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Aliases for TSR3 Gene

Aliases for TSR3 Gene

  • TSR3, Acp Transferase Ribosome Maturation Factor 2 3 5
  • C16orf42 3 4
  • TSR3, 20S RRNA Accumulation, Homolog (S. Cerevisiae) 2
  • Probable Ribosome Biogenesis Protein C16orf42 3
  • Ribosome Biogenesis Protein TSR3 Homolog 3
  • TSR3, 20S RRNA Accumulation, Homolog 3
  • Chromosome 16 Open Reading Frame 42 2
  • UND313L 4

External Ids for TSR3 Gene

Previous HGNC Symbols for TSR3 Gene

  • C16orf42

Previous GeneCards Identifiers for TSR3 Gene

  • GC16M001400
  • GC16M001401
  • GC16M001402
  • GC16M001403

Summaries for TSR3 Gene

GeneCards Summary for TSR3 Gene

TSR3 (TSR3, Acp Transferase Ribosome Maturation Factor) is a Protein Coding gene. Among its related pathways are Gene Expression and rRNA processing in the nucleus and cytosol.

UniProtKB/Swiss-Prot for TSR3 Gene

  • Probable pre-rRNA processing protein involved in ribosome biogenesis.

Gene Wiki entry for TSR3 Gene

Additional gene information for TSR3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TSR3 Gene

Genomics for TSR3 Gene

GeneHancer (GH) Regulatory Elements for TSR3 Gene

Promoters and enhancers for TSR3 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
GH16I001350 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +0.2 209 2.6 MLX ARNT ARID4B SIN3A YY1 ZNF207 ZNF143 FOS CEBPZ ZHX2 GNPTG TSR3 WDR90 ENSG00000261505 TELO2 CRAMP1 BAIAP3 JMJD8 ENSG00000260954 NUBP2
GH16I001377 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 12.9 -26.9 -26930 3.3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 POLR2B ZNF766 CBX5 UNKL CCDC154 GNPTG TSR3 CHTF18 TMEM204 IFT140 BAIAP3 JPT2 GC16P001373
GH16I001296 Enhancer 1.5 Ensembl ENCODE dbSUPER 11.9 +52.7 52727 5.3 HDGF PKNOX1 CLOCK FOXA2 ARID4B NEUROD1 SIN3A ZBTB7B YY1 ZNF766 ENSG00000260710 ENSG00000261505 UBE2I ENSG00000260051 RHOT2 ENSG00000260954 E4F1 BAIAP3 SPSB3 TRAF7
GH16I001413 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 8.1 -63.4 -63434 4.2 ATF1 ARID4B SIN3A ZNF2 ZBTB7B ZNF48 ZNF121 GLIS2 ZNF213 ZNF143 GC16M001479 GC16M001482 GC16P001415 PIR48812 PIR62325 UNKL CCDC154 GNPTG LOC106660606 LMF1
GH16I001271 Enhancer 1.1 ENCODE 11 +80.1 80085 1.6 PKNOX1 SMAD1 SIN3A FEZF1 ZNF2 ZNF213 ZNF302 ZNF416 KLF13 SP3 CRAMP1 WDR90 IFT140 TELO2 ENSG00000260646 TSC2 ENSG00000261505 E4F1 WDR24 ENSG00000260051
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TSR3 on UCSC Golden Path with GeneCards custom track

Genomic Locations for TSR3 Gene

Genomic Locations for TSR3 Gene
chr16:1,349,240-1,351,911
(GRCh38/hg38)
Size:
2,672 bases
Orientation:
Minus strand
chr16:1,399,241-1,401,912
(GRCh37/hg19)

Genomic View for TSR3 Gene

Genes around TSR3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TSR3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TSR3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TSR3 Gene

Proteins for TSR3 Gene

  • Protein details for TSR3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UJK0-TSR3_HUMAN
    Recommended name:
    Ribosome biogenesis protein TSR3 homolog
    Protein Accession:
    Q9UJK0
    Secondary Accessions:
    • Q6PJT8

    Protein attributes for TSR3 Gene

    Size:
    312 amino acids
    Molecular mass:
    33596 Da
    Quaternary structure:
    No Data Available

neXtProt entry for TSR3 Gene

Post-translational modifications for TSR3 Gene

  • Ubiquitination at posLast=103103, posLast=136136, and isoforms=192
  • Modification sites at PhosphoSitePlus

Other Protein References for TSR3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TSR3 Gene

Domains & Families for TSR3 Gene

Gene Families for TSR3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for TSR3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UJK0

UniProtKB/Swiss-Prot:

TSR3_HUMAN :
  • Belongs to the TSR3 family.
Family:
  • Belongs to the TSR3 family.
genes like me logo Genes that share domains with TSR3: view

Function for TSR3 Gene

Molecular function for TSR3 Gene

UniProtKB/Swiss-Prot Function:
Probable pre-rRNA processing protein involved in ribosome biogenesis.

Gene Ontology (GO) - Molecular Function for TSR3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016740 transferase activity EXP 27084949
genes like me logo Genes that share ontologies with TSR3: view

Phenotypes for TSR3 Gene

genes like me logo Genes that share phenotypes with TSR3: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for TSR3 Gene

Localization for TSR3 Gene

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 TSR3 gene
Compartment Confidence
cytosol 5
plasma membrane 1
extracellular 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TSR3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with TSR3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for TSR3 Gene

Pathways & Interactions for TSR3 Gene

genes like me logo Genes that share pathways with TSR3: view

Gene Ontology (GO) - Biological Process for TSR3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000154 rRNA modification TAS --
GO:0006364 rRNA processing IEA --
GO:0030490 maturation of SSU-rRNA IBA --
GO:0042254 ribosome biogenesis IEA --
genes like me logo Genes that share ontologies with TSR3: view

No data available for SIGNOR curated interactions for TSR3 Gene

Drugs & Compounds for TSR3 Gene

No Compound Related Data Available

Transcripts for TSR3 Gene

mRNA/cDNA for TSR3 Gene

Unigene Clusters for TSR3 Gene

TSR3, 20S rRNA accumulation, homolog (S. cerevisiae):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TSR3 Gene

No ASD Table

Relevant External Links for TSR3 Gene

GeneLoc Exon Structure for
TSR3
ECgene alternative splicing isoforms for
TSR3

Expression for TSR3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TSR3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TSR3 Gene

This gene is overexpressed in Adrenal (50.7) and Peripheral blood mononuclear cells (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TSR3 Gene



Protein tissue co-expression partners for TSR3 Gene

NURSA nuclear receptor signaling pathways regulating expression of TSR3 Gene:

TSR3

SOURCE GeneReport for Unigene cluster for TSR3 Gene:

Hs.134846

Evidence on tissue expression from TISSUES for TSR3 Gene

  • Lung(4.3)
  • Bone marrow(4.2)
  • Muscle(2.1)
  • Nervous system(2.1)
genes like me logo Genes that share expression patterns with TSR3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TSR3 Gene

Orthologs for TSR3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TSR3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TSR3 33 34
  • 98.57 (n)
cow
(Bos Taurus)
Mammalia TSR3 33
  • 84.94 (n)
C25H16ORF42 34
  • 82 (a)
OneToOne
dog
(Canis familiaris)
Mammalia TSR3 33 34
  • 83.45 (n)
rat
(Rattus norvegicus)
Mammalia Tsr3 33
  • 81.39 (n)
mouse
(Mus musculus)
Mammalia Tsr3 33 16 34
  • 80.04 (n)
oppossum
(Monodelphis domestica)
Mammalia TSR3 34
  • 65 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TSR3 34
  • 64 (a)
OneToOne
chicken
(Gallus gallus)
Aves C14H16ORF42 33 34
  • 60.83 (n)
lizard
(Anolis carolinensis)
Reptilia TSR3 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tsr3 33
  • 57.95 (n)
zebrafish
(Danio rerio)
Actinopterygii tsr3 33 34
  • 59.58 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4338 33 34
  • 55.34 (n)
worm
(Caenorhabditis elegans)
Secernentea F52C12.2 33 34
  • 51.01 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TSR3 34 36
  • 35 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G10070 33
  • 50.97 (n)
rice
(Oryza sativa)
Liliopsida Os03g0195200 33
  • 50.46 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
OneToOne
Species where no ortholog for TSR3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 TSR3 Gene

ENSEMBL:
Gene Tree for TSR3 (if available)
TreeFam:
Gene Tree for TSR3 (if available)

Paralogs for TSR3 Gene

No data available for Paralogs for TSR3 Gene

Variants for TSR3 Gene

Sequence variations from dbSNP and Humsavar for TSR3 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1016193943 uncertain-significance, Mucolipidosis, Type III Gamma 1,351,924(-) G/C upstream_transcript_variant
rs1041664887 uncertain-significance, Mucolipidosis, Type III Gamma 1,351,906(-) C/T upstream_transcript_variant
rs28654239 likely-benign, Mucolipidosis, Type III Gamma 1,351,894(-) G/A/C upstream_transcript_variant
rs541284873 uncertain-significance, Mucolipidosis, Type III Gamma 1,351,926(-) C/A upstream_transcript_variant
rs547624231 uncertain-significance, Mucolipidosis, Type III Gamma 1,352,116(-) G/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for TSR3 Gene

Variant ID Type Subtype PubMed ID
dgv2692n100 CNV gain 25217958
esv2422427 CNV duplication 17116639
esv2762143 CNV gain 21179565
nsv1046314 CNV loss 25217958
nsv428316 CNV gain+loss 18775914
nsv471066 CNV loss 18288195
nsv952899 CNV deletion 24416366
nsv974746 CNV duplication 23825009

Variation tolerance for TSR3 Gene

Residual Variation Intolerance Score: 37.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.49; 28.96% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TSR3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TSR3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TSR3 Gene

Disorders for TSR3 Gene

Additional Disease Information for TSR3

No disorders were found for TSR3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TSR3 Gene

Publications for TSR3 Gene

  1. Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans. (PMID: 27084949) Meyer B … Entian KD (Nucleic acids research 2016) 2 3 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. The sequence and analysis of duplication-rich human chromosome 16. (PMID: 15616553) Martin J … Pennacchio LA (Nature 2004) 3 4 58
  4. Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. (PMID: 11157797) Daniels RJ … Higgs DR (Human molecular genetics 2001) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for TSR3 Gene

Sources for TSR3 Gene

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