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GDPD4 glycerophosphodiester phosphodiesterase domain containing 4 [ Homo sapiens (human) ]

Gene ID: 220032, updated on 3-Apr-2024

Summary

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Official Symbol
GDPD4provided by HGNC
Official Full Name
glycerophosphodiester phosphodiesterase domain containing 4provided by HGNC
Primary source
HGNC:HGNC:24849
See related
Ensembl:ENSG00000178795 AllianceGenome:HGNC:24849
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GDE6
Summary
Predicted to enable metal ion binding activity and phosphoric diester hydrolase activity. Predicted to be involved in lipid metabolic process. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
11q13.5
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (77216558..77301699, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (77149168..77234313, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (76927603..77012731, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene calpain 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76824170-76824764 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76824765-76825360 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76825361-76825954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76837978-76838700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76838701-76839424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76840147-76840870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76842316-76843037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:76851056-76851622 Neighboring gene olfactory marker protein Neighboring gene myosin VIIA Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:76893658-76894158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76902287-76902788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:76902789-76903288 Neighboring gene TOMM20 pseudogene 1 Neighboring gene p21 (RAC1) activated kinase 1 Neighboring gene NANOG hESC enhancer GRCh37_chr11:77106673-77107174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5303 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5304 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:77159760-77160530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5306 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:77184247-77185163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:77189428-77189933 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:77190945-77191449 Neighboring gene Sharpr-MPRA regulatory region 3332

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. Exome sequencing in Thai patients with familial obesity. Kaewsutthi S, et al. Genet Mol Res, 2016 Jul 14. PMID 27421018
  2. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Fasci D, et al. Mol Cell Proteomics, 2018 Oct. PMID 30021884, Free PMC Article
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
  4. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Huttlin EL, et al. Cell, 2021 May 27. PMID 33961781, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

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

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 glycerophosphodiester phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in lipid metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
glycerophosphodiester phosphodiesterase domain-containing protein 4
Names
GDPD domain containing protein
glycerophosphodiester phosphodiesterase 6
ugpQ

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.

mRNA and Protein(s)

  1. NM_182833.3 → NP_878253.1  glycerophosphodiester phosphodiesterase domain-containing protein 4

    See identical proteins and their annotated locations for NP_878253.1

    Status: VALIDATED

    Source sequence(s)
    AP001855, AP002827
    Consensus CDS
    CCDS8249.1
    UniProtKB/Swiss-Prot
    Q6W3E5, Q7Z5B0
    Related
    ENSP00000320815.4, ENST00000315938.5
    Conserved Domains (2) summary
    cd08610
    Location:179 → 491
    GDPD_GDE6; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE6 and similar proteins
    COG0584
    Location:197 → 456
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    77216558..77301699 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011544834.1 → XP_011543136.1  glycerophosphodiester phosphodiesterase domain-containing protein 4 isoform X3

    UniProtKB/Swiss-Prot
    Q6W3E5, Q7Z5B0
    Related
    ENSP00000365390.2, ENST00000376217.6
    Conserved Domains (2) summary
    COG0584
    Location:223 → 482
    UgpQ; Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]
    cl14615
    Location:205 → 517
    PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

  2. XM_047426557.1 → XP_047282513.1  glycerophosphodiester phosphodiesterase domain-containing protein 4 isoform X1

  3. XM_047426558.1 → XP_047282514.1  glycerophosphodiester phosphodiesterase domain-containing protein 4 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    77149168..77234313 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054368018.1 → XP_054223993.1  glycerophosphodiester phosphodiesterase domain-containing protein 4 isoform X3

  2. XM_054368016.1 → XP_054223991.1  glycerophosphodiester phosphodiesterase domain-containing protein 4 isoform X1

  3. XM_054368017.1 → XP_054223992.1  glycerophosphodiester phosphodiesterase domain-containing protein 4 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6W3E5.1 GenPept UniProtKB/Swiss-Prot:Q6W3E5

Gene LinkOut

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

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