PLXNB3 plexin B3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLXNB3provided by HGNC
Official Full Name: plexin B3provided by HGNC
Primary source: HGNC:HGNC:9105
See related: Ensembl:ENSG00000198753 MIM:300214; AllianceGenome:HGNC:9105
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PLEXR; PLXN6; PLEXB3
Summary: The protein encoded by this gene is a member of the plexin family. It functions as a receptor for semaphorin 5A, and plays a role in axon guidance, invasive growth and cell migration. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
Expression: Broad expression in brain (RPKM 10.9), salivary gland (RPKM 4.4) and 16 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xq28

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (153764249..153779341)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (152037914..152053006)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (153029704..153044796)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

Plexin-B3 expression stimulates MET signaling, breast cancer stem cell specification, and lung metastasis.
Title: Plexin-B3 expression stimulates MET signaling, breast cancer stem cell specification, and lung metastasis.
SEMA5A-PLXNB3 Axis Promotes PDAC Liver Metastasis Outgrowth through Enhancing the Warburg Effect.
Title: SEMA5A-PLXNB3 Axis Promotes PDAC Liver Metastasis Outgrowth through Enhancing the Warburg Effect.
Glycoproteomics Identifies Plexin-B3 as a Targetable Cell Surface Protein Required for the Growth and Invasion of Triple-Negative Breast Cancer Cells.
Title: Glycoproteomics Identifies Plexin-B3 as a Targetable Cell Surface Protein Required for the Growth and Invasion of Triple-Negative Breast Cancer Cells.
Essential roles of plexin-B3(+) oligodendrocyte precursor cells in the pathogenesis of Alzheimer's disease.
Title: Essential roles of plexin-B3(+) oligodendrocyte precursor cells in the pathogenesis of Alzheimer's disease.
Data show that Semaphorin 5A (Sema5A) and plexin-B3 inhibit glioma cell invasion through Rac1 inactivation.
Title: Semaphorin 5A and plexin-B3 regulate human glioma cell motility and morphology through Rac1 and the actin cytoskeleton.
Data represent a novel signaling of semaphorin 5A and plexin B3 in the control of cell motility by indirect inactivation of Rac1 through RhoGDIalpha.
Title: Semaphorin 5A and plexin-B3 inhibit human glioma cell motility through RhoGDIalpha-mediated inactivation of Rac1 GTPase.
A virtual expression database search and RT-PCR analysis showed co-expression of SEMA5A and Plexin B3, and the interaction of SEMA5A with Plexin B3 was confirmed by co-immunoprecipitation studies.
Title: Identification of semaphorin 5A interacting protein by applying apriori knowledge and peptide complementarity related to protein evolution and structure.
Plexin-B3 is a functional receptor for semaphorin 5A
Title: Plexin-B3 is a functional receptor for semaphorin 5A.
plexin B3 may influence cognitive performance, and the development of white matter in vivo in a way similar to its known stimulating effect on neurite outgrowth in vitro
Title: Plexin B3 is genetically associated with verbal performance and white matter volume in human brain.
Data suggest an involvement of homophilic interaction of B3 in semaphorin-independent signaling mechanisms positively influencing neuronal morphogenesis or function.
Title: Plexin B3 promotes neurite outgrowth, interacts homophilically, and interacts with Rin.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A008P20 (e-PCR)
- UniSTS:11170

A004O03 (e-PCR)
- UniSTS:67783

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables Rho GDP-dissociation inhibitor binding	IEA Inferred from Electronic Annotation more info
enables cell-cell adhesion mediator activity	IPI Inferred from Physical Interaction more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of GTPase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of cell adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of lamellipodium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of endothelial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neuron projection development	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 cell shape	IBA Inferred from Biological aspect of Ancestor more info
involved_in semaphorin-plexin signaling pathway	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor 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-B3

Names: plexin 6

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.

Genomic

NG_013255.2 RefSeqGene

Range

5002..20094

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001163257.2 → NP_001156729.1 plexin-B3 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an additional exon in the 5' region compared to variant 1. This results in translation initiation from a start codon (with a strong Kozak signal) found in this exon, and a longer isoform (2) with a distinct N-terminus compared to isoform 1.

Source sequence(s)

AF149019, AK292535, AK295762, AK307894

Consensus CDS

CCDS55536.1

UniProtKB/TrEMBL

A8K920

Related

ENSP00000442736.1, ENST00000538966.5

Conserved Domains (7) summary

cd11277
Location:70 → 495

Sema_plexin_B3; The Sema domain, a protein interacting module, of Plexin B3

cd01179
Location:950 → 1035

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:858 → 949

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 ...

pfam01437
Location:497 → 548

PSI; Plexin repeat

pfam01833
Location:1199 → 1265

TIG; IPT/TIG domain

pfam08337
Location:1350 → 1899

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

cl15674
Location:1038 → 1169

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 ...
NM_005393.3 → NP_005384.2 plexin-B3 isoform 1 precursor

See identical proteins and their annotated locations for NP_005384.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1.

Source sequence(s)

AF149019, AK292535, AK295762

Consensus CDS

CCDS14729.1

UniProtKB/Swiss-Prot

B7Z3E6, F5H773, Q9HDA4, Q9ULL4

UniProtKB/TrEMBL

A8K920

Related

ENSP00000355378.5, ENST00000361971.10

Conserved Domains (7) summary

cd11277
Location:47 → 472

Sema_plexin_B3; The Sema domain, a protein interacting module, of Plexin B3

cd01179
Location:927 → 1012

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:835 → 926

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 ...

pfam01437
Location:474 → 525

PSI; Plexin repeat

pfam01833
Location:1176 → 1242

TIG; IPT/TIG domain

pfam08337
Location:1327 → 1876

Plexin_cytopl; Plexin cytoplasmic RasGAP domain

cl15674
Location:1015 → 1146

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 ...