Aliases for PLXNB1 Gene

Aliases for PLXNB1 Gene

  • Plexin B1 2 3 5
  • Semaphorin Receptor SEP 3 4
  • Plexin-B1 3 4
  • PLXN5 3 4
  • SEP 3 4
  • PLEXIN-B1 3
  • Plexin 5 3
  • KIAA0407 4

External Ids for PLXNB1 Gene

Previous HGNC Symbols for PLXNB1 Gene

  • PLXN5

Previous GeneCards Identifiers for PLXNB1 Gene

  • GC03M048246
  • GC03M047727
  • GC03M048405
  • GC03M048420

Summaries for PLXNB1 Gene

GeneCards Summary for PLXNB1 Gene

PLXNB1 (Plexin B1) is a Protein Coding gene. Diseases associated with PLXNB1 include Breast Cancer and Walker-Warburg Syndrome. Among its related pathways are Signaling by GPCR and Development Slit-Robo signaling. Gene Ontology (GO) annotations related to this gene include GTPase activating protein binding. An important paralog of this gene is PLXNB3.

UniProtKB/Swiss-Prot Summary for PLXNB1 Gene

  • Receptor for SEMA4D (PubMed:19843518, PubMed:20877282, PubMed:21912513). Plays a role in GABAergic synapse development (By similarity). Mediates SEMA4A- and SEMA4D-dependent inhibitory synapse development (By similarity). Plays a role in RHOA activation and subsequent changes of the actin cytoskeleton (PubMed:12196628, PubMed:15210733). Plays a role in axon guidance, invasive growth and cell migration (PubMed:12198496).

Gene Wiki entry for PLXNB1 Gene

Additional gene information for PLXNB1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PLXNB1 Gene

Genomics for PLXNB1 Gene

GeneHancer (GH) Regulatory Elements for PLXNB1 Gene

Promoters and enhancers for PLXNB1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PLXNB1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PLXNB1

Top Transcription factor binding sites by QIAGEN in the PLXNB1 gene promoter:
  • HEN1
  • p53

Genomic Locations for PLXNB1 Gene

Genomic Locations for PLXNB1 Gene
chr3:48,403,854-48,430,324
(GRCh38/hg38)
Size:
26,471 bases
Orientation:
Minus strand
chr3:48,445,261-48,471,594
(GRCh37/hg19)
Size:
26,334 bases
Orientation:
Minus strand

Genomic View for PLXNB1 Gene

Genes around PLXNB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLXNB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLXNB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLXNB1 Gene

Proteins for PLXNB1 Gene

  • Protein details for PLXNB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43157-PLXB1_HUMAN
    Recommended name:
    Plexin-B1
    Protein Accession:
    O43157
    Secondary Accessions:
    • A6H8Y2
    • Q6NY20
    • Q9UIV7
    • Q9UJ92
    • Q9UJ93

    Protein attributes for PLXNB1 Gene

    Size:
    2135 amino acids
    Molecular mass:
    232298 Da
    Quaternary structure:
    • Monomer, and heterodimer with PLXNB2 after proteolytic processing (PubMed:12533544, PubMed:17916560, PubMed:18411422, PubMed:18275816, PubMed:19843518, PubMed:20877282, PubMed:21912513). Binds RAC1 that has been activated by GTP binding (PubMed:11035813, PubMed:17916560, PubMed:18275816, PubMed:19843518). Interaction with SEMA4D promotes binding of cytoplasmic ligands (PubMed:10520995, PubMed:12198496, PubMed:19843518). Interacts with PLXNA1 (By similarity). Interacts with ARHGEF11 and ARHGEF12 (PubMed:12196628). Interacts with ERBB2 (PubMed:15210733). Interacts with MET (PubMed:12198496, PubMed:15184888). Interacts with MST1R (PubMed:15184888). Interacts with RRAS (PubMed:19843518). Interacts with RHOD (PubMed:17916560). Interacts with RND1 (PubMed:12730235, PubMed:17916560, PubMed:18275816, PubMed:19843518). Interacts with NRP1 and NRP2 (PubMed:10520995).
    SequenceCaution:
    • Sequence=BAA23703.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PLXNB1 Gene

    Alternative splice isoforms for PLXNB1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PLXNB1 Gene

Post-translational modifications for PLXNB1 Gene

  • Phosphorylated on tyrosine residues by ERBB2 and MET upon SEMA4D binding.
  • Proteolytic processing favors heterodimerization with PLXNB2 and SEMA4D binding.
  • Glycosylation at Asn31, Asn334, Asn543, Ser691, Ser693, Thr696, Asn1183, Asn1253, and Asn1330
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PLXB1_HUMAN (1612)

No data available for DME Specific Peptides for PLXNB1 Gene

Domains & Families for PLXNB1 Gene

Gene Families for PLXNB1 Gene

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

Suggested Antigen Peptide Sequences for PLXNB1 Gene

GenScript: Design optimal peptide antigens:
  • PLXNB1 protein (A1A4U0_HUMAN)
  • Semaphorin receptor SEP (PLXB1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O43157

UniProtKB/Swiss-Prot:

PLXB1_HUMAN :
  • Belongs to the plexin family.
Family:
  • Belongs to the plexin family.
genes like me logo Genes that share domains with PLXNB1: view

Function for PLXNB1 Gene

Molecular function for PLXNB1 Gene

UniProtKB/Swiss-Prot Function:
Receptor for SEMA4D (PubMed:19843518, PubMed:20877282, PubMed:21912513). Plays a role in GABAergic synapse development (By similarity). Mediates SEMA4A- and SEMA4D-dependent inhibitory synapse development (By similarity). Plays a role in RHOA activation and subsequent changes of the actin cytoskeleton (PubMed:12196628, PubMed:15210733). Plays a role in axon guidance, invasive growth and cell migration (PubMed:12198496).
GENATLAS Biochemistry:
plexin B1,calcium-dependent cell adhesion molecule at the neuronal cell surface,also expressed in hematopoietic and endothelial cells,receptor for the semaphorin,homologous to the hepatocyte growth factor receptor family

Phenotypes From GWAS Catalog for PLXNB1 Gene

Gene Ontology (GO) - Molecular Function for PLXNB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004888 transmembrane signaling receptor activity NAS 10520995
GO:0005096 GTPase activator activity TAS --
GO:0005515 protein binding IPI 12730235
GO:0017154 semaphorin receptor activity IBA,TAS 10520995
GO:0030215 semaphorin receptor binding TAS 10520995
genes like me logo Genes that share ontologies with PLXNB1: view
genes like me logo Genes that share phenotypes with PLXNB1: view

Animal Models for PLXNB1 Gene

MGI Knock Outs for PLXNB1:

Animal Model Products

  • Taconic Biosciences Mouse Models for PLXNB1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLXNB1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PLXNB1 Gene

Localization for PLXNB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLXNB1 Gene

[Isoform 1]: Cell membrane; Single-pass type I membrane protein.
[Isoform 2]: Secreted.
[Isoform 3]: Secreted.

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 PLXNB1 gene
Compartment Confidence
plasma membrane 5
extracellular 4
cytoskeleton 2
nucleus 2
cytosol 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PLXNB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002116 semaphorin receptor complex TAS 19909241
GO:0005576 extracellular region IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS,NAS 10520995
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PLXNB1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PLXNB1 Gene

Pathways & Interactions for PLXNB1 Gene

genes like me logo Genes that share pathways with PLXNB1: view

Pathways by source for PLXNB1 Gene

1 GeneGo (Thomson Reuters) pathway for PLXNB1 Gene
  • Neurophysiological process Receptor-mediated axon growth repulsion
2 Qiagen pathways for PLXNB1 Gene
  • Guidance Cues and Growth Cone Motility
  • Semaphorin Signaling

SIGNOR curated interactions for PLXNB1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for PLXNB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007162 negative regulation of cell adhesion IBA,IDA 15218527
GO:0007165 signal transduction TAS 8570614
GO:0007186 G protein-coupled receptor signaling pathway TAS --
GO:0008360 regulation of cell shape IDA 19843518
GO:0014068 positive regulation of phosphatidylinositol 3-kinase signaling ISS --
genes like me logo Genes that share ontologies with PLXNB1: view

Drugs & Compounds for PLXNB1 Gene

(4) Drugs for PLXNB1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0

(1) Additional Compounds for PLXNB1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PLXNB1: view

Transcripts for PLXNB1 Gene

mRNA/cDNA for PLXNB1 Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
19 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLXNB1

Alternative Splicing Database (ASD) splice patterns (SP) for PLXNB1 Gene

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

ExUns: 20 ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24a · 24b · 24c ^ 25 ^ 26a · 26b ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31a · 31b · 31c ^ 32 ^ 33 ^ 34a · 34b ^ 35a · 35b ^
SP1: - -
SP2: - -
SP3:
SP4: -
SP5:
SP6: - -
SP7: -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

ExUns: 36 ^ 37 ^ 38 ^ 39 ^ 40a · 40b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for PLXNB1 Gene

GeneLoc Exon Structure for
PLXNB1

Expression for PLXNB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PLXNB1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLXNB1 Gene

This gene is overexpressed in Spinal cord (14.6), Serum (7.5), and Frontal cortex (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PLXNB1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PLXNB1

SOURCE GeneReport for Unigene cluster for PLXNB1 Gene:

Hs.476209

mRNA Expression by UniProt/SwissProt for PLXNB1 Gene:

O43157-PLXB1_HUMAN
Tissue specificity: Highly expressed in fetal kidney, and at slightly lower levels in fetal brain, lung and liver.

Evidence on tissue expression from TISSUES for PLXNB1 Gene

  • Nervous system(4.9)
  • Liver(4.3)
  • Bone marrow(4.1)
  • Kidney(2.2)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with PLXNB1: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PLXNB1 Gene

Orthologs for PLXNB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLXNB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLXNB1 31 30
  • 99.63 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PLXNB1 31 30
  • 88.93 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PLXNB1 31 30
  • 87.41 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Plxnb1 17 31 30
  • 85.94 (n)
rat
(Rattus norvegicus)
Mammalia Plxnb1 30
  • 85.54 (n)
oppossum
(Monodelphis domestica)
Mammalia PLXNB1 31
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PLXNB1 31
  • 63 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLXNB1 31 30
  • 68.57 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLXNB1 31
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plxnb1 30
  • 61.53 (n)
Str.10773 30
zebrafish
(Danio rerio)
Actinopterygii plxnb1a 31
  • 76 (a)
OneToMany
plxnb1b 31 30
  • 60.03 (n)
OneToMany
wufb83a09 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011139 30
  • 49.08 (n)
fruit fly
(Drosophila melanogaster)
Insecta plexB 31 32 30
  • 45.09 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea plx-2 31 32
  • 27 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 36 (a)
OneToMany
Species where no ortholog for PLXNB1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 PLXNB1 Gene

ENSEMBL:
Gene Tree for PLXNB1 (if available)
TreeFam:
Gene Tree for PLXNB1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PLXNB1: view image

Paralogs for PLXNB1 Gene

Paralogs for PLXNB1 Gene

(7) SIMAP similar genes for PLXNB1 Gene using alignment to 3 proteins:

  • PLXB1_HUMAN
  • A1A4U0_HUMAN
  • G8JLJ7_HUMAN
genes like me logo Genes that share paralogs with PLXNB1: view

Variants for PLXNB1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PLXNB1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
712054 Benign: not provided 48,419,774(-) C/A MISSENSE_VARIANT
712524 Benign: not provided 48,412,609(-) C/T SYNONYMOUS_VARIANT
712525 Benign: not provided 48,418,036(-) G/A SYNONYMOUS_VARIANT
712526 Benign: not provided 48,424,231(-) G/A SYNONYMOUS_VARIANT
722456 Likely Benign: not provided 48,419,730(-) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for PLXNB1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PLXNB1 Gene

Variant ID Type Subtype PubMed ID
nsv1072254 CNV deletion 25765185
nsv1118969 CNV deletion 24896259
nsv508917 CNV insertion 20534489
nsv590242 CNV loss 21841781
nsv834683 CNV gain 17160897
nsv834684 CNV gain 17160897
nsv954483 CNV deletion 24416366

Variation tolerance for PLXNB1 Gene

Residual Variation Intolerance Score: 21% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.06; 60.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLXNB1 Gene

Human Gene Mutation Database (HGMD)
PLXNB1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLXNB1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLXNB1 Gene

Disorders for PLXNB1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PLXNB1 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
breast cancer
  • breast cancer, familial
walker-warburg syndrome
  • hydrocephalus, agyria, and retinal dysplasia
renal cell carcinoma, papillary, 1
  • rccp1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PLXNB1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PLXNB1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PLXNB1 Gene

Publications for PLXNB1 Gene

  1. The semaphorin receptor plexin-B1 specifically interacts with active Rac in a ligand-dependent manner. (PMID: 11035813) Vikis HG … Guan KL (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4 23 54
  2. Structure and function of the intracellular region of the plexin-b1 transmembrane receptor. (PMID: 19843518) Tong Y … Buck M (The Journal of biological chemistry 2009) 3 4 23 54
  3. Insights into oncogenic mutations of plexin-B1 based on the solution structure of the Rho GTPase binding domain. (PMID: 18275816) Tong Y … Buck M (Structure (London, England : 1993) 2008) 3 4 23 54
  4. Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain. (PMID: 17916560) Tong Y … Buck M (The Journal of biological chemistry 2007) 3 4 23 54
  5. Plexin-B1/RhoGEF-mediated RhoA activation involves the receptor tyrosine kinase ErbB-2. (PMID: 15210733) Swiercz JM … Offermanns S (The Journal of cell biology 2004) 3 4 23 54

Products for PLXNB1 Gene

Sources for PLXNB1 Gene