Human Gene TOP1MT (uc011lkf.2)
  Description: Homo sapiens topoisomerase (DNA) I, mitochondrial (TOP1MT), transcript variant 3, mRNA.
RefSeq Summary (NM_001258447): This gene encodes a mitochondrial DNA topoisomerase that plays a role in the modification of DNA topology. The encoded protein is a type IB topoisomerase and catalyzes the transient breaking and rejoining of DNA to relieve tension and DNA supercoiling generated in the mitochondrial genome during replication and transcription. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012].
Transcript (Including UTRs)
   Position: hg19 chr8:144,391,556-144,407,648 Size: 16,093 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr8:144,391,892-144,407,571 Size: 15,680 Coding Exon Count: 9 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:144,391,556-144,407,648)mRNA (may differ from genome)Protein (477 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsH-INV
HGNCLynxMGIPubMedUniProtKB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TOP1MT
CDC HuGE Published Literature: TOP1MT

-  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: 9.01 RPKM in Testis
Total median expression: 149.49 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 -23.2077-0.301 Picture PostScript Text
3' UTR -137.80336-0.410 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
IPR011010 - DNA_brk_join_enz
IPR001631 - TopoI
IPR018521 - TopoI_AS
IPR025834 - TopoI_C_dom
IPR014711 - TopoI_cat_a-hlx-sub_euk
IPR014727 - TopoI_cat_a/b-sub_euk
IPR013500 - TopoI_cat_euk
IPR008336 - TopoI_DNA-bd_euk
IPR013030 - TopoI_DNA-bd_mixed-a/b_euk
IPR013499 - TopoI_euk
IPR009054 - TopoI_insert_euk

Pfam Domains:
PF01028 - Eukaryotic DNA topoisomerase I, catalytic core
PF02919 - Eukaryotic DNA topoisomerase I, DNA binding fragment
PF14370 - C-terminal topoisomerase domain

SCOP Domains:
46596 - Eukaryotic DNA topoisomerase I, dispensable insert domain
56349 - DNA breaking-rejoining enzymes
56741 - Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment

ModBase Predicted Comparative 3D Structure on B4E061
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 orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003917 DNA topoisomerase type I activity
GO:0016853 isomerase activity

Biological Process:
GO:0006265 DNA topological change

Cellular Component:
GO:0005694 chromosome


-  Descriptions from all associated GenBank mRNAs
  AK316380 - Homo sapiens cDNA, FLJ79279 complete cds, highly similar to DNA topoisomerase I, mitochondrial precursor(EC 5.99.1.2).
AK302372 - Homo sapiens cDNA FLJ50294 complete cds, highly similar to DNA topoisomerase I, mitochondrial precursor (EC 5.99.1.2).
BC027453 - Homo sapiens topoisomerase (DNA) I, mitochondrial, mRNA (cDNA clone IMAGE:4499637), partial cds.
BC071914 - Homo sapiens topoisomerase (DNA) I, mitochondrial, mRNA (cDNA clone MGC:88595 IMAGE:6372930), complete cds.
BC044646 - Homo sapiens topoisomerase (DNA) I, mitochondrial, mRNA (cDNA clone IMAGE:5478964), partial cds.
BC052285 - Homo sapiens topoisomerase (DNA) I, mitochondrial, mRNA (cDNA clone MGC:59993 IMAGE:5443410), complete cds.
AF349017 - Homo sapiens topoisomerase I mRNA, complete cds; nuclear gene for mitochondrial product.
LF385048 - JP 2014500723-A/192551: Polycomb-Associated Non-Coding RNAs.
AK315913 - Homo sapiens cDNA, FLJ78812 complete cds, highly similar to DNA topoisomerase I, mitochondrial precursor (EC 5.99.1.2).
AK311647 - Homo sapiens cDNA, FLJ18689.
AK303237 - Homo sapiens cDNA FLJ51170 complete cds, highly similar to DNA topoisomerase I, mitochondrial precursor (EC 5.99.1.2).
AK308475 - Homo sapiens cDNA, FLJ98516.
AK309005 - Homo sapiens cDNA, FLJ99046.
LF337050 - JP 2014500723-A/144553: Polycomb-Associated Non-Coding RNAs.
MA620625 - JP 2018138019-A/192551: Polycomb-Associated Non-Coding RNAs.
MA572627 - JP 2018138019-A/144553: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK303237, B4E061, B4E061_HUMAN
UCSC ID: uc011lkf.2
RefSeq Accession: NM_001258447
Protein: B4E061

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK303237.1
exon count: 9CDS single in 3' UTR: no RNA size: 1900
ORF size: 1434CDS single in intron: no Alignment % ID: 99.79
txCdsPredict score: 2755.00frame shift in genome: no % Coverage: 81.32
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 682# 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.