Gdpd5 glycerophosphodiester phosphodiesterase domain containing 5 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Gdpd5provided by MGI
Official Full Name: glycerophosphodiester phosphodiesterase domain containing 5provided by MGI
Primary source: MGI:MGI:2686926
See related: Ensembl:ENSMUSG00000035314 AllianceGenome:MGI:2686926
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Gde2
Summary: Enables glycerophosphocholine phosphodiesterase activity. Involved in negative regulation of Notch signaling pathway and positive regulation of cell cycle. Acts upstream of or within neuron differentiation; positive regulation of neuron differentiation; and regulation of timing of cell differentiation. Located in several cellular components, including axon; neuronal cell body; and perinuclear endoplasmic reticulum. Is expressed in several structures, including nervous system and neural retina. Orthologous to human GDPD5 (glycerophosphodiester phosphodiesterase domain containing 5). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in ovary adult (RPKM 14.1), whole brain E14.5 (RPKM 14.1) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 E1; 7 54.07 cM

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (99027976..99111082)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (99381463..99461875)

Chromosome 7 - NC_000073.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of GDE2 leads to complex behavioral changes including memory impairment.
Title: Loss of GDE2 leads to complex behavioral changes including memory impairment.
GDE2 expression in oligodendroglia regulates the pace of oligodendrocyte maturation.
Title: GDE2 expression in oligodendroglia regulates the pace of oligodendrocyte maturation.
GDE2-Dependent Activation of Canonical Wnt Signaling in Neurons Regulates Oligodendrocyte Maturation.
Title: GDE2-Dependent Activation of Canonical Wnt Signaling in Neurons Regulates Oligodendrocyte Maturation.
GDE2 is essential for neuronal survival in the postnatal mammalian spinal cord
Title: GDE2 is essential for neuronal survival in the postnatal mammalian spinal cord.
posttranslational modifications increase glycerophosphocholine by inhibiting GDPD5 phosphodiesterase.
Title: High NaCl- and urea-induced posttranslational modifications that increase glycerophosphocholine by inhibiting GDPD5 phosphodiesterase.
a key role for Gde2 in controlling cortical neuronal fates by regulating the timing of neurogenesis, and loss of Gde2 uncovers additional mechanisms that trigger remaining neuronal progenitors to differentiate at the end of the neurogenic period.
Title: Gde2 regulates cortical neuronal identity by controlling the timing of cortical progenitor differentiation.
Data suggest that neuronal GDE2 controls motor neuron subtype diversity through a non-cell-autonomous feedback mechanism that directly regulates progenitor cell differentiation.
Title: GDE2 regulates subtype-specific motor neuron generation through inhibition of Notch signaling.
Study identified the antioxidant enzyme Prdx1 as an interactor of GDE2 and uncover a developmental role for Prdx1 in regulating neuronal differentiation in the spinal cord.
Title: The antioxidant enzyme Prdx1 controls neuronal differentiation by thiol-redox-dependent activation of GDE2.
GDPD5 is a glycerophosphocholine phosphodiesterase that osmotically regulates the osmoprotective organic osmolyte glycerophosphocholine.
Title: GDPD5 is a glycerophosphocholine phosphodiesterase that osmotically regulates the osmoprotective organic osmolyte GPC.
These results demonstrate that GDE2 expression during neuronal differentiation plays an important role for growing neurites.
Title: Involvement of membrane protein GDE2 in retinoic acid-induced neurite formation in Neuro2A cells.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (4) 1 citation
Endonuclease-mediated (1)

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables glycerophosphocholine phosphodiesterase activity	EXP Inferred from Experiment more info	PubMed
enables glycerophosphocholine phosphodiesterase activity	IDA Inferred from Direct Assay more info	PubMed
enables glycerophosphodiester phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables glycerophosphodiester phosphodiesterase activity	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol phospholipase C activity	IEA Inferred from Electronic Annotation more info
enables phosphoric diester hydrolase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of Notch signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebral cortex neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in lipid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of Notch signaling pathway	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of Notch signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of Notch signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of timing of cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spinal cord motor neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: glycerophosphodiester phosphodiesterase domain-containing protein 5

Names: glycerophosphocholine phosphodiesterase GDPD5; glycerophosphodiester phosphodiesterase 2; phosphoinositide phospholipase C GDPD5

NP_001349095.1

EC 3.1.4.11

EC 3.1.4.2

NP_001349096.1

EC 3.1.4.11

EC 3.1.4.2

NP_001349097.1

EC 3.1.4.11

EC 3.1.4.2

NP_958740.2

EC 3.1.4.11

EC 3.1.4.2

XP_006507696.1

EC 3.1.4.11

EC 3.1.4.2

XP_006507697.1

EC 3.1.4.11

EC 3.1.4.2

XP_006507698.1

EC 3.1.4.11

EC 3.1.4.2

XP_006507700.1

EC 3.1.4.11

EC 3.1.4.2

XP_006507702.1

EC 3.1.4.11

EC 3.1.4.2

XP_011240040.1

EC 3.1.4.11

EC 3.1.4.2

XP_030098348.1

EC 3.1.4.11

EC 3.1.4.2

XP_030098349.1

EC 3.1.4.11

EC 3.1.4.2

XP_036008885.1

EC 3.1.4.11

EC 3.1.4.2

XP_036008886.1

EC 3.1.4.11

EC 3.1.4.2

XP_036008887.1

EC 3.1.4.11

EC 3.1.4.2

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_001362166.1 → NP_001349095.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 1

Status: VALIDATED

Source sequence(s)

AC115858, AC158748

Consensus CDS

CCDS21481.1

UniProtKB/Swiss-Prot

Q640M6, Q8R0T5, Q8R3N5

Conserved Domains (1) summary

cl14615
Location:227 → 576

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
NM_001362167.1 → NP_001349096.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 2

Status: VALIDATED

Source sequence(s)

AC115858, AC158748

Consensus CDS

CCDS90276.1

UniProtKB/TrEMBL

A0A1L1STK0

Related

ENSMUSP00000150361.2, ENSMUST00000213887.2

Conserved Domains (1) summary

cl14615
Location:227 → 581

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
NM_001362168.1 → NP_001349097.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 3

Status: VALIDATED

Source sequence(s)

AC115858, AC158748

Conserved Domains (1) summary

cl14615
Location:170 → 524

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
NM_201352.3 → NP_958740.2 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform 1

See identical proteins and their annotated locations for NP_958740.2

Status: VALIDATED

Source sequence(s)

AC115858, AK141189, BC082585, CO039911

Consensus CDS

CCDS21481.1

UniProtKB/Swiss-Prot

Q640M6, Q8R0T5, Q8R3N5

Related

ENSMUSP00000036175.9, ENSMUST00000037528.10

Conserved Domains (1) summary

cl14615
Location:227 → 576

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000073.7 Reference GRCm39 C57BL/6J

Range

99027976..99111082

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011241738.3 → XP_011240040.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

See identical proteins and their annotated locations for XP_011240040.1

UniProtKB/TrEMBL

A0A1L1STK0

Conserved Domains (1) summary

cl14615
Location:227 → 581

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_036152992.1 → XP_036008885.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X2

UniProtKB/Swiss-Prot

Q640M6, Q8R0T5, Q8R3N5

Conserved Domains (1) summary

cl14615
Location:227 → 576

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_006507634.3 → XP_006507697.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

See identical proteins and their annotated locations for XP_006507697.1

UniProtKB/TrEMBL

A0A1L1STK0

Conserved Domains (1) summary

cl14615
Location:227 → 581

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_006507633.3 → XP_006507696.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X1

See identical proteins and their annotated locations for XP_006507696.1

UniProtKB/TrEMBL

A0A1L1STK0

Conserved Domains (1) summary

cl14615
Location:227 → 581

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_006507635.3 → XP_006507698.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X3

Conserved Domains (1) summary

cl14615
Location:207 → 561

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_036152993.1 → XP_036008886.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X4

Conserved Domains (1) summary

cl14615
Location:170 → 519

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_030242488.2 → XP_030098348.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X5

Conserved Domains (1) summary

cl14615
Location:150 → 504

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_006507637.3 → XP_006507700.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X6

Conserved Domains (1) summary

cl14615
Location:148 → 502

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_036152994.1 → XP_036008887.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X7

Conserved Domains (1) summary

cl14615
Location:148 → 497

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_030242489.2 → XP_030098349.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X8

Conserved Domains (1) summary

cl14615
Location:128 → 482

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily
XM_006507639.3 → XP_006507702.1 glycerophosphodiester phosphodiesterase domain-containing protein 5 isoform X9

Conserved Domains (1) summary

cl14615
Location:227 → 316

PI-PLCc_GDPD_SF; Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily