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Aliases for PLXNB3 Gene

Aliases for PLXNB3 Gene

  • Plexin B3 2 3 5
  • PLXN6 3 4
  • Plexin-B3 3
  • Plexin 6 3
  • KIAA1206 4
  • PLEXB3 3
  • PLEXR 3

External Ids for PLXNB3 Gene

Previous HGNC Symbols for PLXNB3 Gene

  • PLXN6

Previous GeneCards Identifiers for PLXNB3 Gene

  • GC0XP147167
  • GC0XP149484
  • GC0XP150615
  • GC0XP151497
  • GC0XP152550
  • GC0XP152682
  • GC0XP153029
  • GC0XP141686

Summaries for PLXNB3 Gene

Entrez Gene Summary for PLXNB3 Gene

  • 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]

GeneCards Summary for PLXNB3 Gene

PLXNB3 (Plexin B3) is a Protein Coding gene. Diseases associated with PLXNB3 include Glioma. Among its related pathways are Developmental Biology and Semaphorin interactions. Gene Ontology (GO) annotations related to this gene include semaphorin receptor activity. An important paralog of this gene is PLXNB1.

UniProtKB/Swiss-Prot for PLXNB3 Gene

  • Receptor for SEMA5A that plays a role in axon guidance, invasive growth and cell migration. Stimulates neurite outgrowth and mediates Ca(2+)/Mg(2+)-dependent cell aggregation. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1.

Gene Wiki entry for PLXNB3 Gene

Additional gene information for PLXNB3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLXNB3 Gene

Genomics for PLXNB3 Gene

GeneHancer (GH) Regulatory Elements for PLXNB3 Gene

Promoters and enhancers for PLXNB3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ153763 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 650.7 +1.4 1401 3.4 HDGF PKNOX1 SMAD1 FOXA2 ARNT ARID4B SIN3A ZNF2 POLR2B ZNF766 LOC102723591 PLXNB3 BCAP31 DKC1
GH0XJ153776 Promoter 0.9 EPDnew 650.4 +12.7 12661 0.1 KLF1 NCOA1 DEAF1 BRCA1 GABPA SP1 CCNT2 MBD2 EGR1 TARDBP SRPK3 PLXNB3 SSR4
GH0XJ153777 Promoter 0.7 EPDnew 650.4 +13.0 13022 0.1 HIC1 KLF17 KLF8 SRPK3 PLXNB3 SSR4
GH0XJ153779 Promoter 0.7 EPDnew 650.4 +14.8 14811 0.1 ZNF217 CTCF KLF8 PLXNB3 SRPK3 SSR4
GH0XJ153778 Promoter 0.5 EPDnew 650.4 +14.3 14305 0.1 PLXNB3 SRPK3 SSR4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PLXNB3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PLXNB3 gene promoter:
  • Egr-3
  • Nkx2-5
  • COMP1
  • POU2F1
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)

Genomic Locations for PLXNB3 Gene

Genomic Locations for PLXNB3 Gene
chrX:153,764,196-153,779,346
(GRCh38/hg38)
Size:
15,151 bases
Orientation:
Plus strand
chrX:153,029,651-153,044,801
(GRCh37/hg19)
Size:
15,151 bases
Orientation:
Plus strand

Genomic View for PLXNB3 Gene

Genes around PLXNB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLXNB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLXNB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLXNB3 Gene

Proteins for PLXNB3 Gene

  • Protein details for PLXNB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9ULL4-PLXB3_HUMAN
    Recommended name:
    Plexin-B3
    Protein Accession:
    Q9ULL4
    Secondary Accessions:
    • B7Z3E6
    • F5H773
    • Q9HDA4

    Protein attributes for PLXNB3 Gene

    Size:
    1909 amino acids
    Molecular mass:
    206847 Da
    Quaternary structure:
    • Interacts (via cytoplasmic domain) with RAC1 and ARHGDIA (By similarity). Binds MET and MST1R. Interacts (via cytoplasmic domain) with FSCN1. Interacts with RIT2/RIN. May form homodimers (via Sema domain).
    SequenceCaution:
    • Sequence=BAA86520.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for PLXNB3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PLXNB3 Gene

Post-translational modifications for PLXNB3 Gene

  • Glycosylation at isoforms=21218, isoforms=21101, isoforms=2957, isoforms=2900, isoforms=2802, isoforms=2615, isoforms=2231, and isoforms=251
  • Modification sites at PhosphoSitePlus

Other Protein References for PLXNB3 Gene

No data available for DME Specific Peptides for PLXNB3 Gene

Domains & Families for PLXNB3 Gene

Gene Families for PLXNB3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for PLXNB3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9ULL4

UniProtKB/Swiss-Prot:

PLXB3_HUMAN :
  • Belongs to the plexin family.
Family:
  • Belongs to the plexin family.
genes like me logo Genes that share domains with PLXNB3: view

Function for PLXNB3 Gene

Molecular function for PLXNB3 Gene

UniProtKB/Swiss-Prot Function:
Receptor for SEMA5A that plays a role in axon guidance, invasive growth and cell migration. Stimulates neurite outgrowth and mediates Ca(2+)/Mg(2+)-dependent cell aggregation. In glioma cells, SEMA5A stimulation of PLXNB3 results in the disassembly of F-actin stress fibers, disruption of focal adhesions and cellular collapse as well as inhibition of cell migration and invasion through ARHGDIA-mediated inactivation of RAC1.
GENATLAS Biochemistry:
plexin B3,calcium-dependent cell adhesion molecule at the neuronal cell surface

Phenotypes From GWAS Catalog for PLXNB3 Gene

Gene Ontology (GO) - Molecular Function for PLXNB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15184888
GO:0017154 semaphorin receptor activity IDA 15218527
GO:0019904 protein domain specific binding IPI 15218527
GO:0051022 Rho GDP-dissociation inhibitor binding IEA --
GO:0098632 cell-cell adhesion mediator activity IPI 16122393
genes like me logo Genes that share ontologies with PLXNB3: view
genes like me logo Genes that share phenotypes with PLXNB3: view

Animal Models for PLXNB3 Gene

MGI Knock Outs for PLXNB3:

Animal Model Products

  • Taconic Biosciences Mouse Models for PLXNB3

CRISPR Products

miRNA for PLXNB3 Gene

miRTarBase miRNAs that target PLXNB3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLXNB3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PLXNB3 Gene

Localization for PLXNB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLXNB3 Gene

Cell membrane; Single-pass type I membrane protein. Note=Colocalizes with RIT2/RIN at the plasma membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PLXNB3 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PLXNB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002116 semaphorin receptor complex IBA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0009986 cell surface IDA 16122393
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PLXNB3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PLXNB3 Gene

Pathways & Interactions for PLXNB3 Gene

genes like me logo Genes that share pathways with PLXNB3: view

Pathways by source for PLXNB3 Gene

1 KEGG pathway for PLXNB3 Gene

Gene Ontology (GO) - Biological Process for PLXNB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001938 positive regulation of endothelial cell proliferation IMP 19850054
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IDA 16122393
GO:0007162 negative regulation of cell adhesion IDA 15218527
GO:0007165 signal transduction IEA --
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with PLXNB3: view

No data available for SIGNOR curated interactions for PLXNB3 Gene

Drugs & Compounds for PLXNB3 Gene

No Compound Related Data Available

Transcripts for PLXNB3 Gene

mRNA/cDNA for PLXNB3 Gene

Unigene Clusters for PLXNB3 Gene

Plexin B3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLXNB3

Alternative Splicing Database (ASD) splice patterns (SP) for PLXNB3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b · 16c ^ 17 ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^
SP1: - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7: - - - - - -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15: - -

ExUns: 22 ^ 23 ^ 24a · 24b · 24c ^ 25 ^ 26a · 26b · 26c ^ 27 ^ 28a · 28b ^ 29a · 29b · 29c · 29d ^ 30 ^ 31a · 31b ^ 32a · 32b ^ 33 ^ 34 ^ 35a · 35b · 35c ·
SP1: - - -
SP2: - - - -
SP3: -
SP4: - - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: -
SP11:
SP12: - -
SP13:
SP14: -
SP15:

ExUns: 35d ^ 36 ^ 37 ^ 38a · 38b · 38c
SP1:
SP2:
SP3:
SP4:
SP5: -
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for PLXNB3 Gene

GeneLoc Exon Structure for
PLXNB3
ECgene alternative splicing isoforms for
PLXNB3

Expression for PLXNB3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PLXNB3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLXNB3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (30.8), Monocytes (11.0), Frontal cortex (8.7), and Platelet (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PLXNB3 Gene



Protein tissue co-expression partners for PLXNB3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PLXNB3 Gene:

PLXNB3

SOURCE GeneReport for Unigene cluster for PLXNB3 Gene:

Hs.632833

mRNA Expression by UniProt/SwissProt for PLXNB3 Gene:

Q9ULL4-PLXB3_HUMAN
Tissue specificity: Expression detected in Purkinje and granular cells in cerebellum, and in brain neocortex but not in corpus callosum. Expressed in glioma cells and embryonic kidney cells (at protein level). Expressed in brain, liver, pancreas and placenta, with weak expression detected also in lung and kidney. Expressed in several glioma cell lines.

Evidence on tissue expression from TISSUES for PLXNB3 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with PLXNB3: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PLXNB3 Gene

Orthologs for PLXNB3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLXNB3 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
Mammalia PLXNB3 34 33
  • 86.5 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PLXNB3 34 33
  • 84.39 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Plxnb3 16 34 33
  • 82.55 (n)
rat
(Rattus norvegicus)
Mammalia Plxnb3 33
  • 82.39 (n)
oppossum
(Monodelphis domestica)
Mammalia PLXNB3 34
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PLXNB3 34
  • 64 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLXNB3 34
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plxnb3 33
  • 58.41 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.5727 33
zebrafish
(Danio rerio)
Actinopterygii plxnb3 34 33
  • 58.81 (n)
OneToMany
PLXNB3 (3 of 3) 34
  • 41 (a)
OneToMany
PLXNB3 (2 of 3) 34
  • 26 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta plexB 34 35
  • 31 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea plx-2 34 35
  • 26 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 35 (a)
OneToMany
Species where no ortholog for PLXNB3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PLXNB3 Gene

ENSEMBL:
Gene Tree for PLXNB3 (if available)
TreeFam:
Gene Tree for PLXNB3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PLXNB3: view image

Paralogs for PLXNB3 Gene

Paralogs for PLXNB3 Gene

(11) SIMAP similar genes for PLXNB3 Gene using alignment to 7 proteins:

  • PLXB3_HUMAN
  • B7Z3H9_HUMAN
  • F5GWC0_HUMAN
  • F5GZZ4_HUMAN
  • H7BZV5_HUMAN
  • H7C0P4_HUMAN
  • H7C3L0_HUMAN
genes like me logo Genes that share paralogs with PLXNB3: view

Variants for PLXNB3 Gene

Sequence variations from dbSNP and Humsavar for PLXNB3 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1000553617 -- 153,766,110(+) C/T intron_variant
rs1000652835 -- 153,770,740(+) G/A intron_variant
rs1000728365 -- 153,775,267(+) G/A coding_sequence_variant, missense_variant
rs1001444808 -- 153,773,196(+) G/C intron_variant
rs1001497275 -- 153,773,050(+) G/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PLXNB3 Gene

Variant ID Type Subtype PubMed ID
esv2740633 CNV deletion 23290073
esv33199 CNV gain+loss 17666407

Variation tolerance for PLXNB3 Gene

Residual Variation Intolerance Score: 92.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.36; 70.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLXNB3 Gene

Human Gene Mutation Database (HGMD)
PLXNB3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLXNB3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLXNB3 Gene

Disorders for PLXNB3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PLXNB3 Gene - From: GeneCards

Disorder Aliases PubMed IDs
glioma
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PLXNB3

genes like me logo Genes that share disorders with PLXNB3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PLXNB3 Gene

Publications for PLXNB3 Gene

  1. Plexin B3 promotes neurite outgrowth, interacts homophilically, and interacts with Rin. (PMID: 16122393) Hartwig C … Finckh U (BMC neuroscience 2005) 3 4 22 58
  2. Plexin-B3 is a functional receptor for semaphorin 5A. (PMID: 15218527) Artigiani S … Tamagnone L (EMBO reports 2004) 3 4 22 58
  3. Semaphorin 5A and plexin-B3 regulate human glioma cell motility and morphology through Rac1 and the actin cytoskeleton. (PMID: 21706053) Li X … Lee AY (Oncogene 2012) 3 4 58
  4. Semaphorin 5A and plexin-B3 inhibit human glioma cell motility through RhoGDIalpha-mediated inactivation of Rac1 GTPase. (PMID: 20696765) Li X … Lee AY (The Journal of biological chemistry 2010) 3 4 58
  5. Identification of semaphorin 5A interacting protein by applying apriori knowledge and peptide complementarity related to protein evolution and structure. (PMID: 19329067) Sadanandam A … Singh RK (Genomics, proteomics & bioinformatics 2008) 3 22 58

Products for PLXNB3 Gene

Sources for PLXNB3 Gene

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