Human Gene POLRMT (ENST00000588649.7_7) from GENCODE V47lift37
  Description: DNA-dependent RNA polymerase catalyzes the transcription of mitochondrial DNA into RNA using the four ribonucleoside triphosphates as substrates (PubMed:21278163, PubMed:33602924). Component of the mitochondrial transcription initiation complex, composed at least of TFB2M, TFAM and POLRMT that is required for basal transcription of mitochondrial DNA (PubMed:29149603). In this complex, TFAM recruits POLRMT to a specific promoter whereas TFB2M induces structural changes in POLRMT to enable promoter opening and trapping of the DNA non- template strand (PubMed:29149603). Has DNA primase activity (PubMed:18685103, PubMed:33602924). Catalyzes the synthesis of short RNA primers that are necessary for the initiation of lagging-strand DNA synthesis from the origin of light-strand DNA replication (OriL) (PubMed:18685103, PubMed:33602924). (from UniProt O00411)
Gencode Transcript: ENST00000588649.7_7
Gencode Gene: ENSG00000099821.14_12
Transcript (Including UTRs)
   Position: hg19 chr19:617,221-633,537 Size: 16,317 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr19:617,274-633,512 Size: 16,239 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:617,221-633,537)mRNA (may differ from genome)Protein (1230 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsHGNC
MalacardsMGIPubMedReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RPOM_HUMAN
DESCRIPTION: RecName: Full=DNA-directed RNA polymerase, mitochondrial; Short=MtRPOL; EC=2.7.7.6; Flags: Precursor;
FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of mitochondrial DNA into RNA using the four ribonucleoside triphosphates as substrates.
CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
SUBUNIT: Interacts with TFB1M and TFB2M, leading to the stimulation of transcription. Interacts with TEFM.
SUBCELLULAR LOCATION: Mitochondrion.
SIMILARITY: Belongs to the phage and mitochondrial RNA polymerase family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: POLRMT
Diseases sorted by gene-association score: autosomal dominant progressive external ophthalmoplegia (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 46.27 RPKM in Testis
Total median expression: 691.93 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.3025-0.212 Picture PostScript Text
3' UTR -8.2053-0.155 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
IPR024075 - DNA-dir_RNA_pol_helix_hairpin
IPR002092 - DNA-dir_Rpol_phage-type

Pfam Domains:
PF00940 - DNA-dependent RNA polymerase
PF14700 - DNA-directed RNA polymerase N-terminal

SCOP Domains:
56672 - DNA/RNA polymerases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3SPA - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O00411
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 orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006390 transcription from mitochondrial promoter
GO:0006391 transcription initiation from mitochondrial promoter
GO:0007005 mitochondrion organization

Cellular Component:
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0032991 macromolecular complex
GO:0034245 mitochondrial DNA-directed RNA polymerase complex
GO:0042645 mitochondrial nucleoid


-  Descriptions from all associated GenBank mRNAs
  LF208804 - JP 2014500723-A/16307: Polycomb-Associated Non-Coding RNAs.
BC098387 - Homo sapiens polymerase (RNA) mitochondrial (DNA directed), mRNA (cDNA clone MGC:104585 IMAGE:5264127), complete cds.
BC030829 - Homo sapiens cDNA clone IMAGE:4799009.
AK225723 - Homo sapiens mRNA for mitochondrial DNA-directed RNA polymerase precursor variant, clone: TST02840.
AK225865 - Homo sapiens mRNA for mitochondrial DNA-directed RNA polymerase precursor variant, clone: FCC124G05.
AB209920 - Homo sapiens mRNA for DNA-directed RNA polymerase variant protein.
AK302877 - Homo sapiens cDNA FLJ58806 complete cds, highly similar to DNA-directed RNA polymerase, mitochondrial precursor (EC 2.7.7.6).
U75370 - Human mitochondrial RNA polymerase mRNA, nuclear gene encoding mitochondrial protein, complete cds.
JD515976 - Sequence 497000 from Patent EP1572962.
BC024170 - Homo sapiens polymerase (RNA) mitochondrial (DNA directed), mRNA (cDNA clone IMAGE:2820301).
BC070057 - Homo sapiens cDNA clone IMAGE:5296766, containing frame-shift errors.
JD385341 - Sequence 366365 from Patent EP1572962.
KJ897357 - Synthetic construct Homo sapiens clone ccsbBroadEn_06751 POLRMT gene, encodes complete protein.
JD157944 - Sequence 138968 from Patent EP1572962.
AK307525 - Homo sapiens cDNA, FLJ97473.
LF323047 - JP 2014500723-A/130550: Polycomb-Associated Non-Coding RNAs.
JD402831 - Sequence 383855 from Patent EP1572962.
JD248573 - Sequence 229597 from Patent EP1572962.
JD515506 - Sequence 496530 from Patent EP1572962.
JD151741 - Sequence 132765 from Patent EP1572962.
JD479942 - Sequence 460966 from Patent EP1572962.
LF323048 - JP 2014500723-A/130551: Polycomb-Associated Non-Coding RNAs.
JD374239 - Sequence 355263 from Patent EP1572962.
JD076194 - Sequence 57218 from Patent EP1572962.
JD437355 - Sequence 418379 from Patent EP1572962.
JD043084 - Sequence 24108 from Patent EP1572962.
JD383473 - Sequence 364497 from Patent EP1572962.
JD190292 - Sequence 171316 from Patent EP1572962.
JD336775 - Sequence 317799 from Patent EP1572962.
MA558624 - JP 2018138019-A/130550: Polycomb-Associated Non-Coding RNAs.
MA558625 - JP 2018138019-A/130551: Polycomb-Associated Non-Coding RNAs.
MA444381 - JP 2018138019-A/16307: Polycomb-Associated Non-Coding RNAs.

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

Protein O00411 (Reactome details) participates in the following event(s):

R-HSA-163296 Association of TFAM:mt promoter complex with POLRMT:TFB2M
R-HSA-2151201 Transcriptional activation of mitochondrial biogenesis
R-HSA-163282 Mitochondrial transcription initiation
R-HSA-1592230 Mitochondrial biogenesis
R-HSA-75944 Transcription from mitochondrial promoters
R-HSA-1852241 Organelle biogenesis and maintenance
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000588649.1, ENST00000588649.2, ENST00000588649.3, ENST00000588649.4, ENST00000588649.5, ENST00000588649.6, NR_176425, O00411, O60370, POLRMT , RPOM_HUMAN, uc326suw.1, uc326suw.2
UCSC ID: ENST00000588649.7_7
RefSeq Accession: NM_005035.4
Protein: O00411 (aka RPOM_HUMAN)

-  Gene Model Information
  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.