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GDE1 glycerophosphodiester phosphodiesterase 1 [ Homo sapiens (human) ]

Gene ID: 51573, updated on 23-Nov-2023

Summary

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Official Symbol
GDE1provided by HGNC
Official Full Name
glycerophosphodiester phosphodiesterase 1provided by HGNC
Primary source
HGNC:HGNC:29644
See related
Ensembl:ENSG00000006007 MIM:605943; AllianceGenome:HGNC:29644
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
MIR16; 363E6.2
Summary
Predicted to enable glycerophosphodiester phosphodiesterase activity; glycerophosphoinositol glycerophosphodiesterase activity; and lysophospholipase activity. Predicted to be involved in N-acylethanolamine metabolic process; ethanolamine metabolic process; and phospholipid metabolic process. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in colon (RPKM 28.1), fat (RPKM 25.8) and 25 other tissues See more
Orthologs
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Genomic context

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See GDE1 in Genome Data Viewer
Location:
16p12.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (19501693..19522098, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (19432571..19452970, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (19513015..19533420, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene transmembrane channel like 5 Neighboring gene uncharacterized LOC124903659 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19499330-19500018 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:19507832-19508043 Neighboring gene RNA, U4 small nuclear 46, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:19532887-19533621 Neighboring gene centriolar coiled-coil protein 110 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19566659-19567621 Neighboring gene VPS35 endosomal protein sorting factor like Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:19620544-19621743 Neighboring gene NANOG hESC enhancer GRCh37_chr16:19673654-19674240 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:19698132-19698632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19710103-19710758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:19710759-19711413

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. Puerarin Inhibits Proliferation and Induces Apoptosis by Upregulation of miR-16 in Bladder Cancer Cell Line T24. Liu X, et al. Oncol Res, 2018 Sep 14. PMID 29422113, Free PMC Article
  2. Genomic organization, characterization, and molecular 3D model of GDE1, a novel mammalian glycerophosphoinositol phosphodiesterase. Bachmann AS, et al. Gene, 2006 Apr 12. PMID 16472945
  3. Downregulation of exosomal let-7d and miR-16 in idiopathic pulmonary fibrosis. Lacedonia D, et al. BMC Pulm Med, 2021 Jun 4. PMID 34088304, Free PMC Article
  4. Solanine inhibits proliferation and promotes apoptosis of the human leukemia cells by targeting the miR-16/Bcl-2 axis. Zheng Y, et al. J BUON, 2020 May-Jun. PMID 32862612
  5. miR-15a/miR-16 cluster inhibits invasion of prostate cancer cells by suppressing TGF-β signaling pathway. Jin W, et al. Biomed Pharmacother, 2018 Aug. PMID 29803177

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Downregulation of exosomal let-7d and miR-16 in idiopathic pulmonary fibrosis.
    Title: Downregulation of exosomal let-7d and miR-16 in idiopathic pulmonary fibrosis.
  2. Solanine inhibits proliferation and promotes apoptosis of the human leukemia cells by targeting the miR-16/Bcl-2 axis.
    Title: Solanine inhibits proliferation and promotes apoptosis of the human leukemia cells by targeting the miR-16/Bcl-2 axis.
  3. Long Noncoding RNA DLX6-AS1 Promotes the Progression in Cervical Cancer by Targeting miR-16-5p/ARPP19 Axis.
    Title: Long Noncoding RNA DLX6-AS1 Promotes the Progression in Cervical Cancer by Targeting miR-16-5p/ARPP19 Axis.
  4. this study shows that HTR$ gene expression regulation is affected by mir-16 and mir-103 single nucleotide polymorphisms
    Title: miR-16 and miR-103 impact 5-HT(4) receptor signalling and correlate with symptom profile in irritable bowel syndrome.
  5. Sera samples from inflammatory bowel disease (IBD) patients showed higher level of miR-16, miR-21, and miR-223, but not miR-155, compared to controls and was higher in Crohn's disease (CD) than in ulcerative colitis (UC) patients.
    Title: Circulating and Fecal microRNAs as Biomarkers for Inflammatory Bowel Diseases.
  6. Study demonstrated that puerarin could inhibit cell proliferation, promote cell apoptosis, and deactivate NF-kappaB signaling pathway via upregulation of miR-16 in T24 cells
    Title: Puerarin Inhibits Proliferation and Induces Apoptosis by Upregulation of miR-16 in Bladder Cancer Cell Line T24.
  7. MiR15a/16 inhibited the components of TGF-beta signaling pathways.
    Title: miR-15a/miR-16 cluster inhibits invasion of prostate cancer cells by suppressing TGF-β signaling pathway.
  8. Our outcomes suggest that miR-15a/16 maintain the retinal endothelial cell barrier by reducing TGFbeta3/VEGF signaling and increasing levels of key tight junction proteins.
    Title: miR-15a/16 inhibits TGF-beta3/VEGF signaling and increases retinal endothelial cell barrier proteins.
  9. The mRNA of TYRP1 is now found to sequester the tumour suppressor miR-16.
    Title: TYRP1 mRNA goes fishing for miRNAs in melanoma.
  10. we identified cyclin J and far upstream element-binding protein 1 (FUBP1) as novel miR-16 targets, which mediate miR-16 antiproliferative effects.
    Title: MiR-16 mediates trastuzumab and lapatinib response in ErbB-2-positive breast and gastric cancer via its novel targets CCNJ and FUBP1.
Submit: New GeneRIF Correction See all GeneRIFs (23)

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 glycerophosphodiester phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycerophosphodiester phosphodiesterase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables glycerophosphodiester phosphodiesterase activity TAS
Traceable Author Statement
more info
 PubMed 
enables glycerophosphoinositol glycerophosphodiesterase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables glycerophosphoinositol glycerophosphodiesterase activity TAS
Traceable Author Statement
more info
  
enables lysophospholipase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in N-acylethanolamine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in N-acylethanolamine metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in ethanolamine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ethanolamine metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in glycerophospholipid catabolic process TAS
Traceable Author Statement
more info
  
involved_in lipid metabolic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in phospholipid metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phospholipid metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
glycerophosphodiester phosphodiesterase 1
Names
RGS16-interacting membrane protein
glycerophosphoinositol glycerophosphodiesterase GDE1
lysophospholipase D GDE1
membrane interacting protein of RGS16
NP_001310995.1
NP_001310996.1
NP_057725.1

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_001324066.2 → NP_001310995.1  glycerophosphodiester phosphodiesterase 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC003108, AC012621, AC130456
    Conserved Domains (1) summary
    cd08573
    Location:1 → 213
    GDPD_GDE1; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE1 and similar proteins

  2. NM_001324067.2 → NP_001310996.1  glycerophosphodiester phosphodiesterase 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC003108, AC012621, AC130456
    UniProtKB/TrEMBL
    B2R7B1
    Conserved Domains (2) summary
    cd08573
    Location:68 → 292
    GDPD_GDE1; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE1 and similar proteins
    pfam03009
    Location:70 → 275
    GDPD; Glycerophosphoryl diester phosphodiesterase family

  3. NM_016641.4 → NP_057725.1  glycerophosphodiester phosphodiesterase 1 isoform 1

    See identical proteins and their annotated locations for NP_057725.1

    Status: VALIDATED

    Source sequence(s)
    AF306698, BC012153, BQ897064
    Consensus CDS
    CCDS10578.1
    UniProtKB/Swiss-Prot
    O43334, Q6PKF7, Q7KYR4, Q9NZC3
    UniProtKB/TrEMBL
    B2R7B1
    Related
    ENSP00000261386.3, ENST00000353258.8
    Conserved Domains (1) summary
    cd08573
    Location:68 → 323
    GDPD_GDE1; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE1 and similar proteins

RNA

  1. NR_136689.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC003108, AC012621, AC130456

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    19501693..19522098 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    19432571..19452970 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NZC3.1 GenPept UniProtKB/Swiss-Prot:Q9NZC3

Gene LinkOut

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