Plxnd1 plexin D1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Plxnd1provided by RGD
Official Full Name: plexin D1provided by RGD
Primary source: RGD:1310796
See related: EnsemblRapid:ENSRNOG00000025209 AllianceGenome:RGD:1310796
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable protein domain specific binding activity and semaphorin receptor activity. Predicted to be involved in several processes, including negative regulation of neuron apoptotic process; nervous system development; and positive regulation of axonogenesis. Predicted to act upstream of or within circulatory system development; dichotomous subdivision of terminal units involved in salivary gland branching; and kidney development. Predicted to be located in axon; cell body; and lamellipodium. Predicted to be part of semaphorin receptor complex. Predicted to be active in glutamatergic synapse and plasma membrane. Used to study transient cerebral ischemia. Orthologous to human PLXND1 (plexin D1). [provided by Alliance of Genome Resources, Jan 2025]
Expression: Biased expression in Lung (RPKM 183.7), Heart (RPKM 158.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q42

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (150675377..150715706, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (149002786..149043097, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (147854309..147894170, complement)

Chromosome 4 - NC_086022.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study found that depletion of Sema3E/PlexinD1 signaling with lentivirus-mediated PlexinD1-specific-shRNA improves tissue survival and functional outcome following stroke. Sema3E/PlexinD1 inhibition not only increases cortical perfusion but also ameliorates blood-brain barrier damage.
Title: Sema3E/PlexinD1 inhibition is a therapeutic strategy for improving cerebral perfusion and restoring functional loss after stroke in aged rats.

Submit: New GeneRIF Correction

General gene information

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Markers

RH134617 (e-PCR)
- UniSTS:217896

AA964803 (e-PCR)
- UniSTS:261525

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in angiogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within aorta development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within branching involved in blood vessel morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac septum development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within coronary vasculature development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching	ISO Inferred from Sequence Orthology more info
involved_in endothelial cell migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within outflow tract morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell shape	IBA Inferred from Biological aspect of Ancestor more info
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within semaphorin-plexin signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in semaphorin-plexin signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in synaptic target recognition	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in axon	ISO Inferred from Sequence Orthology more info
located_in cell body	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in lamellipodium	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
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_001395052.2 → NP_001381981.2 plexin-D1 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

D4AA77

Related

ENSRNOP00000033101.6, ENSRNOT00000032158.8

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

150675377..150715706 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

RNA

XR_005503232.2 RNA Sequence
XR_005503233.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001107881.1: Suppressed sequence

Description

NM_001107881.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.