Aliases for TPRKB Gene

Aliases for TPRKB Gene

  • TP53RK Binding Protein 2 3 5
  • EKC/KEOPS Complex Subunit TPRKB 3 4
  • CGI-121 2 3
  • CGI121 2 3
  • PRPK (P53-Related Protein Kinase)-Binding Protein 3
  • TP53RK-Binding Protein 4
  • PRPK-Binding Protein 4
  • GAMOS5 3
  • TPRKB 5

External Ids for TPRKB Gene

Previous GeneCards Identifiers for TPRKB Gene

  • GC02M073869
  • GC02M073955
  • GC02M073691

Summaries for TPRKB Gene

GeneCards Summary for TPRKB Gene

TPRKB (TP53RK Binding Protein) is a Protein Coding gene. Diseases associated with TPRKB include Galloway-Mowat Syndrome 5 and Galloway-Mowat Syndrome. Among its related pathways are Gene Expression and tRNA processing. Gene Ontology (GO) annotations related to this gene include protein kinase binding.

UniProtKB/Swiss-Prot Summary for TPRKB Gene

  • Component of the EKC/KEOPS complex that is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine (PubMed:22912744, PubMed:28805828). The complex is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37 (PubMed:22912744, PubMed:28805828). TPRKB acts as an allosteric effector that regulates the t(6)A activity of the complex. TPRKB is not required for tRNA modification (PubMed:22912744, PubMed:28805828).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TPRKB Gene

Genomics for TPRKB Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TPRKB Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J073736 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 611.2 +0.3 306 2.6 SP1 CREB1 GATAD2A PRDM10 ZNF629 TFE3 ZNF512 SIX5 LEF1 POLR2A TPRKB lnc-TPRKB-1 PCGF1 DUSP11 ENSG00000273245 TTC31 CCDC142 MRPL53 WBP1 INO80B
GH02J073762 Promoter 0.3 EPDnew 600.3 -25.3 -25332 0.1 ENSG00000280037 lnc-DUSP11-1 TPRKB DUSP11 lnc-TPRKB-2
GH02J073776 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 22.9 -41.1 -41095 4.6 HNRNPL CREB1 GATAD2A CTCF PRDM10 ZNF629 TFE3 POLR2A RCOR2 JUND DUSP11 lnc-TPRKB-2 TTC31 TPRKB PCGF1 ENSG00000273245 AUP1 MOGS ALMS1P1 CCDC142
GH02J074454 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 12.4 -719.7 -719695 5.8 ZNF221 SP1 HNRNPL CREB1 GATAD2A PRDM10 ZNF629 TFE3 RFX1 SIX5 WBP1 INO80B PCGF1 CCDC142 DUSP11 ENSG00000273245 TTC31 AUP1 MOGS LBX2
GH02J073699 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 21.5 +35.3 35305 5.8 CEBPG IKZF1 REST SP1 BRD9 HDAC1 CEBPA SCRT2 FOXA2 HDAC2 NAT8 NAT8B lnc-C2orf78-1 TPRKB ALMS1P1 piR-41838-015
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TPRKB on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TPRKB

Top Transcription factor binding sites by QIAGEN in the TPRKB gene promoter:
  • FOXC1
  • FOXO3
  • FOXO3a
  • FOXO3b
  • GATA-1
  • GATA-2
  • GATA-3
  • HFH-1
  • Nkx3-1 v3
  • Nkx3-1 v4

Genomic Locations for TPRKB Gene

Genomic Locations for TPRKB Gene
chr2:73,729,104-73,737,406
(GRCh38/hg38)
Size:
8,303 bases
Orientation:
Minus strand
chr2:73,956,231-73,964,527
(GRCh37/hg19)
Size:
8,297 bases
Orientation:
Minus strand

Genomic View for TPRKB Gene

Genes around TPRKB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TPRKB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TPRKB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TPRKB Gene

Proteins for TPRKB Gene

  • Protein details for TPRKB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y3C4-TPRKB_HUMAN
    Recommended name:
    EKC/KEOPS complex subunit TPRKB
    Protein Accession:
    Q9Y3C4
    Secondary Accessions:
    • D6W5H6
    • Q8IWR6
    • Q8IWR7
    • Q9H3K4

    Protein attributes for TPRKB Gene

    Size:
    175 amino acids
    Molecular mass:
    19661 Da
    Quaternary structure:
    • Component of the EKC/KEOPS complex composed of at least GON7, TP53RK, TPRKB, OSGEP and LAGE3; the whole complex dimerizes (PubMed:22912744, PubMed:28805828). Interacts with TP53RK/PRPK (PubMed:12659830).

    Three dimensional structures from OCA and Proteopedia for TPRKB Gene

    Alternative splice isoforms for TPRKB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TPRKB Gene

Post-translational modifications for TPRKB Gene

  • Ubiquitination at Lys21
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TPRKB Gene

Domains & Families for TPRKB Gene

Gene Families for TPRKB Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for TPRKB Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TPRKB Gene

GenScript: Design optimal peptide antigens:
  • PRPK-binding protein (TPRKB_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y3C4

UniProtKB/Swiss-Prot:

TPRKB_HUMAN :
  • Belongs to the CGI121/TPRKB family.
Family:
  • Belongs to the CGI121/TPRKB family.
genes like me logo Genes that share domains with TPRKB: view

Function for TPRKB Gene

Molecular function for TPRKB Gene

UniProtKB/Swiss-Prot Function:
Component of the EKC/KEOPS complex that is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine (PubMed:22912744, PubMed:28805828). The complex is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37 (PubMed:22912744, PubMed:28805828). TPRKB acts as an allosteric effector that regulates the t(6)A activity of the complex. TPRKB is not required for tRNA modification (PubMed:22912744, PubMed:28805828).

Phenotypes From GWAS Catalog for TPRKB Gene

Gene Ontology (GO) - Molecular Function for TPRKB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0019901 protein kinase binding IPI 12659830
genes like me logo Genes that share ontologies with TPRKB: view
genes like me logo Genes that share phenotypes with TPRKB: view

Human Phenotype Ontology for TPRKB Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TPRKB

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TPRKB Gene

Localization for TPRKB Gene

Subcellular locations from UniProtKB/Swiss-Prot for TPRKB Gene

Cytoplasm, cytosol. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TPRKB gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 2
cytoskeleton 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TPRKB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000408 EKC/KEOPS complex IDA 27903914
GO:0005634 nucleus IEA,IDA 12659830
GO:0005737 cytoplasm IEA,IDA 28805828
GO:0005829 cytosol IEA,IDA 12659830
genes like me logo Genes that share ontologies with TPRKB: view

Pathways & Interactions for TPRKB Gene

PathCards logo

SuperPathways for TPRKB Gene

genes like me logo Genes that share pathways with TPRKB: view

Pathways by source for TPRKB Gene

Gene Ontology (GO) - Biological Process for TPRKB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002949 tRNA threonylcarbamoyladenosine modification IDA 28805828
GO:0008033 tRNA processing IEA --
genes like me logo Genes that share ontologies with TPRKB: view

No data available for SIGNOR curated interactions for TPRKB Gene

Drugs & Compounds for TPRKB Gene

No Compound Related Data Available

Transcripts for TPRKB Gene

mRNA/cDNA for TPRKB Gene

8 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TPRKB

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TPRKB Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c · 6d ^ 7a · 7b · 7c · 7d · 7e ^ 8a · 8b · 8c · 8d ^ 9
SP1: - - - - - -
SP2: - - - -
SP3: - - - - - - - -
SP4: - - - - - - - - - - - -
SP5: - - - - - - - -
SP6: - - - -
SP7: - - - - -
SP8: - - - - - - -
SP9: -
SP10: -
SP11: - - - - - -
SP12: - - - - - -
SP13:
SP14: - - - - - - - -
SP15: - - - -
SP16: - - -
SP17: - - -
SP18: - - - - -

Relevant External Links for TPRKB Gene

GeneLoc Exon Structure for
TPRKB

Expression for TPRKB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TPRKB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Liver (Hepatobiliary System)

Protein differential expression in normal tissues from HIPED for TPRKB Gene

This gene is overexpressed in NK cells (6.2) and Spleen (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TPRKB Gene



Protein tissue co-expression partners for TPRKB Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TPRKB

SOURCE GeneReport for Unigene cluster for TPRKB Gene:

Hs.157401

mRNA Expression by UniProt/SwissProt for TPRKB Gene:

Q9Y3C4-TPRKB_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for TPRKB Gene

  • Nervous system(4.5)
  • Kidney(2.3)
  • Skin(2)
genes like me logo Genes that share expression patterns with TPRKB: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TPRKB Gene

Orthologs for TPRKB Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TPRKB Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TPRKB 30 31
  • 99.55 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TPRKB 30 31
  • 92.57 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TPRKB 30 31
  • 91.81 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Tprkb 30
  • 86.86 (n)
Mouse
(Mus musculus)
Mammalia Tprkb 30 17 31
  • 86.1 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TPRKB 31
  • 77 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TPRKB 31
  • 48 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TPRKB 30 31
  • 73.56 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TPRKB 31
  • 68 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tprkb 30
  • 71.1 (n)
MGC75657 30
African clawed frog
(Xenopus laevis)
Amphibia MGC53277 30
Zebrafish
(Danio rerio)
Actinopterygii tprkb 30 31
  • 64.94 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.1574 30
Worm
(Caenorhabditis elegans)
Secernentea W03F8.4 30 31
  • 48.84 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CGI121 31 33
  • 29 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT4G34412 30
  • 46.67 (n)
Rice
(Oryza sativa)
Liliopsida Os01g0142200 30
  • 47.47 (n)
Species where no ortholog for TPRKB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for TPRKB Gene

ENSEMBL:
Gene Tree for TPRKB (if available)
TreeFam:
Gene Tree for TPRKB (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TPRKB: view image

Paralogs for TPRKB Gene

Pseudogenes.org Pseudogenes for TPRKB Gene

genes like me logo Genes that share paralogs with TPRKB: view

No data available for Paralogs for TPRKB Gene

Variants for TPRKB Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TPRKB Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
764552 Benign: not provided 73,730,611(-) C/T SYNONYMOUS_VARIANT
rs1233885358 Pathogenic: GALLOWAY-MOWAT SYNDROME 5. Galloway-Mowat syndrome 5 (GAMOS5) [MIM:617731] 73,730,025(-) T/Cp.Tyr149Cys MISSENSE_VARIANT
rs1553433412 Pathogenic: GALLOWAY-MOWAT SYNDROME 5. Galloway-Mowat syndrome 5 (GAMOS5) [MIM:617731] 73,730,594(-) A/Gp.Leu136Pro MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for TPRKB Gene

Structural Variations from Database of Genomic Variants (DGV) for TPRKB Gene

Variant ID Type Subtype PubMed ID
dgv3870n100 CNV gain 25217958
esv2759060 CNV gain 17122850
nsv1003153 CNV loss 25217958
nsv834260 CNV gain 17160897

Variation tolerance for TPRKB Gene

Residual Variation Intolerance Score: 57.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.59; 12.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TPRKB Gene

Human Gene Mutation Database (HGMD)
TPRKB
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TPRKB

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TPRKB Gene

Disorders for TPRKB Gene

MalaCards: The human disease database

(8) MalaCards diseases for TPRKB Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
galloway-mowat syndrome 5
  • gamos5
galloway-mowat syndrome
  • microcephaly, hiatal hernia, and nephrotic syndrome
galloway-mowat syndrome 1
  • gamos1
bladder calculus
  • urinary bladder calculi
galloway-mowat syndrome 2
- elite association - COSMIC cancer census association via MalaCards
Search TPRKB in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TPRKB_HUMAN
  • Galloway-Mowat syndrome 5 (GAMOS5) [MIM:617731]: A form of Galloway-Mowat syndrome, a severe renal-neurological disease characterized by early-onset nephrotic syndrome associated with microcephaly, central nervous system abnormalities, developmental delays, and a propensity for seizures. Brain anomalies include gyration defects ranging from lissencephaly to pachygyria and polymicrogyria, and cerebellar hypoplasia. Most patients show facial dysmorphism characterized by a small, narrow forehead, large/floppy ears, deep-set eyes, hypertelorism and micrognathia. Additional variable features are visual impairment and arachnodactyly. Most patients die in early childhood. {ECO:0000269 PubMed:28805828}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with TPRKB: view

No data available for Genatlas for TPRKB Gene

Publications for TPRKB Gene

  1. Identification of CGI-121, a novel PRPK (p53-related protein kinase)-binding protein. (PMID: 12659830) Miyoshi A … Ueda N (Biochemical and biophysical research communications 2003) 2 3 4
  2. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4
  3. Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7. (PMID: 27903914) Wan LC … Sicheri F (Nucleic acids research 2017) 3 4
  4. Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly. (PMID: 28805828) Braun DA … Hildebrandt F (Nature genetics 2017) 3 4
  5. The human EKC/KEOPS complex is recruited to Cullin2 ubiquitin ligases by the human tumour antigen PRAME. (PMID: 22912744) Costessi A … Stunnenberg HG (PloS one 2012) 3 4

Products for TPRKB Gene

Sources for TPRKB Gene