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    PLXNB3 plexin B3 [ Homo sapiens (human) ]

    Gene ID: 5365, updated on 27-Nov-2024

    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
    NEW
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    Genomic context

    See PLXNB3 in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153764249..153779341)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152037914..152053006)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153029704..153044796)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152972381-152972881 Neighboring gene Sharpr-MPRA regulatory region 5891 Neighboring gene B cell receptor associated protein 31 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:152990931-152991752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:152998767-152999458 Neighboring gene ATP binding cassette subfamily D member 1 Neighboring gene uncharacterized LOC124905226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153005935-153006435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153008185-153008886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153008887-153009586 Neighboring gene PLXNB3 antisense RNA 1 Neighboring gene uncharacterized LOC124905227 Neighboring gene SRSF protein kinase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153059193-153059920 Neighboring gene isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma Neighboring gene signal sequence receptor subunit 4

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: SRPK3

    Clone Names

    • FLJ76953

    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 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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

    1. NG_013255.2 RefSeqGene

      Range
      5002..20094
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001163257.2NP_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:70495
      Sema_plexin_B3; The Sema domain, a protein interacting module, of Plexin B3
      cd01179
      Location:9501035
      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:858949
      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:497548
      PSI; Plexin repeat
      pfam01833
      Location:11991265
      TIG; IPT/TIG domain
      pfam08337
      Location:13501899
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain
      cl15674
      Location:10381169
      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 ...
    2. NM_005393.3NP_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:47472
      Sema_plexin_B3; The Sema domain, a protein interacting module, of Plexin B3
      cd01179
      Location:9271012
      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:835926
      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:474525
      PSI; Plexin repeat
      pfam01833
      Location:11761242
      TIG; IPT/TIG domain
      pfam08337
      Location:13271876
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain
      cl15674
      Location:10151146
      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 ...

    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

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      153764249..153779341
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      152037914..152053006
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)