Human Gene POLR3E (uc002dkk.4) Description and Page Index
  Description: Homo sapiens polymerase (RNA) III (DNA directed) polypeptide E (80kD) (POLR3E), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr16:22,308,696-22,346,424 Size: 37,729 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr16:22,314,290-22,345,021 Size: 30,732 Coding Exon Count: 20 

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 (chr16:22,308,696-22,346,424)mRNA (may differ from genome)Protein (708 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: RPC5_HUMAN
DESCRIPTION: RecName: Full=DNA-directed RNA polymerase III subunit RPC5; Short=RNA polymerase III subunit C5; AltName: Full=DNA-directed RNA polymerase III 80 kDa polypeptide;
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. Essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters. 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 POLR3D/RPC4.
SUBCELLULAR LOCATION: Nucleus.
SEQUENCE CAUTION: Sequence=BAA95976.1; Type=Erroneous initiation; Sequence=BAB14481.1; Type=Erroneous initiation;

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.13 RPKM in Muscle - Skeletal
Total median expression: 509.30 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 -97.60201-0.486 Picture PostScript Text
3' UTR -357.241403-0.255 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
IPR006886 - RNA_pol_III_Rpc5

Pfam Domains:
PF04801 - Sin-like protein conserved region

ModBase Predicted Comparative 3D Structure on Q9NVU0
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 orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

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

Biological Process:
GO:0002376 immune system process
GO:0006351 transcription, DNA-templated
GO:0006383 transcription from RNA polymerase III promoter
GO:0045087 innate immune response
GO:0051607 defense response to virus

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005666 DNA-directed RNA polymerase III complex
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK026645 - Homo sapiens cDNA: FLJ22992 fis, clone KAT11904.
AK300735 - Homo sapiens cDNA FLJ59434 complete cds, highly similar to DNA-directed RNA polymerases III 80 kDa polypeptide (EC 2.7.7.6).
AK023160 - Homo sapiens cDNA FLJ13098 fis, clone NT2RP3002244.
AK023231 - Homo sapiens cDNA FLJ13169 fis, clone NT2RP3003805.
AK296813 - Homo sapiens cDNA FLJ59568 complete cds, highly similar to DNA-directed RNA polymerases III 80 kDa polypeptide (EC 2.7.7.6).
AK222789 - Homo sapiens mRNA for polymerase (RNA) III (DNA directed) polypeptide E variant, clone: HEP02371.
BC000285 - Homo sapiens polymerase (RNA) III (DNA directed) polypeptide E (80kD), mRNA (cDNA clone MGC:957 IMAGE:3356711), complete cds.
AK001371 - Homo sapiens cDNA FLJ10509 fis, clone NT2RP2000617.
AK222671 - Homo sapiens mRNA, polymerase (RNA) III (DNA directed) polypeptide E variant, clone: CBR03318.
AB040885 - Homo sapiens mRNA for KIAA1452 protein, partial cds.
AK130661 - Homo sapiens cDNA FLJ27151 fis, clone SYN00523.
AK293300 - Homo sapiens cDNA FLJ55674 complete cds, highly similar to DNA-directed RNA polymerases III 80 kDa polypeptide (EC 2.7.7.6).
AB384602 - Synthetic construct DNA, clone: pF1KA1452, Homo sapiens POLR3E gene for DNA-directed RNA polymerase III subunit RPC5, complete cds, without stop codon, in Flexi system.
KJ902865 - Synthetic construct Homo sapiens clone ccsbBroadEn_12259 POLR3E gene, encodes complete protein.
AY092085 - Homo sapiens RNA polymerase III 80 kDa subunit RPC5 mRNA, complete cds.
JD534075 - Sequence 515099 from Patent EP1572962.
JD380828 - Sequence 361852 from Patent EP1572962.
JD175090 - Sequence 156114 from Patent EP1572962.
JD287651 - Sequence 268675 from Patent EP1572962.
JD375879 - Sequence 356903 from Patent EP1572962.
JD312608 - Sequence 293632 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NVU0 (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: KIAA1452, NM_018119, NP_001244964, Q9BWF7, Q9H8W8, Q9H907, Q9NVU0, Q9P276, RPC5_HUMAN, uc002dkk.3
UCSC ID: uc002dkk.4
RefSeq Accession: NM_018119
Protein: Q9NVU0 (aka RPC5_HUMAN)
CCDS: CCDS10605.1, CCDS58432.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018119.3
exon count: 21CDS single in 3' UTR: no RNA size: 3745
ORF size: 2127CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3701.00frame shift in genome: no % Coverage: 99.63
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.