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PLXNC1 plexin C1 [ Homo sapiens (human) ]

Gene ID: 10154, updated on 15-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 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (94148723..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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