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    Polr1a polymerase (RNA) I polypeptide A [ Mus musculus (house mouse) ]

    Gene ID: 20019, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Polr1aprovided by MGI
    Official Full Name
    polymerase (RNA) I polypeptide Aprovided by MGI
    Primary source
    MGI:MGI:1096397
    See related
    Ensembl:ENSMUSG00000049553 AllianceGenome:MGI:1096397
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    mRPA1; 194kDa; RPA194; Rpo1-4; 2900087K15Rik; 3010014K16Rik
    Summary
    Predicted to enable several functions, including DNA-directed 5'-3' RNA polymerase activity; DNA/RNA hybrid binding activity; and metal ion binding activity. Predicted to contribute to RNA polymerase I activity. Predicted to be involved in negative regulation of protein localization to nucleolus and rRNA transcription. Located in chromosome and nucleus. Part of RNA polymerase I complex. Is expressed in several structures, including alimentary system; brain; early conceptus; genitourinary system; and integumental system. Human ortholog(s) of this gene implicated in acrofacial dysostosis Cincinnati type and hypomyelinating leukodystrophy. Orthologous to human POLR1A (RNA polymerase I subunit A). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in ovary adult (RPKM 10.9), adrenal adult (RPKM 8.6) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Polr1a in Genome Data Viewer
    Location:
    6 C1; 6 32.21 cM
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (71886037..71956419)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (71909053..71979435)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene inner membrane protein, mitochondrial Neighboring gene ribosomal protein L7A pseudogene Neighboring gene small nucleolar RNA, C/D box 94 Neighboring gene pentatricopeptide repeat domain 3 Neighboring gene STARR-positive B cell enhancer ABC_E9096 Neighboring gene STARR-positive B cell enhancer ABC_E6439 Neighboring gene STARR-seq mESC enhancer starr_16273 Neighboring gene STARR-seq mESC enhancer starr_16274 Neighboring gene eukaryotic translation initiation factor 3, subunit H pseudogene Neighboring gene STARR-seq mESC enhancer starr_16275 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:71912891-71913074 Neighboring gene predicted gene, 26628 Neighboring gene VISTA enhancer mm1722 Neighboring gene RIKEN cDNA 9130221F21 gene Neighboring gene STARR-seq mESC enhancer starr_16277 Neighboring gene spermine synthase pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Mechanism of transcription termination: PTRF interacts with the largest subunit of RNA polymerase I and dissociates paused transcription complexes from yeast and mouse. Jansa P, et al. Mol Gen Genet, 1999 Oct. PMID 10589839
    2. A kinetic framework for a mammalian RNA polymerase in vivo. Dundr M, et al. Science, 2002 Nov 22. PMID 12446911
    3. POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies. Smallwood K, et al. Am J Hum Genet, 2023 May 4. PMID 37075751, Free PMC Article
    4. Molecular cloning and characterization of the cDNA encoding the largest subunit of mouse RNA polymerase I. Seither P, et al. Mol Gen Genet, 1997 Jun. PMID 9236775
    5. CTCF regulates the local epigenetic state of ribosomal DNA repeats. van de Nobelen S, et al. Epigenetics Chromatin, 2010 Nov 8. PMID 21059229, Free PMC Article

    See all (33) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    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

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    contributes_to DNA-directed 5'-3' RNA polymerase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-directed 5'-3' RNA polymerase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-directed 5'-3' RNA polymerase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA/RNA hybrid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA/RNA hybrid binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    contributes_to RNA polymerase I activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase I activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase I activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of protein localization to nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of protein localization to nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in rRNA transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription by RNA polymerase I 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 
    part_of RNA polymerase I complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 polymerase I subunit RPA1
    Names
    DNA-directed RNA polymerase I largest subunit
    DNA-directed RNA polymerase I subunit A
    RNA polymerase 1-4 (194 kDa subunit)
    RNA polymerase I 194 kDa subunit
    RNA polymerase I subunit A1
    NP_033114.3
    XP_006505867.1

    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_009088.3 → NP_033114.3  DNA-directed RNA polymerase I subunit RPA1

      See identical proteins and their annotated locations for NP_033114.3

      Status: VALIDATED

      Source sequence(s)
      AK147379, AK160970, CJ260853
      Consensus CDS
      CCDS20236.1
      UniProtKB/Swiss-Prot
      O35134, Q7TSA9
      UniProtKB/TrEMBL
      Q3UHI3
      Related
      ENSMUSP00000060858.9, ENSMUST00000055296.11
      Conserved Domains (4) summary
      cd02735
      Location:1206 → 1713
      RNAP_I_Rpa1_C; Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain
      cd01435
      Location:16 → 1011
      RNAP_I_RPA1_N; Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain
      TIGR02390
      Location:10 → 1038
      RNA_pol_rpoA1; DNA-directed RNA polymerase subunit A'
      pfam04998
      Location:965 → 1668
      RNA_pol_Rpb1_5; RNA polymerase Rpb1, domain 5

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      71886037..71956419
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006505804.3 → XP_006505867.1  DNA-directed RNA polymerase I subunit RPA1 isoform X1

      Conserved Domains (2) summary
      cd01435
      Location:1 → 509
      RNAP_I_RPA1_N; Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain
      pfam04998
      Location:463 → 1165
      RNA_pol_Rpb1_5; RNA polymerase Rpb1, domain 5
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O35134.2 GenPept UniProtKB/Swiss-Prot:O35134

    Gene LinkOut

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