Human Gene POLR3D (uc003xbl.3) Description and Page Index
  Description: Homo sapiens polymerase (RNA) III (DNA directed) polypeptide D, 44kDa (POLR3D), mRNA.
RefSeq Summary (NM_001722): This gene complements a temperature-sensitive mutant isolated from the BHK-21 Syrian hamster cell line. It leads to a block in progression through the G1 phase of the cell cycle at nonpermissive temperatures. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1803614.95896.1, SRR1803615.94370.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968189, SAMEA1968540 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000306433.9/ ENSP00000303088.4 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr8:22,102,619-22,108,680 Size: 6,062 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr8:22,102,963-22,108,031 Size: 5,069 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:22,102,619-22,108,680)mRNA (may differ from genome)Protein (398 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: RPC4_HUMAN
DESCRIPTION: RecName: Full=DNA-directed RNA polymerase III subunit RPC4; Short=RNA polymerase III subunit C4; AltName: Full=DNA-directed RNA polymerase III subunit D; AltName: Full=Protein BN51; AltName: Full=RNA polymerase III 47 kDa subunit; AltName: Full=RPC53 homolog;
FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts, such as Epstein-Barr virus-encoded RNAs (EBERs) induce type I interferon and NF- Kappa-B through the RIG-I pathway (By similarity).
SUBUNIT: Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits (By similarity). Interacts with POLR3E/RPC5.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the eukaryotic RPC4/POLR3D RNA polymerase subunit family.
SEQUENCE CAUTION: Sequence=BC000516; Type=Frameshift; Positions=175; Sequence=BC003039; Type=Frameshift; Positions=175;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.76 RPKM in Testis
Total median expression: 223.76 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -38.0083-0.458 Picture PostScript Text
3' UTR -249.12649-0.384 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007811 - RNA_pol_III_Rpc4

Pfam Domains:
PF05132 - RNA polymerase III RPC4

ModBase Predicted Comparative 3D Structure on P05423
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0001056 RNA polymerase III activity

Biological Process:
GO:0002376 immune system process
GO:0006383 transcription from RNA polymerase III promoter
GO:0032728 positive regulation of interferon-beta production
GO:0045087 innate immune response
GO:0045089 positive regulation of innate immune response
GO:0051607 defense response to virus

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005666 DNA-directed RNA polymerase III complex
GO:0005829 cytosol
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AK026588 - Homo sapiens cDNA: FLJ22935 fis, clone KAT07864, highly similar to HUMBN51 Human BN51 mRNA.
M17754 - Human BN51 mRNA, complete cds.
DL491190 - Novel nucleic acids.
BC000516 - Homo sapiens cDNA clone IMAGE:2822828, containing frame-shift errors.
BC003039 - Homo sapiens cDNA clone IMAGE:2822828, containing frame-shift errors.
BC004484 - Homo sapiens polymerase (RNA) III (DNA directed) polypeptide D, 44kDa, mRNA (cDNA clone MGC:10605 IMAGE:3938075), complete cds.
AK295725 - Homo sapiens cDNA FLJ57992 complete cds, highly similar to DNA-directed RNA polymerase III subunit D (EC2.7.7.6).
BC002603 - Homo sapiens polymerase (RNA) III (DNA directed) polypeptide D, 44kDa, mRNA (cDNA clone MGC:2987 IMAGE:3143056), complete cds.
CU678738 - Synthetic construct Homo sapiens gateway clone IMAGE:100019231 5' read POLR3D mRNA.
HQ447310 - Synthetic construct Homo sapiens clone IMAGE:100070622; CCSB004386_02 polymerase (RNA) III (DNA directed) polypeptide D, 44kDa (POLR3D) gene, encodes complete protein.
KJ896507 - Synthetic construct Homo sapiens clone ccsbBroadEn_05901 POLR3D gene, encodes complete protein.
AF346574 - Homo sapiens DNA-directed RNA polymerase III subunit RPC53 mRNA, partial cds.
CR541803 - Homo sapiens full open reading frame cDNA clone RZPDo834E0331D for gene POLR3D, polymerase (RNA) III (DNA directed) polypeptide D, 44kDa; complete cds, without stopcodon.
AY092086 - Homo sapiens RNA polymerase III 53 kDa subunit RPC4 mRNA, complete cds.
CR536509 - Homo sapiens full open reading frame cDNA clone RZPDo834C0820D for gene POLR3D, polymerase (RNA) III (DNA directed) polypeptide D, 44kDa; complete cds, incl. stopcodon.
JD282078 - Sequence 263102 from Patent EP1572962.
JD200459 - Sequence 181483 from Patent EP1572962.
JD537079 - Sequence 518103 from Patent EP1572962.
JD194030 - Sequence 175054 from Patent EP1572962.
JD149084 - Sequence 130108 from Patent EP1572962.
JD102795 - Sequence 83819 from Patent EP1572962.
JD200932 - Sequence 181956 from Patent EP1572962.
JD333039 - Sequence 314063 from Patent EP1572962.
JD560605 - Sequence 541629 from Patent EP1572962.
JD494335 - Sequence 475359 from Patent EP1572962.
JD273078 - Sequence 254102 from Patent EP1572962.
JD179226 - Sequence 160250 from Patent EP1572962.
JD453800 - Sequence 434824 from Patent EP1572962.
JD374966 - Sequence 355990 from Patent EP1572962.
JD083769 - Sequence 64793 from Patent EP1572962.
JD049715 - Sequence 30739 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00230 - Purine metabolism
hsa00240 - Pyrimidine metabolism
hsa01100 - Metabolic pathways
hsa03020 - RNA polymerase
hsa04623 - Cytosolic DNA-sensing pathway

Reactome (by CSHL, EBI, and GO)

Protein P05423 (Reactome details) participates in the following event(s):

R-HSA-76056 Recruitment of RNA polymerase III to TFIIIB:TFIIIC:TFIIIA:Type 1 Promoter Complex
R-HSA-83803 Recruitment of RNA Polymerase III to TFIIIB:SNAPc:Type 3 Promoter Complex
R-HSA-83805 Recruitment of RNA Polymerase III to the TFIIIB:TFIIIC: Type 2 Promoter Complex
R-HSA-113454 RNA Polymerase III Termination and release of transcribed RNA
R-HSA-76060 RNA Polymerase III Promoter Opening at Type 1 Promoters
R-HSA-112150 RNA Polymerase III Promoter Opening at Type 2 Promoters
R-HSA-112152 RNA Polymerase III Promoter Opening at Type 3 Promoters
R-HSA-112055 RNA Polymerase III Abortive Initiation At Type 1 Open Promoters
R-HSA-112153 RNA Polymerase III Simple Start Sequence Initiation At Type 1 Promoters
R-HSA-112149 RNA Polymerase III Abortive Initiation At Type 2 Open Promoters
R-HSA-112155 RNA Polymerase III Simple Start Sequence Initiation At Type 2 Promoters
R-HSA-112054 RNA Polymerase III Abortive Initiation At Type 3 Open Promoters
R-HSA-112156 RNA Polymerase III Simple Start Sequence Initiation At Type 3 Promoters
R-HSA-113442 RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites
R-HSA-113446 Initiation of RNA Polymerase III Productive Transcription
R-HSA-113449 RNA Polymerase III Transcriptional Pause at Terminator Sequence
R-HSA-113451 Resumption of RNA Polymerase III Productive Transcription
R-HSA-113705 RNA Polymerase III Productive Transcription
R-HSA-76061 RNA Polymerase III Transcription Initiation From Type 1 Promoter
R-HSA-76071 RNA Polymerase III Transcription Initiation From Type 3 Promoter
R-HSA-76066 RNA Polymerase III Transcription Initiation From Type 2 Promoter
R-HSA-73980 RNA Polymerase III Transcription Termination
R-HSA-749476 RNA Polymerase III Abortive And Retractive Initiation
R-HSA-73780 RNA Polymerase III Chain Elongation
R-HSA-76046 RNA Polymerase III Transcription Initiation
R-HSA-74158 RNA Polymerase III Transcription
R-HSA-1834949 Cytosolic sensors of pathogen-associated DNA
R-HSA-74160 Gene expression (Transcription)
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: BN51, BN51T, NM_001722, NP_001713, P05423, Q6FI28, Q9BPV7, Q9BPZ1, Q9BXB3, RPC4_HUMAN
UCSC ID: uc003xbl.3
RefSeq Accession: NM_001722
Protein: P05423 (aka RPC4_HUMAN)
CCDS: CCDS34858.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001722.2
exon count: 9CDS single in 3' UTR: no RNA size: 1946
ORF size: 1197CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2509.00frame shift in genome: no % Coverage: 99.13
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.