POLR1C RNA polymerase I subunit C [Homo sapiens (human)] - Gene

Summary

Official Symbol: POLR1Cprovided by HGNC
Official Full Name: RNA polymerase I subunit Cprovided by HGNC
Primary source: HGNC:HGNC:20194
See related: Ensembl:ENSG00000171453 MIM:610060; Vega:OTTHUMG00000014739
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: AC40; RPA5; TCS3; HLD11; RPA39; RPA40; RPAC1; RPC40
Summary: The protein encoded by this gene is a subunit of both RNA polymerase I and RNA polymerase III complexes. The encoded protein is part of the Pol core element. Mutations in this gene have been associated with Treacher Collins syndrome (TCS) and hypomyelinating leukodystrophy 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Orthologs: mouse all

Genomic context

See POLR1C in Genome Data Viewer Map Viewer

Location:: 6p21.1

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
108	current	GRCh38.p7 (GCF_000001405.33)	6	NC_000006.12 (43517024..43562404)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (43484777..43497114)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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 Jun 15 11:32:44 2016

Bibliography

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GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

We report a clinical and extensive molecular study, including TCOF1, POLR1D, POLR1C, and EFTUD2 genes, in a series of 146 patients with TCS.
Title: Treacher Collins syndrome: a clinical and molecular study based on a large series of patients.
This study is the first to show that distinct mutations in a gene coding for a shared subunit of two RNA polymerases lead to selective modification of the enzymes' availability leading to two different clinical conditions.
Title: Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III.
Mutations in TCOF1, POLR1C and POLR1D have all been implicated in causing TCS
Title: Treacher Collins Syndrome: the genetics of a craniofacial disease.
mutations in both alleles of POLR1C in three individuals with Treacher Collins syndrome.
Title: Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome.
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
Title: A kinetic framework for a mammalian RNA polymerase in vivo.

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

Associated conditions

Description	Tests
Leukodystrophy, hypomyelinating, 11 MedGen: C4225305 OMIM: 616494 GeneReviews: POLR3-Related Leukodystrophy	Compare labs
Mandibulofacial dysostosis, Treacher Collins type, autosomal recessive MedGen: C1855433 OMIM: 248390 GeneReviews: Treacher Collins Syndrome	Compare labs

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 BioSystems

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B-WICH complex positively regulates rRNA expression, organism-specific biosystem (from REACTOME)
B-WICH complex positively regulates rRNA expression, organism-specific biosystemThe B-WICH complex is a large 3 Mdalton complex containing SMARCA5 (SNF2H), BAZ1B (WSTF), ERCC6 (CSB), MYO1C (Nuclear myosin 1c) (Cavellan et al. 2006, Percipalle et al. 2006, Vintermist et al. 2001,...
Cytosolic DNA-sensing pathway, organism-specific biosystem (from KEGG)
Cytosolic DNA-sensing pathway, organism-specific biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
Cytosolic DNA-sensing pathway, conserved biosystem (from KEGG)
Cytosolic DNA-sensing pathway, conserved biosystemSpecific families of pattern recognition receptors are responsible for detecting foreign DNA from invading microbes or host cells and generating innate immune responses. DAI is the first identified s...
Cytosolic sensors of pathogen-associated DNA, organism-specific biosystem (from REACTOME)
Cytosolic sensors of pathogen-associated DNA, organism-specific biosystemPresence of pathogen-associated DNA in cytosol induces type I IFN production. Several intracellular receptors have been implicated to some degree. These include DNA-dependent activator of interferon ...
Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
Epstein-Barr virus infection, organism-specific biosystem (from KEGG)
Epstein-Barr virus infection, organism-specific biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
Epstein-Barr virus infection, conserved biosystem (from KEGG)
Epstein-Barr virus infection, conserved biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
Gene Expression, organism-specific biosystem (from REACTOME)
Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
Immune System, organism-specific biosystem (from REACTOME)
Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
Innate Immune System, organism-specific biosystem (from REACTOME)
Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
Metabolic pathways, organism-specific biosystem (from KEGG)
Metabolic pathways, organism-specific biosystem
Metabolic pathways
Negative epigenetic regulation of rRNA expression, organism-specific biosystem (from REACTOME)
Negative epigenetic regulation of rRNA expression, organism-specific biosystemTranscription of rRNA genes is controlled by epigenetic activation and repression (reviewed in McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2013). About half of the roughl...
NoRC negatively regulates rRNA expression, organism-specific biosystem (from REACTOME)
NoRC negatively regulates rRNA expression, organism-specific biosystemOnly about half of the rRNA gene copies in a cell are expressed. The remaining copies are silenced by modifications to histones and DNA (reviewed in Santoro and Grummt 2001, Grummt 2007, Preuss and P...
Positive epigenetic regulation of rRNA expression, organism-specific biosystem (from REACTOME)
Positive epigenetic regulation of rRNA expression, organism-specific biosystemTranscription of rRNA genes is controlled by epigenetic activation and repression (reviewed in Percipalle and Farrants 2006, McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2...
Purine metabolism, organism-specific biosystem (from KEGG)
Purine metabolism, organism-specific biosystem
Purine metabolism
Purine metabolism, conserved biosystem (from KEGG)
Purine metabolism, conserved biosystem
Purine metabolism
Pyrimidine metabolism, organism-specific biosystem (from KEGG)
Pyrimidine metabolism, organism-specific biosystem
Pyrimidine metabolism
Pyrimidine metabolism, conserved biosystem (from KEGG)
Pyrimidine metabolism, conserved biosystem
Pyrimidine metabolism
RNA Polymerase I Chain Elongation, organism-specific biosystem (from REACTOME)
RNA Polymerase I Chain Elongation, organism-specific biosystem
RNA Polymerase I Chain Elongation
RNA Polymerase I Promoter Clearance, organism-specific biosystem (from REACTOME)
RNA Polymerase I Promoter Clearance, organism-specific biosystemPromoter clearance is one of the rate-limiting steps in Polymerase I transcription. This step is composed of three phases, promoter opening, transcription initiation and promoter escape.
RNA Polymerase I Promoter Escape, organism-specific biosystem (from REACTOME)
RNA Polymerase I Promoter Escape, organism-specific biosystemAs the active RNA Polymerase I complex leaves the promoter Rrn3 dissociates from the complex. RNA polymerase I Promoter Clearance is complete and Chain Elongation begins.
RNA Polymerase I Transcription, organism-specific biosystem (from REACTOME)
RNA Polymerase I Transcription, organism-specific biosystemThe rRNA genes are transcribed by RNA polymerase I, one of three eukaryotic nuclear RNA polymerases. The polymerase is a multisubunit complex, composed of two large subunits (the most conserved porti...
RNA Polymerase I Transcription Initiation, organism-specific biosystem (from REACTOME)
RNA Polymerase I Transcription Initiation, organism-specific biosystemDuring initiation the double-stranded DNA must be melted and transcription begins. SL1 forms and interacts with UBF-1 and the rDNA promoter. It is this platform that will recruit active RNA polymeras...
RNA Polymerase I Transcription Termination, organism-specific biosystem (from REACTOME)
RNA Polymerase I Transcription Termination, organism-specific biosystemTermination of transcription by RNA polymerase I is a 4 step process. Initially TTF-1 binds the template rDNA. This complex pauses polymerase I allowing PTRF to interact with the quaternary complex ...
RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription, organism-specific biosystem (from REACTOME)
RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription, organism-specific biosystemTranscription by RNA Polymerase I, RNA Polymerase III and transcription from mitochondrial promoters.
RNA Polymerase III Abortive And Retractive Initiation, organism-specific biosystem (from REACTOME)
RNA Polymerase III Abortive And Retractive Initiation, organism-specific biosystemAbortive initiation, the repetitive formation of short oligonucleotides, is a ubiquitous feature of transcriptional initiation. This Pathway contains events inferred from events in Saccharomyces cer...
RNA Polymerase III Chain Elongation, organism-specific biosystem (from REACTOME)
RNA Polymerase III Chain Elongation, organism-specific biosystemPol III initiation complexes open the promoter spontaneously similar to the mechanism employed in archaeal and bacterial transcription.
RNA Polymerase III Transcription, organism-specific biosystem (from REACTOME)
RNA Polymerase III Transcription, organism-specific biosystemRNA polymerase III is one of three types of nuclear RNA polymerases present in eucaryotic cells. About 10% of the total transcription in dividing cells can be attributed to its activity. It synthes...
RNA Polymerase III Transcription Initiation, organism-specific biosystem (from REACTOME)
RNA Polymerase III Transcription Initiation, organism-specific biosystemThere are three basic types of RNA polymerase III promoters. The three types of RNA polymerase III promoters are known as type 1, type 2, and type 3 promoters. Type 1 promoters are found in the 5S ...
RNA Polymerase III Transcription Initiation From Type 1 Promoter, organism-specific biosystem (from REACTOME)
RNA Polymerase III Transcription Initiation From Type 1 Promoter, organism-specific biosystemThe type 1 promoters recruit TFIIIA, the founding member of the C2H2 zinc finger family of DNA-binding proteins (Engelke et al., 1980; Sakonju et al., 1981). The binding of TFIIIA then allows the bi...
RNA Polymerase III Transcription Initiation From Type 2 Promoter, organism-specific biosystem (from REACTOME)
RNA Polymerase III Transcription Initiation From Type 2 Promoter, organism-specific biosystemThe type 2 promoters can recruit TFIIIC without the help of TFIIIA because TFIIIC binds directly to the A and B boxes. As for the type 1 promoters, this then allows the binding of Brf1-TFIIIB and RN...
RNA Polymerase III Transcription Initiation From Type 3 Promoter, organism-specific biosystem (from REACTOME)
RNA Polymerase III Transcription Initiation From Type 3 Promoter, organism-specific biosystemThe metazoan-specific type 3 promoters, which are exemplified by the human U6 promoter, recruit a complex variously called the snRNA activating protein complex (SNAPc) (Sadowski et al., 1993), the PS...
RNA Polymerase III Transcription Termination, organism-specific biosystem (from REACTOME)
RNA Polymerase III Transcription Termination, organism-specific biosystem
RNA Polymerase III Transcription Termination
RNA polymerase, organism-specific biosystem (from KEGG)
RNA polymerase, organism-specific biosystem
RNA polymerase
RNA polymerase, conserved biosystem (from KEGG)
RNA polymerase, conserved biosystem
RNA polymerase
RNA polymerase I, eukaryotes, organism-specific biosystem (from KEGG)
RNA polymerase I, eukaryotes, organism-specific biosystemStructural complex; Genetic information processing; RNA polymerase
RNA polymerase I, eukaryotes, conserved biosystem (from KEGG)
RNA polymerase I, eukaryotes, conserved biosystemStructural complex; Genetic information processing; RNA polymerase
RNA polymerase III, eukaryotes, organism-specific biosystem (from KEGG)
RNA polymerase III, eukaryotes, organism-specific biosystemStructural complex; Genetic information processing; RNA polymerase
RNA polymerase III, eukaryotes, conserved biosystem (from KEGG)
RNA polymerase III, eukaryotes, conserved biosystemStructural complex; Genetic information processing; RNA polymerase

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-107161 (e-PCR)
- UniSTS:170276

SHGC-53217 (e-PCR)
- UniSTS:42815

D6S1340 (e-PCR)
- UniSTS:21838

D6S1161E (e-PCR)
- UniSTS:67687

D6S1888 (e-PCR)
- UniSTS:65163

RH18413 (e-PCR)
- UniSTS:20974

Homology

Homologs of the POLR1C gene: The POLR1C gene is conserved in chimpanzee, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 223 organisms have orthologs with human gene POLR1C
The Hierarchical Catalog of Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA binding	IEA Inferred from Electronic Annotation more info
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 III activity	IBA Inferred from Biological aspect of Ancestor more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein dimerization activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
positive regulation of gene expression, epigenetic	TAS Traceable Author Statement more info
positive regulation of type I interferon production	TAS Traceable Author Statement more info
termination of RNA polymerase I transcription	TAS Traceable Author Statement more info
transcription elongation from RNA polymerase I promoter	TAS Traceable Author Statement more info
transcription from RNA polymerase I promoter	TAS Traceable Author Statement more info	PubMed
transcription from RNA polymerase III promoter	IEA Inferred from Electronic Annotation more info
transcription initiation from RNA polymerase I promoter	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
DNA-directed RNA polymerase I complex	IBA Inferred from Biological aspect of Ancestor more info
DNA-directed RNA polymerase III complex	IDA Inferred from Direct Assay more info	PubMed
cytosol	TAS Traceable Author Statement more info
nucleoplasm	TAS Traceable Author Statement more info
nucleus	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: DNA-directed RNA polymerases I and III subunit RPAC1

Names: DNA-directed RNA polymerase I subunit C; DNA-directed RNA polymerases I and III 40 kDa polypeptide; RNA polymerases I and III subunit AC1; polymerase (RNA) I polypeptide C, 30kDa; polymerase (RNA) I subunit C

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

NG_028283.2 RefSeqGene

Range

4986..9488

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001318876.1 → NP_001305805.1 DNA-directed RNA polymerases I and III subunit RPAC1 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' terminal exon, resulting in a different 3' coding region and 3' UTR compared to variant 1. The encoded isoform (2) has a shorter, distinct C-terminus compared to isoform 1.

Source sequence(s)

AF047441, BC008863, DW415914

UniProtKB/Swiss-Prot

O15160

Related

ENSP00000307212.3, OTTHUMP00000016468, ENST00000304004.7, OTTHUMT00000040650

Conserved Domains (2) summary

cd07032
Location:49 → 307

RNAP_I_II_AC40; AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

smart00662
Location:61 → 267

RPOLD; RNA polymerases D
NM_203290.3 → NP_976035.1 DNA-directed RNA polymerases I and III subunit RPAC1 isoform 1

See identical proteins and their annotated locations for NP_976035.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL355802, BC008863, DW415914

Consensus CDS

CCDS4901.1

UniProtKB/Swiss-Prot

O15160

Related

ENSP00000361465.3, OTTHUMP00000016470, ENST00000372389.7, OTTHUMT00000040652

Conserved Domains (1) summary

cd07032
Location:49 → 339

RNAP_I_II_AC40; AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

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

Reference GRCh38.p7 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p7 Primary Assembly

Range

43517024..43562404

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011515000.2 → XP_011513302.1 DNA-directed RNA polymerases I and III subunit RPAC1 isoform X1

Conserved Domains (2) summary

cd07032
Location:49 → 307

RNAP_I_II_AC40; AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III

smart00662
Location:61 → 267

RPOLD; RNA polymerases D

Alternate CHM1_1.1

Genomic

NC_018917.2 Alternate CHM1_1.1

Range

43487894..43500246

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_004875.2: Suppressed sequence

Description

NM_004875.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.