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    PLXNA3 plexin A3 [ Homo sapiens (human) ]

    Gene ID: 55558, updated on 14-Nov-2024

    Summary

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    Official Symbol
    PLXNA3provided by HGNC
    Official Full Name
    plexin A3provided by HGNC
    Primary source
    HGNC:HGNC:9101
    See related
    Ensembl:ENSG00000130827 MIM:300022; AllianceGenome:HGNC:9101
    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
    6.3; PLXN3; PLXN4; XAP-6; HSSEXGENE
    Summary
    This gene encodes a member of the plexin class of proteins. The encoded protein is a class 3 semaphorin receptor, and may be involved in cytoskeletal remodeling and as well as apoptosis. Studies of a similar gene in zebrafish suggest that it is important for axon pathfinding in the developing nervous system. This gene may be associated with tumor progression. [provided by RefSeq, Aug 2013]
    Expression
    Ubiquitous expression in skin (RPKM 7.2), ovary (RPKM 7.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PLXNA3 in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154458281..154477779)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152694791..152714288)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153686621..153706118)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153665032-153665532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153666887-153667386 Neighboring gene GDP dissociation inhibitor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153672115-153672682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153673251-153673818 Neighboring gene family with sequence similarity 50 member A Neighboring gene microRNA 6858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:153687524-153688076 Neighboring gene Sharpr-MPRA regulatory region 3405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21109 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153707495-153707994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30063 Neighboring gene L antigen family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153713643-153714401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:153714402-153715160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30064 Neighboring gene ubiquitin like 4A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21112 Neighboring gene solute carrier family 10 member 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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?
    1. Semaphorin-Plexin Signaling: From Axonal Guidance to a New X-Linked Intellectual Disability Syndrome.
      Title: Semaphorin-Plexin Signaling: From Axonal Guidance to a New X-Linked Intellectual Disability Syndrome.
    2. Exome analysis of Kuwaiti multiple sclerosis patients revealed a missense variant (rs5945430) in Plexin A3 (PLXNA3) gene (Xq28) associated with male-specific MS severity and disability.
      Title: PLXNA3 Variant rs5945430 is Associated with Severe Clinical Course in Male Multiple Sclerosis Patients.
    3. Data indicate that plexin A1-4 (PLXNA1-4) mediation of neuroanatomical traits can be detected using in vivo neuroimaging techniques.
      Title: PlexinA polymorphisms mediate the developmental trajectory of human corpus callosum microstructure.
    4. in vitro analysis on PLXNA3 also suggest that this gene may have some form of growth suppressive role in breast cancer, in addition to a similar role for the gene previously reported in ovarian cancer.
      Title: Semaphorin-plexin signalling genes associated with human breast tumourigenesis.
    5. Data show that the expression of Sema3A receptors (neuropilin-1 (NRP-1), NRP-2, plexin A1, plexin A2, and plexin A3) significantly increased during M-CSF-mediated differentiation of monocytes into macrophages.
      Title: Expression and function of semaphorin 3A and its receptors in human monocyte-derived macrophages.
    Submit: New GeneRIF Correction

    Phenotypes

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    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

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein 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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in axon extension involved in axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in branchiomotor neuron axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in facial nerve structural organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in gonadotrophin-releasing hormone neuronal migration to the hypothalamus IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within hippocampus development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in motor neuron axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative chemotaxis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of axon extension involved in axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within neuron projection guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in olfactory nerve formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within pyramidal neuron development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cell migration 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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in semaphorin-plexin signaling pathway NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in trigeminal nerve structural organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    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
    		  
    part_of semaphorin receptor complex TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    plexin-A3
    Names
    Sex chromosome X transmembrane protein of HGF receptor family 3
    plexin-4
    semaphorin receptor SEX

    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

    1. NG_021298.2 RefSeqGene

      Range
      5007..20372
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_017514.5 → NP_059984.3  plexin-A3 precursor

      Status: REVIEWED

      Source sequence(s)
      AC244090, AW001914, BF798844, BG820285, BQ718472, BQ720233, CN427844, CN484803, HY098587, HY158513, X87852
      Consensus CDS
      CCDS14752.1
      UniProtKB/Swiss-Prot
      P51805, Q5HY36
      Related
      ENSP00000358696.3, ENST00000369682.4
      Conserved Domains (8) summary
      cd11273
      Location:21 → 489
      Sema_plexin_A3; The Sema domain, a protein interacting module, of Plexin A3
      smart00423
      Location:788 → 831
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00603
      Location:1125 → 1208
      IPT_PCSR; IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the ...
      cd01179
      Location:935 → 1021
      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:840 → 934
      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 ...
      cd01181
      Location:1023 → 1123
      IPT_plexin_repeat3; Third 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:490 → 530
      PSI; Plexin repeat
      pfam08337
      Location:1294 → 1841
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain

    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
      154458281..154477779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442247.1 → XP_047298203.1  plexin-A3 isoform X1

    RNA

    1. XR_007068193.1 RNA Sequence

    2. XR_430556.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      152694791..152714288
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054327369.1 → XP_054183344.1  plexin-A3 isoform X1

    RNA

    1. XR_008485494.1 RNA Sequence

    2. XR_008485493.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P51805.3 GenPept UniProtKB/Swiss-Prot:P51805

    Gene LinkOut

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