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Aliases for RPUSD1 Gene

Aliases for RPUSD1 Gene

  • RNA Pseudouridylate Synthase Domain Containing 1 2 3 5
  • Ribosomal Large Subunit Pseudouridine Synthase C-Like Protein 3 4
  • C16orf40 3 4
  • RLUCL 3 4
  • RNA Pseudouridylate Synthase Domain-Containing Protein 1 3
  • Chromosome 16 Open Reading Frame 40 2

External Ids for RPUSD1 Gene

Previous HGNC Symbols for RPUSD1 Gene

  • C16orf40

Previous GeneCards Identifiers for RPUSD1 Gene

  • GC16M000779
  • GC16M000834
  • GC16M000756
  • GC16M000802
  • GC16M000822
  • GC16M000841
  • GC16M000866
  • GC16M000871
  • GC16M000904
  • GC16M000921

Summaries for RPUSD1 Gene

GeneCards Summary for RPUSD1 Gene

RPUSD1 (RNA Pseudouridylate Synthase Domain Containing 1) is a Protein Coding gene. Diseases associated with RPUSD1 include Basal Cell Nevus Syndrome. Gene Ontology (GO) annotations related to this gene include RNA binding and pseudouridine synthase activity.

Additional gene information for RPUSD1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPUSD1 Gene

Genomics for RPUSD1 Gene

GeneHancer (GH) Regulatory Elements for RPUSD1 Gene

Promoters and enhancers for RPUSD1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I000787 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 -0.2 -223 2.8 PKNOX1 ARID4B SIN3A ZNF2 ZNF207 ZNF143 FOS SP3 MXD4 REST CHTF18 RPUSD1 GC16M000948 WDR90 CRAMP1 ENSG00000261207 WDR24 ENSG00000260051 MSLN MSLNL
GH16I000323 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 10.3 +462.0 461965 5.3 PKNOX1 CLOCK ARNT NEUROD1 SIN3A FEZF1 ZNF2 YY1 ZNF766 ZNF213 LUC7L WDR90 ENSG00000228779 RHOT2 UBE2I ENSG00000261505 WDR24 JMJD8 ENSG00000262528 TMEM8A
GH16I000709 Enhancer 1.3 Ensembl ENCODE dbSUPER 12.6 +77.9 77896 3 ARID4B SIN3A ZNF2 GLIS2 ZNF213 ZNF143 FOS KLF13 ZNF263 REST ENSG00000259840 FBXL16 CHTF18 RPUSD1 WFIKKN1 ENSG00000262528 ENSG00000279255
GH16I001296 Enhancer 1.5 Ensembl ENCODE dbSUPER 10.3 -510.8 -510787 5.3 HDGF PKNOX1 CLOCK FOXA2 ARID4B NEUROD1 SIN3A ZBTB7B YY1 ZNF766 ENSG00000260710 ENSG00000261505 UBE2I ENSG00000260051 RHOT2 ENSG00000260954 E4F1 BAIAP3 SPSB3 TRAF7
GH16I000635 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 5.1 +151.3 151325 4.1 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 METTL26 GC16P000992 MCRIP2 TRG-CCC2-2 LOC100287175 WFIKKN1 CRAMP1 NARFL ENSG00000269482 ENSG00000268836
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RPUSD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RPUSD1 gene promoter:

Genomic Locations for RPUSD1 Gene

Genomic Locations for RPUSD1 Gene
3,424 bases
Minus strand

Genomic View for RPUSD1 Gene

Genes around RPUSD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPUSD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPUSD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPUSD1 Gene

Proteins for RPUSD1 Gene

  • Protein details for RPUSD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    RNA pseudouridylate synthase domain-containing protein 1
    Protein Accession:
    Secondary Accessions:
    • D3DU66

    Protein attributes for RPUSD1 Gene

    312 amino acids
    Molecular mass:
    34756 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for RPUSD1 Gene

neXtProt entry for RPUSD1 Gene

Post-translational modifications for RPUSD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RPUSD1 Gene

Domains & Families for RPUSD1 Gene

Gene Families for RPUSD1 Gene

Protein Domains for RPUSD1 Gene

Suggested Antigen Peptide Sequences for RPUSD1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the pseudouridine synthase RluA family.
  • Belongs to the pseudouridine synthase RluA family.
genes like me logo Genes that share domains with RPUSD1: view

Function for RPUSD1 Gene

Phenotypes From GWAS Catalog for RPUSD1 Gene

Gene Ontology (GO) - Molecular Function for RPUSD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0003723 RNA binding IEA --
GO:0009982 pseudouridine synthase activity IEA,IBA --
GO:0019239 contributes_to deaminase activity IBA --
genes like me logo Genes that share ontologies with RPUSD1: view

Phenotypes for RPUSD1 Gene

genes like me logo Genes that share phenotypes with RPUSD1: view

Animal Model Products

miRNA for RPUSD1 Gene

miRTarBase miRNAs that target RPUSD1

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPUSD1 Gene

Localization for RPUSD1 Gene

Subcellular locations from

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 RPUSD1 gene
Compartment Confidence
cytosol 3
extracellular 2
nucleus 2
golgi apparatus 2
plasma membrane 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for RPUSD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
genes like me logo Genes that share ontologies with RPUSD1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for RPUSD1 Gene

Pathways & Interactions for RPUSD1 Gene

SuperPathways for RPUSD1 Gene

No Data Available

Interacting Proteins for RPUSD1 Gene

Gene Ontology (GO) - Biological Process for RPUSD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000455 enzyme-directed rRNA pseudouridine synthesis IBA --
GO:0001522 pseudouridine synthesis IEA --
GO:0008150 biological_process ND --
GO:0009451 RNA modification IEA --
GO:0031119 tRNA pseudouridine synthesis IBA --
genes like me logo Genes that share ontologies with RPUSD1: view

No data available for Pathways by source and SIGNOR curated interactions for RPUSD1 Gene

Drugs & Compounds for RPUSD1 Gene

(1) Additional Compounds for RPUSD1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 5-(b-D-Ribofuranosyl)uracil
  • 5-(b-delta-Ribofuranosyl)uracil
  • 5-b-D-Ribofuranosyl-Uracil
  • 5-beta-delta-Ribofuranosyl-Uracil
  • 5-Ribosyluracil
genes like me logo Genes that share compounds with RPUSD1: view

Transcripts for RPUSD1 Gene

Unigene Clusters for RPUSD1 Gene

RNA pseudouridylate synthase domain containing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RPUSD1 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b · 5c · 5d
SP1: - -
SP2: -
SP3: - -
SP4: - -

Relevant External Links for RPUSD1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RPUSD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RPUSD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RPUSD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of RPUSD1 Gene:


SOURCE GeneReport for Unigene cluster for RPUSD1 Gene:


Evidence on tissue expression from TISSUES for RPUSD1 Gene

  • Lung(4.2)
genes like me logo Genes that share expression patterns with RPUSD1: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPUSD1 Gene

Orthologs for RPUSD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RPUSD1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RPUSD1 33 34
  • 98.82 (n)
(Bos Taurus)
Mammalia RPUSD1 33 34
  • 85.5 (n)
(Canis familiaris)
Mammalia RPUSD1 33 34
  • 82.39 (n)
(Rattus norvegicus)
Mammalia Rpusd1 33
  • 80.39 (n)
(Mus musculus)
Mammalia Rpusd1 33 16 34
  • 79.96 (n)
(Monodelphis domestica)
Mammalia RPUSD1 34
  • 67 (a)
(Ornithorhynchus anatinus)
Mammalia RPUSD1 34
  • 63 (a)
(Gallus gallus)
Aves RPUSD1 33 34
  • 70.52 (n)
(Anolis carolinensis)
Reptilia RPUSD1 34
  • 66 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rpusd1 33
  • 63.1 (n)
(Danio rerio)
Actinopterygii rpusd1 33 34
  • 65.39 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004401 33
  • 50.3 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PUS6 34
  • 16 (a)
Species where no ortholog for RPUSD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RPUSD1 Gene

Gene Tree for RPUSD1 (if available)
Gene Tree for RPUSD1 (if available)

Paralogs for RPUSD1 Gene

No data available for Paralogs for RPUSD1 Gene

Variants for RPUSD1 Gene

Sequence variations from dbSNP and Humsavar for RPUSD1 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs193920771 uncertain-significance, Malignant tumor of prostate 786,368(-) T/C/G 3_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1000261081 -- 789,879(-) G/A/T upstream_transcript_variant
rs1001515157 -- 789,743(-) T/G upstream_transcript_variant
rs1001808659 -- 785,547(-) C/A 3_prime_UTR_variant
rs1002088427 -- 784,826(-) G/C downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RPUSD1 Gene

Variant ID Type Subtype PubMed ID
dgv4827n54 CNV loss 21841781
dgv4828n54 CNV gain 21841781
esv2422427 CNV duplication 17116639
esv3637582 CNV gain 21293372
nsv1160325 CNV duplication 26073780
nsv1160326 CNV duplication 26073780
nsv457312 CNV loss 19166990
nsv471063 CNV loss 18288195
nsv517488 CNV loss 19592680
nsv526903 CNV loss 19592680
nsv571040 CNV loss 21841781
nsv571042 CNV loss 21841781
nsv571043 CNV loss 21841781
nsv817712 CNV loss 17921354
nsv9321 CNV gain+loss 18304495
nsv952898 CNV deletion 24416366

Variation tolerance for RPUSD1 Gene

Residual Variation Intolerance Score: 43.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.86; 67.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPUSD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPUSD1 Gene

Disorders for RPUSD1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RPUSD1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
basal cell nevus syndrome
  • bcns
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RPUSD1

genes like me logo Genes that share disorders with RPUSD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RPUSD1 Gene

Publications for RPUSD1 Gene

  1. 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
  2. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58
  3. N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB. (PMID: 22814378) Van Damme P … Aldabe R (Proceedings of the National Academy of Sciences of the United States of America 2012) 4 58
  4. Toward an understanding of the protein interaction network of the human liver. (PMID: 21988832) Wang J … Yang X (Molecular systems biology 2011) 3 58
  5. Transcriptome analysis of human gastric cancer. (PMID: 16341674) Oh JH … Kim NS (Mammalian genome : official journal of the International Mammalian Genome Society 2005) 3 58

Products for RPUSD1 Gene

Sources for RPUSD1 Gene

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