Human Gene TOP2B (ENST00000264331.9_7) from GENCODE V47lift37
  Description: DNA topoisomerase II beta, transcript variant 1 (from RefSeq NM_001330700.2)
Gencode Transcript: ENST00000264331.9_7
Gencode Gene: ENSG00000077097.17_21
Transcript (Including UTRs)
   Position: hg19 chr3:25,639,475-25,706,398 Size: 66,924 Total Exon Count: 36 Strand: -
Coding Region
   Position: hg19 chr3:25,639,798-25,705,788 Size: 65,991 Coding Exon Count: 36 

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 (chr3:25,639,475-25,706,398)mRNA (may differ from genome)Protein (1626 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TOP2B_HUMAN
DESCRIPTION: RecName: Full=DNA topoisomerase 2-beta; EC=5.99.1.3; AltName: Full=DNA topoisomerase II, beta isozyme;
FUNCTION: Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Indirectly involved in vitamin D- coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR- mediated transrepression of the CYP27B1 gene.
CATALYTIC ACTIVITY: ATP-dependent breakage, passage and rejoining of double-stranded DNA.
SUBUNIT: Homodimer. Component of the WINAC complex, at least composed of SMARCA2, SMARCA4, SMARCB1, SMARCC1, SMARCC2, SMARCD1, SMARCE1, ACTL6A, BAZ1B/WSTF, ARID1A, SUPT16H, CHAF1A and TOP2B.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
MISCELLANEOUS: Eukaryotic topoisomerase I and II can relax both negative and positive supercoils, whereas prokaryotic enzymes relax only negative supercoils.
SIMILARITY: Belongs to the type II topoisomerase family.
SIMILARITY: Contains 1 Toprim domain.

-  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: TOP2B
Diseases sorted by gene-association score: non-functioning pancreatic endocrine tumor (4)

-  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: 55.35 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 1323.39 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 -339.60610-0.557 Picture PostScript Text
3' UTR -51.70323-0.160 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
IPR024946 - Arg_repress_C-like
IPR003594 - ATPase-like_ATP-bd
IPR012542 - DTHCT
IPR020568 - Ribosomal_S5_D2-typ_fold
IPR014721 - Ribosomal_S5_D2-typ_fold_subgr
IPR001241 - Topo_IIA
IPR002205 - Topo_IIA_A/C
IPR013758 - Topo_IIA_A/C_ab
IPR013757 - Topo_IIA_A_a
IPR013759 - Topo_IIA_B/N_ab
IPR013506 - Topo_IIA_bsu_dom2
IPR013760 - Topo_IIA_cen
IPR018522 - TopoIIA_CS
IPR006171 - Toprim_domain

Pfam Domains:
PF00204 - DNA gyrase B
PF00521 - DNA gyrase/topoisomerase IV, subunit A
PF01751 - Toprim domain
PF02518 - Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
PF08070 - DTHCT (NUC029) region
PF16898 - C-terminal associated domain of TOPRIM

SCOP Domains:
55874 - ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
54211 - Ribosomal protein S5 domain 2-like
56719 - Type II DNA topoisomerase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3QX3 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q02880
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 orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003916 DNA topoisomerase activity
GO:0003918 DNA topoisomerase type II (ATP-hydrolyzing) activity
GO:0005080 protein kinase C binding
GO:0005524 ATP binding
GO:0008022 protein C-terminus binding
GO:0016853 isomerase activity
GO:0019899 enzyme binding
GO:0042826 histone deacetylase binding
GO:0043021 ribonucleoprotein complex binding
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity
GO:0061505 DNA topoisomerase II activity

Biological Process:
GO:0000712 resolution of meiotic recombination intermediates
GO:0000819 sister chromatid segregation
GO:0001764 neuron migration
GO:0006259 DNA metabolic process
GO:0006265 DNA topological change
GO:0007409 axonogenesis
GO:0030900 forebrain development
GO:0044774 mitotic DNA integrity checkpoint

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:1990904 ribonucleoprotein complex
GO:0000792 heterochromatin
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  LF209941 - JP 2014500723-A/17444: Polycomb-Associated Non-Coding RNAs.
LP895460 - Sequence 324 from Patent EP3253886.
BC157118 - Synthetic construct Homo sapiens clone IMAGE:100063468, MGC:190784 topoisomerase (DNA) II beta 180kDa (TOP2B) mRNA, encodes complete protein.
X68060 - H.sapiens topIIb mRNA for topoisomerase IIb.
BC156330 - Synthetic construct Homo sapiens clone IMAGE:100061836, MGC:190111 topoisomerase (DNA) II beta 180kDa (TOP2B) mRNA, encodes complete protein.
AK296510 - Homo sapiens cDNA FLJ55300 partial cds, highly similar to DNA topoisomerase 2-beta (EC 5.99.1.3).
AK307450 - Homo sapiens cDNA, FLJ97398.
Z15111 - H.sapiens TOP2 mRNA for DNA topoisomerase II (partial).
MA445518 - JP 2018138019-A/17444: Polycomb-Associated Non-Coding RNAs.
U54831 - Human topoisomerase IIb mRNA, partial cds.
BC021863 - Homo sapiens, clone IMAGE:4999541, mRNA, partial cds.
AK297171 - Homo sapiens cDNA FLJ50986 complete cds, highly similar to DNA topoisomerase 2-beta (EC 5.99.1.3).
Z15115 - H.sapiens TOP2 mRNA for DNA topoisomerase II (partial).
AB208879 - Homo sapiens mRNA for DNA topoisomerase II, beta isozyme variant protein.
AK316492 - Homo sapiens cDNA, FLJ79391 complete cds, highly similar to DNA topoisomerase 2-beta (EC 5.99.1.3).
JD548584 - Sequence 529608 from Patent EP1572962.
JD046879 - Sequence 27903 from Patent EP1572962.
LF332953 - JP 2014500723-A/140456: Polycomb-Associated Non-Coding RNAs.
LF332952 - JP 2014500723-A/140455: Polycomb-Associated Non-Coding RNAs.
X53662 - H.sapiens mRNA for DNA topoisomerase II.
LF332951 - JP 2014500723-A/140454: Polycomb-Associated Non-Coding RNAs.
LF332950 - JP 2014500723-A/140453: Polycomb-Associated Non-Coding RNAs.
BC054482 - Homo sapiens topoisomerase (DNA) II beta 180kDa, mRNA (cDNA clone IMAGE:6725385), containing frame-shift errors.
LF332949 - JP 2014500723-A/140452: Polycomb-Associated Non-Coding RNAs.
LF332948 - JP 2014500723-A/140451: Polycomb-Associated Non-Coding RNAs.
LF332947 - JP 2014500723-A/140450: Polycomb-Associated Non-Coding RNAs.
M27504 - Homo sapiens topoisomerase type II (Topo II) mRNA, partial cds.
LF332946 - JP 2014500723-A/140449: Polycomb-Associated Non-Coding RNAs.
LF332945 - JP 2014500723-A/140448: Polycomb-Associated Non-Coding RNAs.
LF332942 - JP 2014500723-A/140445: Polycomb-Associated Non-Coding RNAs.
LF332941 - JP 2014500723-A/140444: Polycomb-Associated Non-Coding RNAs.
LF332940 - JP 2014500723-A/140443: Polycomb-Associated Non-Coding RNAs.
LF332938 - JP 2014500723-A/140441: Polycomb-Associated Non-Coding RNAs.
LF332934 - JP 2014500723-A/140437: Polycomb-Associated Non-Coding RNAs.
LF332933 - JP 2014500723-A/140436: Polycomb-Associated Non-Coding RNAs.
LF332932 - JP 2014500723-A/140435: Polycomb-Associated Non-Coding RNAs.
LF332930 - JP 2014500723-A/140433: Polycomb-Associated Non-Coding RNAs.
LF332929 - JP 2014500723-A/140432: Polycomb-Associated Non-Coding RNAs.
MA568530 - JP 2018138019-A/140456: Polycomb-Associated Non-Coding RNAs.
MA568529 - JP 2018138019-A/140455: Polycomb-Associated Non-Coding RNAs.
MA568528 - JP 2018138019-A/140454: Polycomb-Associated Non-Coding RNAs.
MA568527 - JP 2018138019-A/140453: Polycomb-Associated Non-Coding RNAs.
MA568526 - JP 2018138019-A/140452: Polycomb-Associated Non-Coding RNAs.
MA568525 - JP 2018138019-A/140451: Polycomb-Associated Non-Coding RNAs.
MA568524 - JP 2018138019-A/140450: Polycomb-Associated Non-Coding RNAs.
MA568523 - JP 2018138019-A/140449: Polycomb-Associated Non-Coding RNAs.
MA568522 - JP 2018138019-A/140448: Polycomb-Associated Non-Coding RNAs.
MA568519 - JP 2018138019-A/140445: Polycomb-Associated Non-Coding RNAs.
MA568518 - JP 2018138019-A/140444: Polycomb-Associated Non-Coding RNAs.
MA568517 - JP 2018138019-A/140443: Polycomb-Associated Non-Coding RNAs.
MA568515 - JP 2018138019-A/140441: Polycomb-Associated Non-Coding RNAs.
MA568511 - JP 2018138019-A/140437: Polycomb-Associated Non-Coding RNAs.
MA568510 - JP 2018138019-A/140436: Polycomb-Associated Non-Coding RNAs.
MA568509 - JP 2018138019-A/140435: Polycomb-Associated Non-Coding RNAs.
MA568507 - JP 2018138019-A/140433: Polycomb-Associated Non-Coding RNAs.
MA568506 - JP 2018138019-A/140432: Polycomb-Associated Non-Coding RNAs.
LF332927 - JP 2014500723-A/140430: Polycomb-Associated Non-Coding RNAs.
HZ409324 - JP 2015528002-A/1921: CHIRAL CONTROL.
HZ459713 - WO 2015182781-A/416: Kit or device and method for detecting pancreatic cancer.
HZ460816 - WO 2015190584-A/313: Kit or device and method for detecting prostate cancer.
HZ461442 - WO 2015190586-A/255: Kit and method for detecting colon cancer.
HZ462308 - WO 2015190591-A/463: Kit and method for detecting breast cancer.
HZ463163 - WO 2015194535-A/257: Kit and method for detecting stomach cancer.
HZ463797 - WO 2015194610-A/233: Kit and method for detecting lung cancer.
HZ464619 - WO 2015194615-A/437: Kit or device and method for detecting hepatic cancer.
HZ465251 - WO 2015194627-A/304: Kit and method for detecting esophageal cancer.
LG052658 - KR 1020150036642-A/1924: CHIRAL CONTROL.
LY481153 - KR 1020170010856-A/416: PANCREATIC CANCER DETECTION KIT, DEVICE, AND DETECTION METHOD.
LY496434 - KR 1020170018406-A/304: ESOPHAGEAL CANCER DETECTION KIT OR DEVICE, AND DETECTION METHOD.
LY497085 - KR 1020170016485-A/255: COLORECTAL CANCER DETECTION KIT OR DEVICE, AND DETECTION METHOD.
LY497698 - KR 1020170018409-A/233: KIT OR DEVICE FOR DETECTING LUNG CANCER, AND LUNG CANCER DETECTION METHOD.
LY498520 - KR 1020170018411-A/437: LIVER CANCER DETECTION KIT OR DEVICE, AND DETECTION METHOD.
LY499311 - KR 1020170018412-A/463: BREAST CANCER DETECTION KIT OR DEVICE, AND METHOD FOR DETECTING BREAST CANCER.
LY499976 - KR 1020170019425-A/257: STOMACH CANCER DETECTION KIT OR DEVICE, AND DETECTION METHOD.
LY500689 - KR 1020170016490-A/313: PROSTATE CANCER DETECTION KIT OR DEVICE, AND DETECTION METHOD.
LZ238724 - WO 2017171048-A/385: Kit, device and method for detecting early pancreatic cancer or precancerous lesion of pancreas.
MS869608 - Sequence 313 from Patent EP3156483.
MS880626 - Sequence 463 from Patent EP3156498.
MS884272 - Sequence 255 from Patent EP3156499.
MS885095 - Sequence 257 from Patent EP3156503.
MS994442 - Sequence 304 from Patent EP3159406.
MS996764 - Sequence 233 from Patent EP3159416.
MA568504 - JP 2018138019-A/140430: Polycomb-Associated Non-Coding RNAs.
MA822747 - WO 2019004436-A/560: Kit, device, and method for detection of lung cancer.
LY616488 - KR 1020180129785-A/385: KIT OR DEVICE FOR DETECTING EARLY STAGE PANCREATIC CANCER OR PANCREATIC CANCER PRECURSOR LESIONS AND DETECTION METHOD THEREFOR.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_vdrPathway - Control of Gene Expression by Vitamin D Receptor
h_DNAfragmentPathway - Apoptotic DNA fragmentation and tissue homeostasis

Reactome (by CSHL, EBI, and GO)

Protein Q02880 (Reactome details) participates in the following event(s):

R-HSA-4641345 SUMOylation of TOP2B with SUMO1
R-HSA-4615885 SUMOylation of DNA replication proteins
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-2990846 SUMOylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000264331.1, ENST00000264331.2, ENST00000264331.3, ENST00000264331.4, ENST00000264331.5, ENST00000264331.6, ENST00000264331.7, ENST00000264331.8, NM_001330700, Q02880, Q13600, Q9UMG8, Q9UQP8, TOP2B_HUMAN, uc317hri.1, uc317hri.2
UCSC ID: ENST00000264331.9_7
RefSeq Accession: NM_001330700.2
Protein: Q02880 (aka TOP2B_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.