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

    Gene ID: 64425, updated on 28-Oct-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 and RNA polymerase I general transcription initiation factor binding activity. Involved in nucleolar large rRNA transcription by RNA polymerase I and transcription initiation at RNA polymerase I promoter. Located in fibrillar center and nucleoplasm. Part of RNA polymerase I complex. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 15.6), endometrium (RPKM 8.0) and 25 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (37485948..37503697)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (37509662..37527361)
    RS_2024_09 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 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. RNA polymerase I-specific subunit CAST/hPAF49 has a role in the activation of transcription by upstream binding factor. Panov KI, et al. Mol Cell Biol, 2006 Jul. PMID 16809778, Free PMC Article
    5. PAF49: An RNA Polymerase I subunit essential for rDNA transcription and stabilization of PAF53. McNamar R, et al. J Biol Chem, 2023 Aug. PMID 37356716, Free PMC Article

    See all (79) 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_2024_08

    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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