216..86105886 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    86022315..86107956 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95602.2 GenPept UniProtKB/Swiss-Prot:O95602

Gene LinkOut

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