PLXND1 plexin D1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLXND1provided by HGNC
Official Full Name: plexin D1provided by HGNC
Primary source: HGNC:HGNC:9107
See related: Ensembl:ENSG00000004399 MIM:604282; AllianceGenome:HGNC:9107
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: CHTD9; PLEXD1
Summary: Enables protein domain specific binding activity. Predicted to be involved in several processes, including positive regulation of axonogenesis; semaphorin-plexin signaling pathway; and synapse assembly. Predicted to act upstream of or within circulatory system development; dichotomous subdivision of terminal units involved in salivary gland branching; and kidney development. Located in lamellipodium. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in placenta (RPKM 37.7), fat (RPKM 32.1) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q22.1

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (129555214..129606676, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (132299641..132351112, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (129274057..129325519, complement)

Chromosome 3 - NC_000003.12 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 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 circ_PLXND1 inhibits tumorigenesis of non-small cell lung carcinoma via miR-1287-5p/ERBB3 axis.
Title: Downregulation of circ_PLXND1 inhibits tumorigenesis of non-small cell lung carcinoma via miR-1287-5p/ERBB3 axis.
Biallelic alterations in PLXND1 cause common arterial trunk and other cardiac malformations in humans.
Title: Biallelic alterations in PLXND1 cause common arterial trunk and other cardiac malformations in humans.
PLXND1/SEMA3E Promotes Epithelial-Mesenchymal Transition Partly via the PI3K/AKT-Signaling Pathway and Induces Heterogenity in Colorectal Cancer.
Title: PLXND1/SEMA3E Promotes Epithelial-Mesenchymal Transition Partly via the PI3K/AKT-Signaling Pathway and Induces Heterogenity in Colorectal Cancer.
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.
Identification of plexin D1 on circulating extracellular vesicles as a potential biomarker of polymyositis and dermatomyositis.
Title: Identification of plexin D1 on circulating extracellular vesicles as a potential biomarker of polymyositis and dermatomyositis.
Semaphorin4A-Plexin D1 Axis Induces Th2 and Th17 While Represses Th1 Skewing in an Autocrine Manner.
Title: Semaphorin4A-Plexin D1 Axis Induces Th2 and Th17 While Represses Th1 Skewing in an Autocrine Manner.
In the absence of neuropilins, plexin-A4 formed complexes with plexin-D1, and was required in addition to plexin-D1 to enable Sema3C-induced signal transduction.
Title: Complexes of plexin-A4 and plexin-D1 convey semaphorin-3C signals to induce cytoskeletal collapse in the absence of neuropilins.
The role of Plexin D1 in tumor development and progression is thereby garnering research interest for its potential as a biomarker and as a therapeutic target.
Title: Divergent roles of Plexin D1 in cancer.
Anti-plexin D1 antibodies are a novel biomarker for immunotherapy-responsive neuropathic pain.
Title: A Novel Autoantibody against Plexin D1 in Patients with Neuropathic Pain.
the receptor Plexin-D1 contains a sorting motif that interacts with the adaptor protein GIPC1 to facilitate transport to recycling endosomes.
Title: Post-endocytic sorting of Plexin-D1 controls signal transduction and development of axonal and vascular circuits.

Submit: New GeneRIF Correction See all GeneRIFs (30)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Congenital heart defects, multiple types, 9 MedGen: C5830367 OMIM: 620294 GeneReviews: Not available	not available

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

D10Bir17 (e-PCR), detects polymorphism
- UniSTS:141482

SHGC-77334 (e-PCR)
- UniSTS:50875

D3S3945 (e-PCR)
- UniSTS:503

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IPI Inferred from Physical Interaction more info	PubMed
enables semaphorin receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in aorta development	IEA Inferred from Electronic Annotation more info
involved_in branching involved in blood vessel morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in cardiac septum development	IEA Inferred from Electronic Annotation more info
involved_in coronary vasculature development	IEA Inferred from Electronic Annotation more info
involved_in dichotomous subdivision of terminal units involved in salivary gland branching	IEA Inferred from Electronic Annotation more info
involved_in endothelial cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in kidney 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	IEA Inferred from Electronic Annotation more info
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
involved_in regulation of angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell migration	ISS Inferred from Sequence or Structural Similarity 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
involved_in semaphorin-plexin signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in synapse assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in synaptic target recognition	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cell body	IEA Inferred from Electronic Annotation more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in lamellipodium	IDA Inferred from Direct Assay more info	PubMed
located_in lamellipodium 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	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement 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_015103.3 → NP_055918.3 plexin-D1 precursor

Status: VALIDATED

Source sequence(s)

AC023162, AC080007

Consensus CDS

CCDS33854.1

UniProtKB/Swiss-Prot

A7E2C6, C9JPZ6, Q6PJS9, Q8IZJ2, Q9BTQ2, Q9Y4D7

Related

ENSP00000317128.4, ENST00000324093.9

Conserved Domains (8) summary

cd11247
Location:49 → 547

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

smart00423
Location:711 → 753

PSI; domain found in Plexins, Semaphorins and Integrins

cd01179
Location:981 → 1067

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:891 → 979

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:1069 → 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:549 → 601

PSI; Plexin repeat

pfam08337
Location:1345 → 1888

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

pfam17960
Location:627 → 700

TIG_plexin; TIG domain

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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

129555214..129606676 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011512589.2 → XP_011510891.1 plexin-D1 isoform X2

Conserved Domains (6) summary

cd11247
Location:49 → 547

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

cd01179
Location:851 → 937

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:761 → 849

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:939 → 1044

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:549 → 601

PSI; Plexin repeat

pfam08337
Location:1215 → 1758

Plexin_cytopl; Plexin cytoplasmic RasGAP domain
XM_011512588.3 → XP_011510890.1 plexin-D1 isoform X1

Conserved Domains (7) summary

cd11247
Location:49 → 547

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

smart00423
Location:711 → 753

PSI; domain found in Plexins, Semaphorins and Integrins

cd01179
Location:981 → 1067

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:891 → 979

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:1069 → 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:549 → 601

PSI; Plexin repeat

pfam08337
Location:1345 → 1887

Plexin_cytopl; Plexin cytoplasmic RasGAP domain
XM_011512592.1 → XP_011510894.1 plexin-D1 isoform X6

Conserved Domains (4) summary

cd01179
Location:37 → 123

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 ...

cd01181
Location:125 → 230

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 ...

pfam08337
Location:401 → 944

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

cl15674
Location:3 → 35

IPT; Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor ...
XM_047447765.1 → XP_047303721.1 plexin-D1 isoform X3
XM_011512590.3 → XP_011510892.1 plexin-D1 isoform X4

Conserved Domains (7) summary

cd11247
Location:49 → 547

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

smart00423
Location:711 → 753

PSI; domain found in Plexins, Semaphorins and Integrins

cd01179
Location:981 → 1067

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:891 → 979

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:1069 → 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:549 → 601

PSI; Plexin repeat

cl02569
Location:1344 → 1439

RasGAP; Ras GTPase Activating Domain
XM_047447766.1 → XP_047303722.1 plexin-D1 isoform X5