Plxnd1 plexin D1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Plxnd1provided by MGI
Official Full Name: plexin D1provided by MGI
Primary source: MGI:MGI:2154244
See related: Ensembl:ENSMUSG00000030123 AllianceGenome:MGI:2154244
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: b2b553Clo; b2b1863Clo; 6230425C21Rik
Summary: Enables semaphorin receptor activity. Involved in several processes, including endothelial cell migration; semaphorin-plexin signaling pathway; and synapse assembly. Acts upstream of or within several processes, including circulatory system development; dichotomous subdivision of terminal units involved in salivary gland branching; and positive regulation of protein binding activity. Is integral component of plasma membrane. Is expressed in several structures, including cardiovascular system; genitourinary system; liver; nervous system; and spleen. Used to study DiGeorge syndrome. Orthologous to human PLXND1 (plexin D1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in thymus adult (RPKM 164.2), adrenal adult (RPKM 135.5) and 20 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 E3; 6 53.72 cM

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (115931772..115972300, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (115954811..115995339, complement)

Chromosome 6 - NC_000072.7 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?

Association of PLXND1 with a novel subtype of anomalous pulmonary venous return.
Title: Association of PLXND1 with a novel subtype of anomalous pulmonary venous return.
Vascular Sema3E-Plexin-D1 Signaling Reactivation Promotes Post-stroke Recovery through VEGF Downregulation in Mice.
Title: Vascular Sema3E-Plexin-D1 Signaling Reactivation Promotes Post-stroke Recovery through VEGF Downregulation in Mice.
PlexinD1 Deficiency in Lung Interstitial Macrophages Exacerbates House Dust Mite-Induced Allergic Asthma.
Title: PlexinD1 Deficiency in Lung Interstitial Macrophages Exacerbates House Dust Mite-Induced Allergic Asthma.
plexin D1 (PLXND1) has a role in mechanosensation and mechanically induced disease pathogenesis; results establish a previously undescribed mechanosensor in endothelial cells that regulates cardiovascular pathophysiology, and provide a mechanism by which a single receptor can exhibit a binary biochemical nature
Title: The guidance receptor plexin D1 is a mechanosensor in endothelial cells.
Results describe new roles of Sema3E/PlexinD1 signaling during development and in adult hippocampal formation and provide evidence for an implication of Sema3E/PlexinD1 in the layer-specific development of the entorhino-hippocampal connection.
Title: New functions of Semaphorin 3E and its receptor PlexinD1 during developing and adult hippocampal formation.
Authors found that the PlexinD1 cleavage product binds to actin rods, pathological aggregate-like structures which had so far been described for age-related neurodegenerative diseases. Data suggest a novel disease mechanism for SMA involving formation of actin rods as a molecular sink for a cleaved PlexinD1 fragment leading to dysregulation of receptor signaling.
Title: Metalloprotease-mediated cleavage of PlexinD1 and its sequestration to actin rods in the motoneuron disease spinal muscular atrophy (SMA).
GIPC1 forms a domain-swapped dimer in an autoinhibited conformation that hinders binding of both PlexinD1 and myosin VI. PlexinD1 binding to GIPC1 releases the autoinhibition, promoting its interaction with myosin VI. GIPCs and myosin VI interact through two distinct interfaces and form an open-ended alternating array.
Title: Structure analyses reveal a regulated oligomerization mechanism of the PlexinD1/GIPC/myosin VI complex.
Sema3G induces cell collapse in an Nrp2/PlexinD1-dependent manner.
Title: Semaphorin 3G Provides a Repulsive Guidance Cue to Lymphatic Endothelial Cells via Neuropilin-2/PlexinD1.
Our results demonstrate that sema3e/plexin D1 modulates IS formation and Ag-scanning activities of thymocytes within thymic tissues.
Title: Sema3e/Plexin D1 Modulates Immunological Synapse and Migration of Thymocytes by Rap1 Inhibition.
Sema3E/PlexinD1 signaling controls the motogenic potential of Cajal-Retzius (CR) cells in vitro and in vivo. Absence of Sema3E/PlexinD1 signalling increased the migratory properties of CR cells.
Title: Sema3E/PlexinD1 regulates the migration of hem-derived Cajal-Retzius cells in developing cerebral cortex.

Submit: New GeneRIF Correction See all GeneRIFs (28)

Variation

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Alleles

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

Targeted (8) 1 citation
Chemically induced (ENU) (3)
Endonuclease-mediated (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables semaphorin receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables semaphorin receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables semaphorin receptor activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within aorta development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within branching involved in blood vessel morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cardiac septum development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within coronary vasculature development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching	IDA Inferred from Direct Assay more info	PubMed
involved_in endothelial cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in endothelial cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within kidney development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within outflow tract morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in outflow tract morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of protein binding	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of GTPase activity	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell shape	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within semaphorin-plexin signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in semaphorin-plexin signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in semaphorin-plexin signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in synaptic target recognition	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic target recognition	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 body	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in lamellipodium	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IC Inferred by Curator more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
part_of semaphorin receptor complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: plexin-D1

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_026376.4 → NP_080652.2 plexin-D1 precursor

See identical proteins and their annotated locations for NP_080652.2

Status: VALIDATED

Source sequence(s)

AC139761

Consensus CDS

CCDS20448.1

UniProtKB/Swiss-Prot

Q3UH93, Q68HV1

UniProtKB/TrEMBL

Q6ZQ83

Related

ENSMUSP00000015511.9, ENSMUST00000015511.15

Conserved Domains (7) summary

cd11247
Location:51 → 549

Sema_plexin_D1; The Sema domain, a protein interacting module, of Plexin D1

smart00423
Location:713 → 755

PSI; domain found in Plexins, Semaphorins and Integrins

cd01179
Location:983 → 1069

IPT_plexin_repeat2; Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01180
Location:893 → 981

IPT_plexin_repeat1; First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

cd01181
Location:1071 → 1174

IPT_plexin_repeat3; Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present ...

pfam01437
Location:551 → 603

PSI; Plexin repeat

pfam08337
Location:1345 → 1888

Plexin_cytopl; Plexin cytoplasmic RasGAP domain