GDE1 glycerophosphodiester phosphodiesterase 1 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 16p12.3

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (19501693..19522098, complement)
110	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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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-HT4 receptor signalling and correlate with symptom profile in irritable bowel syndrome.
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.
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.
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.
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.
The mRNA of TYRP1 is now found to sequester the tumour suppressor miR-16.
Title: TYRP1 mRNA goes fishing for miRNAs in melanoma.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH78973 (e-PCR)
- UniSTS:50970

SHGC-61116 (e-PCR)
- UniSTS:71988

RH93458 (e-PCR)
- UniSTS:91872

SHGC-60880 (e-PCR)
- UniSTS:63486

Homology

Homologs of the GDE1 gene: The GDE1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, and frog.
Orthologs from Annotation Pipeline: 461 organisms have orthologs with human gene GDE1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables glycerophosphodiester phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	PubMed
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	PubMed
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	PubMed
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	PubMed
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

EC 3.1.4.44

NP_001310996.1

EC 3.1.4.44

NP_057725.1

EC 3.1.4.44

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)

NM_001324066.2 → NP_001310995.1 glycerophosphodiester phosphodiesterase 1 isoform 2

Status: VALIDATED

Source sequence(s)

AC003108, AC012621, AC130456

UniProtKB/TrEMBL

A0A024QYU1

Conserved Domains (1) summary

cd08573
Location:1 → 213

GDPD_GDE1; Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE1 and similar proteins
NM_001324067.2 → NP_001310996.1 glycerophosphodiester phosphodiesterase 1 isoform 3

Status: VALIDATED

Source sequence(s)

AC003108, AC012621, AC130456

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
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

Q7KYR4, Q9NZC3

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