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PLXNB2 Gene(Protein Coding)

Plexin B2

GCID:
GC22M050274
GIFtS:
45
Genes Participants
UDN Logo

Aliases for PLXNB2 Gene

Aliases for PLXNB2 Gene

  • Plexin B2 2 3 5
  • MM1 3 4
  • DJ402G11.3 3
  • Nbla00445 3
  • Plexin-B2 3
  • KIAA0315 4
  • PLEXB2 3

External Ids for PLXNB2 Gene

Previous GeneCards Identifiers for PLXNB2 Gene

  • GC22M047264
  • GC22M048895
  • GC22M049016
  • GC22M049055
  • GC22M050713
  • GC22M033610

Summaries for PLXNB2 Gene

Entrez Gene Summary for PLXNB2 Gene

  • Members of the B class of plexins, such as PLXNB2 are transmembrane receptors that participate in axon guidance and cell migration in response to semaphorins (Perrot et al. (2002) [PubMed 12183458]).[supplied by OMIM, Mar 2008]

GeneCards Summary for PLXNB2 Gene

PLXNB2 (Plexin B2) is a Protein Coding gene. Among its related pathways are Axon guidance. Gene Ontology (GO) annotations related to this gene include receptor activity and semaphorin receptor activity. An important paralog of this gene is PLXNB1.

UniProtKB/Swiss-Prot for PLXNB2 Gene

  • Cell surface receptor for SEMA4C, SEMA4D and SEMA4G that plays an important role in cell-cell signaling. Binding to class 4 semaphorins promotes downstream activation of RHOA and phosphorylation of ERBB2 at Tyr-1248. Required for normal differentiation and migration of neuronal cells during brain corticogenesis and for normal embryonic brain development. Regulates the migration of cerebellar granule cells in the developing brain. Plays a role in RHOA activation and subsequent changes of the actin cytoskeleton. Plays a role in axon guidance, invasive growth and cell migration. May modulate the activity of RAC1 and CDC42. Down-regulates macrophage migration in wound-healing assays (in vitro) (By similarity).

Gene Wiki entry for PLXNB2 Gene

Additional gene information for PLXNB2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLXNB2 Gene

Genomics for PLXNB2 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for PLXNB2 Gene

Promoters and enhancers for PLXNB2 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
GH22I050292 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 565.6 +6.5 6535 17.7 HDGF FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 PLXNB2 PIM3 BRD1 NCAPH2 RABL2B TYMP TUBGCP6 DENND6B LOC105373100 ODF3B
GH22I050626 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 33.1 -320.4 -320381 2.4 HDGF ZNF493 ARID4B SIN3A YBX1 GLI4 ZNF2 ZNF280A GLIS2 KLF7 ARSA BRD1 ZBED4 RABL2B ENSG00000272836 TUBGCP6 PLXNB2 ALG12 CHKB LOC105373095
GH22I050339 Enhancer 0.9 ENCODE 59.8 -32.6 -32582 2.1 HDGF ZNF493 ZNF2 KLF7 ZNF488 ZNF585B GLIS1 MYNN NBN ZNF300 BRD1 RABL2B ALG12 PLXNB2 ENSG00000272836 CHKB TUBGCP6 ZBED4 LMF2 ENSG00000273192
GH22I050188 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 13.1 +116.6 116563 5.6 HDGF PKNOX1 ATF1 SIN3A ZNF2 IRF4 ZNF766 GLIS2 ZNF143 KLF7 TRABD ENSG00000273188 TUBGCP6 MAPK12 HDAC10 BRD1 ENSG00000273253 MAPK11 PLXNB2 MLC1
GH22I049942 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 17.7 +358.4 358401 13.5 HDGF PKNOX1 CLOCK FOXA2 MLX ARNT ZFP64 ARID4B NEUROD1 SIN3A ALG12 ENSG00000272836 RABL2B PLXNB2 TUBGCP6 ZBED4 LMF2 NCAPH2 CHKB BRD1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PLXNB2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PLXNB2 gene promoter:

Genomic Locations for PLXNB2 Gene

Genomic Locations for PLXNB2 Gene
chr22:50,274,979-50,307,642
(GRCh38/hg38)
Size:
32,664 bases
Orientation:
Minus strand
chr22:50,713,408-50,746,056
(GRCh37/hg19)

Genomic View for PLXNB2 Gene

Genes around PLXNB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLXNB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLXNB2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PLXNB2 Gene

Proteins for PLXNB2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for PLXNB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15031-PLXB2_HUMAN
    Recommended name:
    Plexin-B2
    Protein Accession:
    O15031
    Secondary Accessions:
    • A6QRH0
    • Q7KZU3
    • Q9BSU7

    Protein attributes for PLXNB2 Gene

    Size:
    1838 amino acids
    Molecular mass:
    205127 Da
    Quaternary structure:
    • Monomer, and heterodimer with PLXNB1. Interacts with SEMA4C, SEMA4D and SEMA4G (By similarity). Binds MET, ARHGEF11 and ARHGEF12. May also interact with MST1R.
    SequenceCaution:
    • Sequence=BAA21571.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PLXNB2 Gene

neXtProt entry for PLXNB2 Gene

Protein Expression for PLXNB2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PLXNB2 Gene

  • Ubiquitination at isoforms=1423
  • Glycosylation at isoforms=127, isoforms=242, isoforms=391, Asn402, Asn528, Asn733, Asn759, isoforms=795, Asn844, isoforms=1002, isoforms=1049, isoforms=1068, and Asn1099

Other Protein References for PLXNB2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PLXNB2 Gene

Domains & Families for PLXNB2 Gene

Gene Families for PLXNB2 Gene

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

Protein Domains for PLXNB2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PLXNB2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O15031

UniProtKB/Swiss-Prot:

PLXB2_HUMAN :
  • Belongs to the plexin family.
Family:
  • Belongs to the plexin family.
genes like me logo Genes that share domains with PLXNB2: view

Function for PLXNB2 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for PLXNB2 Gene

GENATLAS Biochemistry:
plexin B2,calcium-dependent cell adhesion molecule at the neuronal cell surface,receptor for the semaphorin 7A (SEMA7A),expressed in brain and differentially in brain tumors
UniProtKB/Swiss-Prot Function:
Cell surface receptor for SEMA4C, SEMA4D and SEMA4G that plays an important role in cell-cell signaling. Binding to class 4 semaphorins promotes downstream activation of RHOA and phosphorylation of ERBB2 at Tyr-1248. Required for normal differentiation and migration of neuronal cells during brain corticogenesis and for normal embryonic brain development. Regulates the migration of cerebellar granule cells in the developing brain. Plays a role in RHOA activation and subsequent changes of the actin cytoskeleton. Plays a role in axon guidance, invasive growth and cell migration. May modulate the activity of RAC1 and CDC42. Down-regulates macrophage migration in wound-healing assays (in vitro) (By similarity).

Phenotypes From GWAS Catalog for PLXNB2 Gene

Gene Ontology (GO) - Molecular Function for PLXNB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15184888
GO:0017154 semaphorin receptor activity IEA,ISS --
genes like me logo Genes that share ontologies with PLXNB2: view
genes like me logo Genes that share phenotypes with PLXNB2: view

Animal Models for PLXNB2 Gene

MGI Knock Outs for PLXNB2:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PLXNB2 Gene

Localization for PLXNB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLXNB2 Gene

Cell membrane; Single-pass type I membrane protein.

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 PLXNB2 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for PLXNB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane ISS --
GO:0009986 cell surface IDA,HDA 19581412
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PLXNB2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PLXNB2 Gene

Pathways & Interactions for PLXNB2 Gene

SuperPathways for PLXNB2 Gene

PathCards logo More details on SuperPathways for PLXNB2
SuperPathway Contained pathways
1 Axon guidance
Axon guidance
-
genes like me logo Genes that share pathways with PLXNB2: view

Pathways by source for PLXNB2 Gene

1 KEGG pathway for PLXNB2 Gene

Gene Ontology (GO) - Biological Process for PLXNB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001843 neural tube closure ISS --
GO:0001932 regulation of protein phosphorylation ISS --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IDA 16122393
GO:0007162 negative regulation of cell adhesion IBA --
GO:0007165 signal transduction IEA --
genes like me logo Genes that share ontologies with PLXNB2: view

No data available for SIGNOR curated interactions for PLXNB2 Gene

Drugs & Compounds for PLXNB2 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for PLXNB2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PLXNB2 Gene

(8) REFSEQ mRNAs :
(17) Additional mRNA sequences :
(478) Selected AceView cDNA sequences:
(14) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PLXNB2 Gene

Plexin B2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLXNB2 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b · 12c ^ 13a · 13b ·
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6: - -
SP7:
SP8:
SP9:
SP10: - - - - - - - - - - - - - - - - - - - - - -
SP11:
SP12: - -
SP13: - -
SP14: - -
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:
SP23: - - - -
SP24: -
SP25:
SP26:
SP27:
SP28:
SP29:
SP30:

ExUns: 13c ^ 14a · 14b · 14c ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18a · 18b · 18c ^ 19a · 19b ^ 20a · 20b · 20c ^ 21 ^ 22 ^ 23 ^ 24a · 24b ^ 25 ^ 26 ^ 27a · 27b ^
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: -
SP9:
SP10: - - - - - - - - - - - - - - - - - - - - - - - - - -
SP11:
SP12:
SP13:
SP14:
SP15: -
SP16: -
SP17: -
SP18:
SP19:
SP20:
SP21:
SP22:
SP23:
SP24:
SP25: - - -
SP26:
SP27:
SP28:
SP29:
SP30:

ExUns: 28a · 28b ^ 29a · 29b ^ 30a · 30b · 30c ^ 31 ^ 32 ^ 33a · 33b · 33c ^ 34a · 34b · 34c ^ 35 ^ 36a · 36b ^ 37
SP1:
SP2: -
SP3: -
SP4: -
SP5: -
SP6:
SP7:
SP8:
SP9:
SP10: - - - - -
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:
SP21:
SP22:
SP23:
SP24:
SP25:
SP26:
SP27:
SP28: - -
SP29:
SP30:

Relevant External Links for PLXNB2 Gene

GeneLoc Exon Structure for
PLXNB2
ECgene alternative splicing isoforms for
PLXNB2

Expression for PLXNB2 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PLXNB2 Gene

mRNA expression in normal human tissues for PLXNB2 Gene
mRNA expression by GTEx for PLXNB2 GenemRNA expression by BioGPS for PLXNB2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PLXNB2 Gene

This gene is overexpressed in Nasal epithelium (27.0) and Bone (17.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PLXNB2 Gene



Protein tissue co-expression partners for PLXNB2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PLXNB2 Gene:

PLXNB2

SOURCE GeneReport for Unigene cluster for PLXNB2 Gene:

Hs.3989

Evidence on tissue expression from TISSUES for PLXNB2 Gene

  • Nervous system(4.8)
  • Liver(4.3)
  • Intestine(3.1)
  • Lung(2.4)
  • Eye(2.3)
  • Kidney(2.2)
  • Pancreas(2.1)
  • Skin(2)
genes like me logo Genes that share expression patterns with PLXNB2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PLXNB2 Gene

Orthologs for PLXNB2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLXNB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PLXNB2 33
  • 97.32 (n)
dog
(Canis familiaris)
 Mammalia PLXNB2 33 34
  • 87.4 (n)
cow
(Bos Taurus)
 Mammalia PLXNB2 33 34
  • 86.42 (n)
mouse
(Mus musculus)
 Mammalia Plxnb2 33 16 34
  • 84.58 (n)
rat
(Rattus norvegicus)
 Mammalia Plxnb2 33
  • 83.99 (n)
oppossum
(Monodelphis domestica)
 Mammalia PLXNB2 34
  • 77 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia PLXNB2 34
  • 63 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PLXNB2 33 34
  • 63.52 (n)
lizard
(Anolis carolinensis)
 Reptilia PLXNB2 34
  • 66 (a)
 OneToOne
zebrafish
(Danio rerio)
 Actinopterygii plxnb2a 33 34 34
  • 58.79 (n)
plxnb2b 34
  • 37 (a)
 OneToMany
PLXNB2 (4 of 5) 34
  • 35 (a)
 OneToMany
PLXNB2 (3 of 5) 34
  • 34 (a)
 OneToMany
wufb75d06 33
fruit fly
(Drosophila melanogaster)
 Insecta plexB 34
  • 28 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea plx-2 34
  • 26 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 36 (a)
 OneToMany
Species where no ortholog for PLXNB2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for PLXNB2 Gene

ENSEMBL:
Gene Tree for PLXNB2 (if available)
TreeFam:
Gene Tree for PLXNB2 (if available)

Paralogs for PLXNB2 Gene

Paralogs for PLXNB2 Gene

(12) SIMAP similar genes for PLXNB2 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with PLXNB2: view

Variants for PLXNB2 Gene

Sequence variations from dbSNP and Humsavar for PLXNB2 Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000023005 -- 50,303,056(-) C/T genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant, upstream_transcript_variant
rs1000051783 -- 50,303,309(-) G/A genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant, upstream_transcript_variant
rs1000095053 -- 50,280,860(-) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1000106239 -- 50,275,462(-) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000176906 -- 50,307,333(-) C/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PLXNB2 Gene

Variant ID Type Subtype PubMed ID
dgv781n67 CNV gain 20364138
esv1272171 CNV insertion 17803354
esv1579920 CNV insertion 17803354
esv2724763 CNV deletion 23290073
esv3344719 CNV duplication 20981092
esv3452071 CNV duplication 20981092
nsv1066496 CNV loss 25217958
nsv1136698 CNV deletion 24896259
nsv191216 CNV insertion 16902084
nsv471876 CNV novel sequence insertion 20440878
nsv472275 CNV novel sequence insertion 20440878
nsv474467 CNV novel sequence insertion 20440878
nsv474978 CNV novel sequence insertion 20440878
nsv478597 CNV novel sequence insertion 20440878
nsv480026 CNV novel sequence insertion 20440878
nsv480233 CNV novel sequence insertion 20440878
nsv589208 CNV gain 21841781
nsv589209 CNV loss 21841781
nsv955199 CNV deletion 24416366

Variation tolerance for PLXNB2 Gene

Residual Variation Intolerance Score: 4.46% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.07; 75.29% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLXNB2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLXNB2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLXNB2 Gene

Disorders for PLXNB2 Gene

Additional Disease Information for PLXNB2

ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PLXNB2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PLXNB2 Gene

Publications for PLXNB2 Gene

  1. Plexin B regulates Rho through the guanine nucleotide exchange factors leukemia-associated Rho GEF (LARG) and PDZ-RhoGEF. (PMID: 12183458) Perrot V … Gutkind JS (The Journal of biological chemistry 2002) 2 3 4 22 58
  2. Functional regulation of semaphorin receptors by proprotein convertases. (PMID: 12533544) Artigiani S … Tamagnone L (The Journal of biological chemistry 2003) 3 4 22 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Interplay between scatter factor receptors and B plexins controls invasive growth. (PMID: 15184888) Conrotto P … Giordano S (Oncogene 2004) 3 4 58
  5. Plexins are a large family of receptors for transmembrane, secreted, and GPI-anchored semaphorins in vertebrates. (PMID: 10520995) Tamagnone L … Comoglio PM (Cell 1999) 2 3 58

Products for PLXNB2 Gene

Sources for PLXNB2 Gene

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