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PUDP pseudouridine 5'-phosphatase [ Homo sapiens (human) ]

Gene ID: 8226, updated on 11-Apr-2024

Summary

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Official Symbol
PUDPprovided by HGNC
Official Full Name
pseudouridine 5'-phosphataseprovided by HGNC
Primary source
HGNC:HGNC:16818
See related
Ensembl:ENSG00000130021 MIM:306480; AllianceGenome:HGNC:16818
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GS1; HDHD1; HDHD1A; FAM16AX; DXF68S1E
Summary
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]
Expression
Ubiquitous expression in placenta (RPKM 6.4), colon (RPKM 5.4) and 25 other tissues See more
Orthologs
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Genomic context

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See PUDP in Genome Data Viewer
Location:
Xp22.31
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (6705838..7148153, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (6259733..6701938, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (6966961..7066194, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene S232-VCX3A recombination region Neighboring gene uncharacterized LOC124905240 Neighboring gene variable charge X-linked 3A Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:6582190-6583002 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:6610973-6611531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29381 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:6849955-6850621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:6850622-6851287 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:6876827-6877452 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:6877453-6878076 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:6884751-6885264 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:6894281-6894451 Neighboring gene uncharacterized LOC107987331 Neighboring gene RPS27A pseudogene 17 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:6975911-6976411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:6986912-6987412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:7000180-7000680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:7000681-7001181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:7033895-7034396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:7034397-7034896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29391 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:7154725-7155349 Neighboring gene microRNA 4767 Neighboring gene Sharpr-MPRA regulatory region 5189 Neighboring gene NANOG hESC enhancer GRCh37_chrX:7208639-7209140 Neighboring gene steroid sulfatase Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:7290864-7292063 Neighboring gene NANOG hESC enhancer GRCh37_chrX:7366971-7367514 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:7510918-7511520 Neighboring gene uncharacterized LOC124905241 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:7682068-7682794 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:7682795-7683521 Neighboring gene variable charge X-linked

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. HDHD1, which is often deleted in X-linked ichthyosis, encodes a pseudouridine-5'-phosphatase. Preumont A, et al. Biochem J, 2010 Oct 15. PMID 20722631
  2. Cloning and sequencing of ribosomal protein L27a and a gene similar to human GS1 in Drosophila. Soehnge H, et al. Gene, 1997 Feb 7. PMID 9055824
  3. Isolation of a new gene from the distal short arm of the human X chromosome that escapes X-inactivation. Yen PH, et al. Hum Mol Genet, 1992 Apr. PMID 1284467
  4. The human enamel protein gene amelogenin is expressed from both the X and the Y chromosomes. Salido EC, et al. Am J Hum Genet, 1992 Feb. PMID 1734713, Free PMC Article
  5. Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Suzuki Y, et al. Genome Res, 2001 May. PMID 11337467, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. STS and PUDP Deletion Identified by Targeted Panel Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature Review.
    Title: STS and PUDP Deletion Identified by Targeted Panel Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature Review.
  2. HDHD1 is a phosphatase specifically involved in dephosphorylation of a modified nucleotide present in RNA.
    Title: HDHD1, which is often deleted in X-linked ichthyosis, encodes a pseudouridine-5'-phosphatase.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular_function ND
No biological Data available
more info
  
enables phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables pseudouridine 5'-phosphatase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in nucleotide metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
pseudouridine-5'-phosphatase
Names
5'-PsiMPase
family with sequence similarity 16, member A, X-linked
haloacid dehalogenase-like hydrolase domain containing 1
haloacid dehalogenase-like hydrolase domain containing 1A
haloacid dehalogenase-like hydrolase domain-containing protein 1
haloacid dehalogenase-like hydrolase domain-containing protein 1A
pseudouridine-5'-monophosphatase
NP_001129037.1
NP_001171606.1
NP_001171607.1
NP_036212.3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_021256.2 RefSeqGene

    Range
    5000..104233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001135565.2 → NP_001129037.1  pseudouridine-5'-phosphatase isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC073583, BC012494, DR156836
    Consensus CDS
    CCDS48076.1
    UniProtKB/Swiss-Prot
    Q08623
    Related
    ENSP00000396452.2, ENST00000424830.6
    Conserved Domains (2) summary
    TIGR02009
    Location:11 → 217
    PGMB-YQAB-SF; beta-phosphoglucomutase family hydrolase
    cl21460
    Location:15 → 251
    HAD_like; Haloacid Dehalogenase-like Hydrolases

  2. NM_001178135.2 → NP_001171606.1  pseudouridine-5'-phosphatase isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an alternate 3' exon compared to variant 1. The resulting isoform (c) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC073583, AK300740, DC388394
    Consensus CDS
    CCDS55366.1
    UniProtKB/Swiss-Prot
    Q08623
    Related
    ENSP00000430995.2, ENST00000486446.3
    Conserved Domains (1) summary
    cl21460
    Location:15 → 166
    HAD_like; Haloacid Dehalogenase-like Hydrolases

  3. NM_001178136.2 → NP_001171607.1  pseudouridine-5'-phosphatase isoform d

    See identical proteins and their annotated locations for NP_001171607.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame segment in the CDS compared to variant 1. The resulting isoform (d) lacks an internal segment compared to isoform 1.
    Source sequence(s)
    AC073583, AK300985, BC012494
    Consensus CDS
    CCDS55367.1
    UniProtKB/Swiss-Prot
    Q08623
    Related
    ENSP00000406260.2, ENST00000412827.6
    Conserved Domains (2) summary
    TIGR02009
    Location:11 → 151
    PGMB-YQAB-SF; beta-phosphoglucomutase family hydrolase
    cl21460
    Location:15 → 185
    HAD_like; Haloacid Dehalogenase-like Hydrolases

  4. NM_012080.5 → NP_036212.3  pseudouridine-5'-phosphatase isoform b

    See identical proteins and their annotated locations for NP_036212.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC073583, BC012494, DA653367, DC388394
    Consensus CDS
    CCDS48075.1
    UniProtKB/Swiss-Prot
    B2R7X6, B4DV93, B7Z6Q3, E9PAV8, F5GWZ2, Q08623, Q53F84, Q96EB8
    Related
    ENSP00000370467.6, ENST00000381077.10
    Conserved Domains (2) summary
    TIGR02009
    Location:11 → 194
    PGMB-YQAB-SF; beta-phosphoglucomutase family hydrolase
    cl21460
    Location:15 → 228
    HAD_like; Haloacid Dehalogenase-like Hydrolases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    6705838..7148153 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_007068202.1 RNA Sequence

  2. XR_001755734.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    6259733..6701938 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_008485510.1 RNA Sequence

  2. XR_008485511.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q08623.3 GenPept UniProtKB/Swiss-Prot:Q08623

Gene LinkOut

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