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    PLXNC1 plexin C1 [ Homo sapiens (human) ]

    Gene ID: 10154, updated on 17-Jun-2019

    Summary

    Official Symbol
    PLXNC1provided by HGNC
    Official Full Name
    plexin C1provided by HGNC
    Primary source
    HGNC:HGNC:9106
    See related
    Ensembl:ENSG00000136040 MIM:604259
    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
    CD232; VESPR; PLXN-C1
    Summary
    This gene encodes a member of the plexin family. Plexins are transmembrane receptors for semaphorins, a large family of proteins that regulate axon guidance, cell motility and migration, and the immune response. The encoded protein and its ligand regulate melanocyte adhesion, and viral semaphorins may modulate the immune response by binding to this receptor. The encoded protein may be a tumor suppressor protein for melanoma. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jan 2011]
    Expression
    Broad expression in appendix (RPKM 8.1), testis (RPKM 6.6) and 23 other tissues See more
    Orthologs

    Genomic context

    See PLXNC1 in Genome Data Viewer
    Location:
    12q22
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (94148577..94307675)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (94542499..94701451)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369913 Neighboring gene REST corepressor 2 pseudogene Neighboring gene centrosomal protein 83 Neighboring gene RNA, 7SL, cytoplasmic 330, pseudogene Neighboring gene RNA binding motif single stranded interacting protein 2 pseudogene 1

    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 FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    A genome-wide scan for breast cancer risk haplotypes among African American women.
    NHGRI GWA Catalog
    TSPYL5 SNPs: association with plasma estradiol concentrations and aromatase expression.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Axon guidance, organism-specific biosystem (from KEGG)
      Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
    • Axon guidance, conserved biosystem (from KEGG)
      Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
    • Axon guidance, organism-specific biosystem (from REACTOME)
      Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • Other semaphorin interactions, organism-specific biosystem (from REACTOME)
      Other semaphorin interactions, organism-specific biosystemThere are eight classes of semaphorins and four types of plexins. Semaphorin (SEMA) classes 1 and 2 are found in invertebrates and classes 3-7 are vertebrate sempahorines. Sempahorin class 3 is secre...
    • Semaphorin interactions, organism-specific biosystem (from REACTOME)
      Semaphorin interactions, organism-specific biosystemSemaphorins are a large family of cell surface and secreted guidance molecules divided into eight classes on the basis of their structures. They all have an N-terminal conserved sema domain. Semaphor...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    semaphorin receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    signaling receptor binding TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    cell adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation of cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    regulation of GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    regulation of cell shape IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin-plexin signaling pathway involved in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    membrane HDA PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    semaphorin receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    plexin-C1
    Names
    plexin (semaphorin receptor)
    receptor for viral semaphorin protein
    receptor for virally-encoded semaphorin
    virus-encoded semaphorin protein receptor

    NCBI Reference Sequences (RefSeq)

    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_050648.1 RefSeqGene

      Range
      5001..163953
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005761.3NP_005752.1  plexin-C1 precursor

      See identical proteins and their annotated locations for NP_005752.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the functional protein.
      Source sequence(s)
      AC073655, AC123567
      Consensus CDS
      CCDS9049.1
      UniProtKB/Swiss-Prot
      O60486
      Related
      ENSP00000258526.4, ENST00000258526.9
      Conserved Domains (6) summary
      cd11246
      Location:44453
      Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
      smart00423
      Location:591635
      PSI; domain found in Plexins, Semaphorins and Integrins
      smart00429
      Location:753841
      IPT; ig-like, plexins, transcription factors
      pfam01437
      Location:454507
      PSI; Plexin repeat
      pfam01833
      Location:664750
      TIG; IPT/TIG domain
      pfam08337
      Location:10121535
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain

    RNA

    1. NR_037687.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks multiple 5' exons but contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest in-frame ORF. Translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA609130, AB208934, AC073655, AK304327

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

      Range
      94148577..94307675
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006719186.4XP_006719249.1  plexin-C1 isoform X1

      Conserved Domains (6) summary
      cd11246
      Location:44453
      Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
      smart00423
      Location:591635
      PSI; domain found in Plexins, Semaphorins and Integrins
      smart00429
      Location:753841
      IPT; ig-like, plexins, transcription factors
      pfam01437
      Location:454507
      PSI; Plexin repeat
      pfam01833
      Location:664750
      TIG; IPT/TIG domain
      pfam08337
      Location:10121522
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    2. XM_017018672.2XP_016874161.1  plexin-C1 isoform X4

    3. XM_017018671.2XP_016874160.1  plexin-C1 isoform X2

    4. XM_011537730.3XP_011536032.1  plexin-C1 isoform X3

      Conserved Domains (6) summary
      cd11246
      Location:44453
      Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
      smart00423
      Location:591635
      PSI; domain found in Plexins, Semaphorins and Integrins
      smart00429
      Location:753841
      IPT; ig-like, plexins, transcription factors
      pfam01437
      Location:454507
      PSI; Plexin repeat
      pfam01833
      Location:664750
      TIG; IPT/TIG domain
      pfam08337
      Location:10121292
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain
    5. XM_011537731.3XP_011536033.1  plexin-C1 isoform X5

      Conserved Domains (6) summary
      cd11246
      Location:44453
      Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
      smart00423
      Location:591635
      PSI; domain found in Plexins, Semaphorins and Integrins
      smart00429
      Location:753841
      IPT; ig-like, plexins, transcription factors
      pfam01437
      Location:454507
      PSI; Plexin repeat
      pfam01833
      Location:664750
      TIG; IPT/TIG domain
      cl02569
      Location:10101029
      RasGAP; Ras GTPase Activating Domain
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