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    GDE1 glycerophosphodiester phosphodiesterase 1 [ Homo sapiens (human) ]

    Gene ID: 51573, updated on 10-Dec-2024

    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 membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Dec 2024]
    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

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    See GDE1 in Genome Data Viewer
    Location:
    16p12.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (19501693..19522098, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (19432571..19452970, complement)
    RS_2024_09 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: 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. Genomic organization, characterization, and molecular 3D model of GDE1, a novel mammalian glycerophosphoinositol phosphodiesterase. Bachmann AS, et al. Gene, 2006 Apr 12. PMID 16472945
    2. 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
    3. Micro-RNA-15a and micro-RNA-16 expression and chromosome 13 deletions in multiple myeloma. Corthals SL, et al. Leuk Res, 2010 May. PMID 20031211
    4. miR-15a/16 inhibits TGF-beta3/VEGF signaling and increases retinal endothelial cell barrier proteins. Ye EA, et al. Vision Res, 2017 Oct. PMID 28774775, Free PMC Article
    5. TYRP1 mRNA goes fishing for miRNAs in melanoma. Soengas MS, et al. Nat Cell Biol, 2017 Oct 31. PMID 29087386

    See all (45) 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)

    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_2024_08

    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

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

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