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    PLXNC1 plexin C1 [ Homo sapiens (human) ]

    Gene ID: 10154, updated on 1-Mar-2024

    Summary

    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
    NEW
    Try the new Gene table
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    Genomic context

    See PLXNC1 in Genome Data Viewer
    Location:
    12q22
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (94148577..94307675)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (94129732..94288500)
    105.20220307 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

    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?

    Phenotypes

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 GTPase activity 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
     
    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 
    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

    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)

    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_050648.2 RefSeqGene

      Range
      5002..164100
      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, Q59H25
      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_037687.2 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_2023_10

    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_006719186.5XP_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_047428050.1XP_047284006.1  plexin-C1 isoform X2

    3. XM_011537730.4XP_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
    4. XM_011537731.4XP_011536033.1  plexin-C1 isoform X4

      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

    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_054370727.1XP_054226702.1  plexin-C1 isoform X1

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

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

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