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    PLXNC1 plexin C1 [ Homo sapiens (human) ]

    Gene ID: 10154, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PLXNC1provided by HGNC
    Official Full Name
    plexin C1provided by HGNC
    Primary source
    HGNC:HGNC:9106
    See related
    Ensembl:ENSG00000136040 MIM:604259; AllianceGenome:HGNC:9106
    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
    mouse all
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    Genomic context

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    See PLXNC1 in Genome Data Viewer
    Location:
    12q22
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (94148577..94307675)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (94129732..94288500)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (94542353..94701451)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6774 Neighboring gene uncharacterized LOC124902986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4720 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6778 Neighboring gene REST corepressor 2 pseudogene Neighboring gene uncharacterized LOC124902988 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:94563164-94563859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:94564987-94565496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:94579005-94579506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:94580673-94581173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6782 Neighboring gene uncharacterized LOC124902987 Neighboring gene MPRA-validated peak1895 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:94654721-94655463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4726 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94657254-94658018 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94658019-94658782 Neighboring gene centrosomal protein 83 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:94698110-94698989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4727 Neighboring gene RNA, 7SL, cytoplasmic 330, pseudogene Neighboring gene RNA binding motif single stranded interacting protein 2 pseudogene 1

    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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    Related articles in PubMed

    1. Soluble CD100 functions on human monocytes and immature dendritic cells require plexin C1 and plexin B1, respectively. Chabbert-de Ponnat I, et al. Int Immunol, 2005 Apr. PMID 15746246
    2. Identification of genes with abnormal expression changes in acute myeloid leukemia. Stirewalt DL, et al. Genes Chromosomes Cancer, 2008 Jan. PMID 17910043
    3. The Relationship Between Plexin C1 Overexpression and Survival in Hepatocellular Carcinoma: a Turkish Oncology Group (TOG) Study. NazimTurhal S, et al. J Gastrointest Cancer, 2022 Jun. PMID 33656690
    4. Molecular profiling of the "plexinome" in melanoma and pancreatic cancer. Balakrishnan A, et al. Hum Mutat, 2009 Aug. PMID 19462467, Free PMC Article
    5. Mechanical tension alters semaphorin expression in the periodontium. Spencer AY, et al. J Periodontol, 2009 Oct. PMID 19792857

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Semaphorin 7A promotes endothelial permeability and inflammation via plexin C1 and integrin beta1 in Kawasaki disease.
      Title: Semaphorin 7A promotes endothelial permeability and inflammation via plexin C1 and integrin β1 in Kawasaki disease.
    2. PLXNC1 interference alleviates the inflammatory injury, apoptosis and extracellular matrix degradation of IL-1beta-exposed chondrocytes via suppressing GRP78 expression.
      Title: PLXNC1 interference alleviates the inflammatory injury, apoptosis and extracellular matrix degradation of IL-1β-exposed chondrocytes via suppressing GRP78 expression.
    3. The Relationship Between Plexin C1 Overexpression and Survival in Hepatocellular Carcinoma: a Turkish Oncology Group (TOG) Study.
      Title: The Relationship Between Plexin C1 Overexpression and Survival in Hepatocellular Carcinoma: a Turkish Oncology Group (TOG) Study.
    4. Results indicated that PLXNC1 was a direct target of miR-4500. Its knockdown inhibits proliferation and invasion of papillary thyroid cancer (PTC) cells. On the contrary, its overexpression of impairs miR-4500-induced inhibition of PTC malignancy.
      Title: MiR-4500 Regulates PLXNC1 and Inhibits Papillary Thyroid Cancer Progression.
    5. Results indicate that long non-coding RNA (lncRNA) CASC2 can promote PLXNC1 expression by sponging miR-181a, thereby inhibiting the proliferation and invasion of melanoma cells.
      Title: Long non-coding RNA CASC2 inhibits tumorigenesis via the miR-181a/PLXNC1 axis in melanoma.
    6. Plexin C1 deficiency permits synaptotagmin 7-mediated macrophage migration and enhances mammalian lung fibrosis
      Title: Plexin C1 deficiency permits synaptotagmin 7-mediated macrophage migration and enhances mammalian lung fibrosis.
    7. loss of Plexin C1 in melanoma may promote early steps in melanoma progression through suppression of migration and proliferation
      Title: The neural guidance receptor Plexin C1 delays melanoma progression.
    8. Study reports the structures of Sema7A and A39R complexed with the Semaphorin-binding module of PlexinC1; both structures show two PlexinC1 molecules symmetrically bridged by Semaphorin dimers.
      Title: Structural basis of semaphorin-plexin recognition and viral mimicry from Sema7A and A39R complexes with PlexinC1.
    9. significant loss of Plexin C1 in metastatic melanoma compared with primary melanoma, suggesting the possibility that the Plexin C1 receptor is a tumor suppressor protein for melanoma
      Title: The semaphorin 7A receptor Plexin C1 is lost during melanoma metastasis.
    10. Plexin C1, a receptor for semaphorin 7a, inactivates cofilin and is a potential tumor suppressor for melanoma progression.
      Title: Plexin C1, a receptor for semaphorin 7a, inactivates cofilin and is a potential tumor suppressor for melanoma progression.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

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

    Variation

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    See Variation Viewer (GRCh37.p13)

    Pathways from PubChem

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    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 signaling receptor binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cell shape IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of synapse pruning IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cerebellar climbing fiber to Purkinje cell synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane HDA 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
    		  

    General protein information

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    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)

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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_050648.2 RefSeqGene

      Range
      5002..164100
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005761.3 → NP_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, Q59H25
      Related
      ENSP00000258526.4, ENST00000258526.9
      Conserved Domains (6) summary
      cd11246
      Location:44 → 453
      Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
      smart00423
      Location:591 → 635
      PSI; domain found in Plexins, Semaphorins and Integrins
      smart00429
      Location:753 → 841
      IPT; ig-like, plexins, transcription factors
      pfam01437
      Location:454 → 507
      PSI; Plexin repeat
      pfam01833
      Location:664 → 750
      TIG; IPT/TIG domain
      pfam08337
      Location:1012 → 1535
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain

    RNA

    1. NR_037687.2 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)
      AC073655

    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_000012.12 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_006719186.5 → XP_006719249.1  plexin-C1 isoform X1

      Conserved Domains (6) summary
      cd11246
      Location:44 → 453
      Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
      smart00423
      Location:591 → 635
      PSI; domain found in Plexins, Semaphorins and Integrins
      smart00429
      Location:753 → 841
      IPT; ig-like, plexins, transcription factors
      pfam01437
      Location:454 → 507
      PSI; Plexin repeat
      pfam01833
      Location:664 → 750
      TIG; IPT/TIG domain
      pfam08337
      Location:1012 → 1522
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain

    2. XM_047428050.1 → XP_047284006.1  plexin-C1 isoform X2

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

      Conserved Domains (6) summary
      cd11246
      Location:44 → 453
      Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
      smart00423
      Location:591 → 635
      PSI; domain found in Plexins, Semaphorins and Integrins
      smart00429
      Location:753 → 841
      IPT; ig-like, plexins, transcription factors
      pfam01437
      Location:454 → 507
      PSI; Plexin repeat
      pfam01833
      Location:664 → 750
      TIG; IPT/TIG domain
      pfam08337
      Location:1012 → 1292
      Plexin_cytopl; Plexin cytoplasmic RasGAP domain

    4. XM_011537731.4 → XP_011536033.1  plexin-C1 isoform X4

      Conserved Domains (6) summary
      cd11246
      Location:44 → 453
      Sema_plexin_C1; The Sema domain, a protein interacting module, of Plexin C1
      smart00423
      Location:591 → 635
      PSI; domain found in Plexins, Semaphorins and Integrins
      smart00429
      Location:753 → 841
      IPT; ig-like, plexins, transcription factors
      pfam01437
      Location:454 → 507
      PSI; Plexin repeat
      pfam01833
      Location:664 → 750
      TIG; IPT/TIG domain
      cl02569
      Location:1010 → 1029
      RasGAP; Ras GTPase Activating Domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      94129732..94288500
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370727.1 → XP_054226702.1  plexin-C1 isoform X1

    2. XM_054370728.1 → XP_054226703.1  plexin-C1 isoform X2

    3. XM_054370729.1 → XP_054226704.1  plexin-C1 isoform X3

    4. XM_054370730.1 → XP_054226705.1  plexin-C1 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60486.1 GenPept UniProtKB/Swiss-Prot:O60486

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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