U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from OMIM

    • Showing Current items.

    SEMA3C semaphorin 3C [ Homo sapiens (human) ]

    Gene ID: 10512, updated on 28-Oct-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    SEMA3Cprovided by HGNC
    Official Full Name
    semaphorin 3Cprovided by HGNC
    Primary source
    HGNC:HGNC:10725
    See related
    Ensembl:ENSG00000075223 MIM:602645; AllianceGenome:HGNC:10725
    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
    SemE; SEMAE
    Summary
    This gene encodes a secreted glycoprotein that belongs to the semaphorin class 3 family of neuronal guidance cues. The encoded protein contains an N-terminal sema domain, integrin and immunoglobulin-like domains, and a C-terminal basic domain. Homodimerization and proteolytic cleavage of the C-terminal propeptide are necessary for the function of the encoded protein. It binds a neuropilin co-receptor before forming a heterotrimeric complex with an associated plexin. An increase in the expression of this gene correlates with an increase in cancer cell invasion and adhesion. Naturally occurring mutations in this gene are associated with Hirschsprung disease. [provided by RefSeq, May 2017]
    Expression
    Broad expression in prostate (RPKM 41.1), urinary bladder (RPKM 40.3) and 20 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See SEMA3C in Genome Data Viewer
    Location:
    7q21.11
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (80742538..80922389, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (81993843..82173749, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (80371854..80551705, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901685 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:80157849-80158348 Neighboring gene NANOG hESC enhancer GRCh37_chr7:80162485-80162986 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:80163190-80164389 Neighboring gene CD36 molecule (CD36 blood group) Neighboring gene Sharpr-MPRA regulatory region 7331 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_100118 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:80393335-80394071 Neighboring gene uncharacterized LOC124901686 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:80512613-80513812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18334 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:80627598-80627796 Neighboring gene NANOG hESC enhancer GRCh37_chr7:80642207-80642710 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:80703763-80704962 Neighboring gene HNF1 motif-containing MPRA enhancer 195 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:80809759-80810307 Neighboring gene voltage dependent anion channel 3 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:80924025-80924526 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:80983381-80984580 Neighboring gene eukaryotic translation initiation factor 4E pseudogene 4

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Class 3 semaphorins are transcriptionally regulated by 1,25(OH)(2)D(3) in osteoblasts. Ryynänen J, et al. J Steroid Biochem Mol Biol, 2017 Oct. PMID 28189595, Free PMC Article
    2. Semaphorin-3C Is Upregulated in Polycystic Kidney Epithelial Cells and Inhibits Angiogenesis of Glomerular Endothelial Cells. Kim BH, et al. Am J Nephrol, 2020. PMID 32610315
    3. Semaphorin 3 C is a Novel Adipokine Representing Exercise-Induced Improvements of Metabolism in Metabolically Healthy Obese Young Males. Nam JS, et al. Sci Rep, 2020 Jun 19. PMID 32561824, Free PMC Article
    4. The Anti-Tumorigenic Activity of Sema3C in the Chick Embryo Chorioallantoic Membrane Model. Valiulytė I, et al. Int J Mol Sci, 2019 Nov 12. PMID 31726800, Free PMC Article
    5. Semaphorins in kidney development and disease: modulators of ureteric bud branching, vascular morphogenesis, and podocyte-endothelial crosstalk. Reidy K, et al. Pediatr Nephrol, 2011 Sep. PMID 21336944, Free PMC Article

    See all (79) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Semaphorin 3C (Sema3C) reshapes stromal microenvironment to promote hepatocellular carcinoma progression.
      Title: Semaphorin 3C (Sema3C) reshapes stromal microenvironment to promote hepatocellular carcinoma progression.
    2. Clinically-observed FOXA1 mutations upregulate SEMA3C through transcriptional derepression in prostate cancer.
      Title: Clinically-observed FOXA1 mutations upregulate SEMA3C through transcriptional derepression in prostate cancer.
    3. Semaphorin 3C exacerbates liver fibrosis.
      Title: Semaphorin 3C exacerbates liver fibrosis.
    4. Semaphorin 3C promotes de novo steroidogenesis in prostate cancer cells.
      Title: Semaphorin 3C promotes de novo steroidogenesis in prostate cancer cells.
    5. Sema3C signaling is an alternative activator of the canonical WNT pathway in glioblastoma.
      Title: Sema3C signaling is an alternative activator of the canonical WNT pathway in glioblastoma.
    6. SEMA3C induces androgen synthesis in prostatic stromal cells through paracrine signaling.
      Title: SEMA3C induces androgen synthesis in prostatic stromal cells through paracrine signaling.
    7. MAOA promotes prostate cancer cell perineural invasion through SEMA3C/PlexinA2/NRP1-cMET signaling.
      Title: MAOA promotes prostate cancer cell perineural invasion through SEMA3C/PlexinA2/NRP1-cMET signaling.
    8. MiR-146a Regulates Migration and Invasion by Targeting NRP2 in Circulating-Tumor Cell Mimicking Suspension Cells.
      Title: MiR-146a Regulates Migration and Invasion by Targeting NRP2 in Circulating-Tumor Cell Mimicking Suspension Cells.
    9. Semaphorin-3C Is Upregulated in Polycystic Kidney Epithelial Cells and Inhibits Angiogenesis of Glomerular Endothelial Cells.
      Title: Semaphorin-3C Is Upregulated in Polycystic Kidney Epithelial Cells and Inhibits Angiogenesis of Glomerular Endothelial Cells.
    10. Whole-genome sequencing identifies functional noncoding variation in SEMA3C that cosegregates with dyslexia in a multigenerational family.
      Title: Whole-genome sequencing identifies functional noncoding variation in SEMA3C that cosegregates with dyslexia in a multigenerational family.
    Submit: New GeneRIF Correction See all GeneRIFs (40)

    Phenotypes

    Go to the top of the page Help

    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
    Genome-wide association meta-analysis for total serum bilirubin levels.
    EBI GWAS Catalog

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in axon guidance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in blood vessel remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cardiac endothelial to mesenchymal transition ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cardiac right ventricle morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in dichotomous subdivision of terminal units involved in salivary gland branching IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in immune response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in limb bud formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neural tube development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in outflow tract septum morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in post-embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in pulmonary myocardium development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to xenobiotic stimulus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    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 somitogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    semaphorin-3C
    Names
    sema E
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C
    semaphorin E

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_054744.2 RefSeqGene

      Range
      8338..184851
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001350120.2 → NP_001337049.1  semaphorin-3C isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AA853650, AB000220, AC004972, AK304294, BC030690, BM473251, CN334967, CN334969, DC415474
      UniProtKB/TrEMBL
      B4E2I9
      Conserved Domains (3) summary
      cd05871
      Location:593 → 682
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11251
      Location:63 → 532
      Sema_3C; The Sema domain, a protein interacting module, of semaphorin 3C (Sema3C)
      smart00423
      Location:531 → 568
      PSI; domain found in Plexins, Semaphorins and Integrins

    2. NM_001350121.2 → NP_001337050.1  semaphorin-3C isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC004880, AC073850, AC093683
      UniProtKB/TrEMBL
      B4E2I9
      Conserved Domains (3) summary
      cd05871
      Location:517 → 606
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11251
      Location:1 → 456
      Sema_3C; The Sema domain, a protein interacting module, of semaphorin 3C (Sema3C)
      smart00423
      Location:455 → 492
      PSI; domain found in Plexins, Semaphorins and Integrins

    3. NM_006379.5 → NP_006370.1  semaphorin-3C isoform 2 precursor

      See identical proteins and their annotated locations for NP_006370.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AA853650, AB000220, AK304294, BC030690, BM473251, CN334967, CN334969
      Consensus CDS
      CCDS5596.1
      UniProtKB/Swiss-Prot
      B4DRL8, Q99985
      UniProtKB/TrEMBL
      B4E2I9
      Related
      ENSP00000265361.3, ENST00000265361.8
      Conserved Domains (3) summary
      cd05871
      Location:575 → 664
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11251
      Location:45 → 514
      Sema_3C; The Sema domain, a protein interacting module, of semaphorin 3C (Sema3C)
      smart00423
      Location:513 → 550
      PSI; domain found in Plexins, Semaphorins and Integrins

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      80742538..80922389 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      81993843..82173749 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99985.2 GenPept UniProtKB/Swiss-Prot:Q99985

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools