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

    Gene ID: 8226, updated on 10-Dec-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (6705838..7148153, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (6259733..6701938, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 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. STS and PUDP Deletion Identified by Targeted Panel Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature Review. Park J, et al. Genes (Basel), 2023 Oct 10. PMID 37895274, Free PMC Article
    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. 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
    5. 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

    See all (19) 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)

    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 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 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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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