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Aliases for PUDP Gene

Aliases for PUDP Gene

  • Pseudouridine 5'-Phosphatase 2
  • Pseudouridine 5-Phosphatase 2 3 5
  • Haloacid Dehalogenase-Like Hydrolase Domain-Containing Protein 1A 3 4
  • Haloacid Dehalogenase-Like Hydrolase Domain-Containing Protein 1 3 4
  • Haloacid Dehalogenase-Like Hydrolase Domain Containing 1A 2 3
  • Haloacid Dehalogenase-Like Hydrolase Domain Containing 1 2 3
  • Family With Sequence Similarity 16, Member A, X-Linked 2 3
  • Pseudouridine-5-Monophosphatase 3 4
  • 5-PsiMPase 3 4
  • DXF68S1E 3 4
  • FAM16AX 3 4
  • HDHD1A 3 4
  • HDHD1 3 4
  • GS1 3 4
  • Pseudouridine-5-Phosphatase 3
  • Protein GS1 4
  • EC 3.1.3.96 4

External Ids for PUDP Gene

Previous HGNC Symbols for PUDP Gene

  • FAM16AX
  • HDHD1A
  • HDHD1

Summaries for PUDP Gene

Entrez Gene Summary for PUDP Gene

  • This gene encodes a member of the haloacid dehalogenase-like (HAD) hydrolase superfamily. The encoded protein has no known biological function. This gene has a pseudogene on chromosome 1. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2010]

GeneCards Summary for PUDP Gene

PUDP (Pseudouridine 5'-Phosphatase) is a Protein Coding gene. Among its related pathways are Metabolism and Purine metabolism.

UniProtKB/Swiss-Prot for PUDP Gene

  • Dephosphorylates pseudouridine 5-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine.

Gene Wiki entry for PUDP Gene

Additional gene information for PUDP Gene

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

Genomics for PUDP Gene

Regulatory Elements for PUDP Gene

Enhancers for PUDP Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XH007131 1.4 Ensembl ENCODE dbSUPER 11.7 +15.5 15482 2 HDAC1 NFIB SIN3A BRCA1 RAD21 RFX5 TCF12 GATA2 ZNF143 FOS PUDP GC0XM007135 ENSG00000228550
GH0XH007108 1.4 Ensembl ENCODE dbSUPER 11 +38.1 38145 3 HDGF PKNOX1 ARNT RAD21 TCF12 ATF7 ETV6 RUNX3 CREM IKZF2 PUDP ENSG00000228550 GC0XP007028
GH0XH007119 1.3 Ensembl ENCODE dbSUPER 11.6 +27.3 27265 2 SOX13 FOXA2 NFIB FEZF1 EBF1 CEBPG RARA ATF7 GATAD2A SMARCE1 PUDP ENSG00000228550 GC0XM007135
GH0XH007145 1.5 Ensembl ENCODE dbSUPER 9.1 +0.9 880 3 HDGF PKNOX1 ATF1 SIN3A YY1 ZNF766 ELK1 ZNF143 ZNF207 ATF7 PUDP MIR4767 STS
GH0XH007085 1.2 Ensembl ENCODE dbSUPER 11.2 +61.8 61826 1 PKNOX1 TBL1XR1 ELF1 DPF2 EGR1 IKZF1 EED ETV6 MLLT1 RUNX3 PUDP ENSG00000228550 GC0XP007028
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PUDP on UCSC Golden Path with GeneCards custom track

Promoters for PUDP Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000244039 190 2001 HDGF PKNOX1 SIN3A YY1 ZNF766 ELK1 ZNF207 ATF7 RUNX3 SMARCA4

Genomic Location for PUDP Gene

Chromosome:
X
Start:
7,048,920 bp from pter
End:
7,148,190 bp from pter
Size:
99,271 bases
Orientation:
Minus strand

Genomic View for PUDP Gene

Genes around PUDP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PUDP Gene

Proteins for PUDP Gene

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

    Protein Symbol:
    Q08623-HDHD1_HUMAN
    Recommended name:
    Pseudouridine-5-phosphatase
    Protein Accession:
    Q08623
    Secondary Accessions:
    • B2R7X6
    • B4DV93
    • B7Z6Q3
    • E9PAV8
    • F5GWZ2
    • Q53F84
    • Q96EB8

    Protein attributes for PUDP Gene

    Size:
    228 amino acids
    Molecular mass:
    25249 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAA58622.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH12494.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAD97125.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAG35973.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PUDP Gene

    Alternative splice isoforms for PUDP Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PUDP Gene

Post-translational modifications for PUDP Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PUDP Gene

Domains & Families for PUDP Gene

Protein Domains for PUDP Gene

Suggested Antigen Peptide Sequences for PUDP Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q08623

UniProtKB/Swiss-Prot:

HDHD1_HUMAN :
  • Belongs to the HAD-like hydrolase superfamily. CbbY/CbbZ/Gph/YieH family.
Family:
  • Belongs to the HAD-like hydrolase superfamily. CbbY/CbbZ/Gph/YieH family.
genes like me logo Genes that share domains with PUDP: view

Function for PUDP Gene

Molecular function for PUDP Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.38 uM for 5-PsiMP {ECO:0000269 PubMed:20722631}; KM=1.5 mM for 3-AMP {ECO:0000269 PubMed:20722631}; KM=5.9 mM for Fructose-6-P {ECO:0000269 PubMed:20722631}; KM=9.4 mM for 5-UMP {ECO:0000269 PubMed:20722631};
UniProtKB/Swiss-Prot CatalyticActivity:
Pseudouridine 5-phosphate + H(2)O = pseudouridine + phosphate.
UniProtKB/Swiss-Prot Function:
Dephosphorylates pseudouridine 5-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine.
UniProtKB/Swiss-Prot Induction:
Inhibited by low concentrations of calcium.

Enzyme Numbers (IUBMB) for PUDP Gene

Gene Ontology (GO) - Molecular Function for PUDP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0016787 hydrolase activity TAS --
GO:0016791 phosphatase activity IBA --
GO:0046872 metal ion binding IEA --
GO:1990738 pseudouridine 5-phosphatase activity IEA --
genes like me logo Genes that share ontologies with PUDP: view

Phenotypes for PUDP Gene

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

Animal Model Products

CRISPR Products

miRNA for PUDP Gene

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PUDP
  • Applied Biological Materials Clones for PUDP
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PUDP Gene

Localization for PUDP 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 PUDP gene
Compartment Confidence
extracellular 5
cytosol 5
mitochondrion 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PUDP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with PUDP: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for PUDP Gene

Pathways & Interactions for PUDP Gene

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

Pathways by source for PUDP Gene

Gene Ontology (GO) - Biological Process for PUDP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008150 biological_process ND --
GO:0008152 metabolic process IEA --
GO:0009117 nucleotide metabolic process IEA --
GO:0016311 dephosphorylation IEA --
GO:0043097 pyrimidine nucleoside salvage TAS --
genes like me logo Genes that share ontologies with PUDP: view

No data available for SIGNOR curated interactions for PUDP Gene

Drugs & Compounds for PUDP Gene

(2) Drugs for PUDP Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pseudouridine
  • 5-(b-D-Ribofuranosyl)uracil
  • 5-(b-delta-Ribofuranosyl)uracil
  • 5-b-D-Ribofuranosyl-Uracil
  • 5-beta-delta-Ribofuranosyl-Uracil
  • 5-Ribosyluracil
1445-07-4
genes like me logo Genes that share compounds with PUDP: view

Transcripts for PUDP Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PUDP
  • Applied Biological Materials Clones for PUDP
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

No ASD Table

Relevant External Links for PUDP Gene

GeneLoc Exon Structure for
PUDP
ECgene alternative splicing isoforms for
PUDP

Expression for PUDP Gene

NURSA nuclear receptor signaling pathways regulating expression of PUDP Gene:

PUDP

Evidence on tissue expression from TISSUES for PUDP Gene

  • Nervous system(4.6)
  • Intestine(4.2)
  • Blood(4.1)
No Expression Related Data Available

Primer Products

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PUDP Gene

Orthologs for PUDP Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PUDP Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia HDHD1 33 34
  • 83.19 (n)
cow
(Bos Taurus)
Mammalia HDHD1A 34
  • 79 (a)
OneToOne
HDHD1 33
  • 77.78 (n)
rat
(Rattus norvegicus)
Mammalia Hdhd1 33
  • 75.19 (n)
mouse
(Mus musculus)
Mammalia Hdhd1a 33 34
  • 74.92 (n)
Pudp 16
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 65 (a)
OneToMany
-- 34
  • 62 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia HDHD1 34
  • 63 (a)
OneToOne
chicken
(Gallus gallus)
Aves HDHD1 33 34
  • 70.1 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 62 (a)
OneToMany
-- 34
  • 53 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia hdhd1 33
  • 67.6 (n)
Str.11029 33
zebrafish
(Danio rerio)
Actinopterygii hdhd1 33 34
  • 66.2 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5250 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003372 33
  • 59.09 (n)
fruit fly
(Drosophila melanogaster)
Insecta Gs1l 33 34
  • 58.18 (n)
CG31924 34
  • 43 (a)
OneToMany
CG5565 34
  • 40 (a)
OneToMany
CG5561 34
  • 22 (a)
OneToMany
CG5556 34
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea R151.10 34
  • 42 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 34
  • 33 (a)
OneToOne
-- 36
thale cress
(Arabidopsis thaliana)
eudicotyledons GPP1 33
  • 53.54 (n)
rice
(Oryza sativa)
Liliopsida Os08g0243600 33
  • 55.01 (n)
wheat
(Triticum aestivum)
Liliopsida Ta.6535 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 49 (a)
OneToOne
Species where no ortholog for PUDP 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • 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)

Evolution for PUDP Gene

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

Paralogs for PUDP Gene

Pseudogenes.org Pseudogenes for PUDP Gene

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

No data available for Paralogs for PUDP Gene

Variants for PUDP Gene

Sequence variations from dbSNP and Humsavar for PUDP Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs1000001688 -- 6,870,976(+) GGGAT(A/T)ACAGG intron-variant
rs1000002216 -- 6,884,782(+) CTGCA(G/T)AAGTT intron-variant
rs1000017707 -- 7,039,530(+) AAGAG(A/G)AGATG intron-variant
rs1000018923 -- 7,127,530(+) TTTAA(C/G)AAATG intron-variant
rs1000053282 -- 6,789,057(+) AGCTG(A/G)GGCAG intron-variant

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

Variant ID Type Subtype PubMed ID
esv3309109 CNV mobile element insertion 20981092
esv3395909 CNV insertion 20981092
esv3573508 CNV loss 25503493
esv3573510 CNV loss 25503493
esv3576734 CNV gain 25503493
esv3576753 CNV gain 25503493

Variation tolerance for PUDP Gene

Residual Variation Intolerance Score: 62.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.15; 84.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PUDP Gene

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

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

Disorders for PUDP Gene

Relevant External Links for PUDP

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PUDP
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PUDP

No disorders were found for PUDP Gene.

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

Publications for PUDP Gene

  1. HDHD1, which is often deleted in X-linked ichthyosis, encodes a pseudouridine-5'-phosphatase. (PMID: 20722631) Preumont A … Van Schaftingen E (The Biochemical journal 2010) 2 3 4 60
  2. Isolation of a new gene from the distal short arm of the human X chromosome that escapes X-inactivation. (PMID: 1284467) Yen PH … Shapiro L (Human molecular genetics 1992) 2 3 4 60
  3. 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 60
  4. Cloning and sequencing of ribosomal protein L27a and a gene similar to human GS1 in Drosophila. (PMID: 9055824) Soehnge H … Stern M (Gene 1997) 3 22 60
  5. The human enamel protein gene amelogenin is expressed from both the X and the Y chromosomes. (PMID: 1734713) Salido EC … Shapiro LJ (American journal of human genetics 1992) 2 3 60

Products for PUDP Gene

  • Addgene plasmids for PUDP

Sources for PUDP Gene

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