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SEMA3C semaphorin 3C [ Homo sapiens (human) ]

Gene ID: 10512, updated on 2-Nov-2024

Summary

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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
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Genomic context

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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

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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. 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

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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 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

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Preferred Names
semaphorin-3C
Names
sema E
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C
semaphorin E

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_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.

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