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... See more...

Aliases for SEMA3C Gene

Aliases for SEMA3C Gene

  • Semaphorin 3C 2 3 5
  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3C 2 3
  • Semaphorin-3C 3 4
  • Sema E 3 4
  • SEMAE 3 4
  • Semaphorin E 3
  • Semaphorin-E 4
  • SemE 3

External Ids for SEMA3C Gene

Previous HGNC Symbols for SEMA3C Gene

  • SEMAE

Previous GeneCards Identifiers for SEMA3C Gene

  • GC07M078907
  • GC07M079970
  • GC07M079983
  • GC07M080016
  • GC07M080209
  • GC07M080371
  • GC07M074974

Summaries for SEMA3C Gene

Entrez Gene Summary for SEMA3C Gene

  • 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]

GeneCards Summary for SEMA3C Gene

SEMA3C (Semaphorin 3C) is a Protein Coding gene. Diseases associated with SEMA3C include Hirschsprung Disease 1 and Posterior Cortical Atrophy. Among its related pathways are Axon guidance. Gene Ontology (GO) annotations related to this gene include semaphorin receptor binding. An important paralog of this gene is SEMA3F.

UniProtKB/Swiss-Prot Summary for SEMA3C Gene

  • Binds to plexin family members and plays an important role in the regulation of developmental processes. Required for normal cardiovascular development during embryogenesis. Functions as attractant for growing axons, and thereby plays an important role in axon growth and axon guidance (By similarity).

Gene Wiki entry for SEMA3C Gene

Additional gene information for SEMA3C Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEMA3C Gene

Genomics for SEMA3C Gene

GeneHancer (GH) Regulatory Elements for SEMA3C Gene

Promoters and enhancers for SEMA3C Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07J080916 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 +2.1 2056 8.6 ZNF217 EP300 CTCF ZSCAN5C TCF12 NRF1 TEAD4 ZFX ZIC2 FOXA1 lnc-CD36-6 SEMA3C lnc-GNAT3-7
GH07J081208 Promoter/Enhancer 1.5 EPDnew FANTOM5 Ensembl ENCODE 512.5 -288.1 -288145 4 EP300 JUND CTBP1 NCOR1 NFRKB ZNF316 MAFF MYNN TRIM24 ZNF592 SEMA3C lnc-CD36-4 ENSG00000226671 HSALNG0059228
GH07J080940 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 11.2 -20.0 -20002 4.7 ZNF217 TCF12 JUND FOS REST CLOCK CHD1 EP300 GATAD2B CTBP1 lnc-SEMA3C-3 SEMA3C CD36 piR-31199-335
GH07J080880 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.7 +39.3 39317 6.1 ZNF217 ZSCAN5C TCF12 JUND FOS ZNF639 ZNF10 ZIC2 REST TRIM28 SEMA3C GNAT3 piR-41405-090 lnc-GNAT3-7 KR153203-008
GH07J080876 Enhancer 1.3 Ensembl ENCODE dbSUPER 11 +45.2 45158 2 ZNF217 ZSCAN5C TCF12 JUND ZNF639 ZNF10 ZIC2 FOXA1 ZNF623 ZNF423 SEMA3C GNAT3 piR-41405-090 lnc-GNAT3-7 KR153203-008
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA3C on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEMA3C

Top Transcription factor binding sites by QIAGEN in the SEMA3C gene promoter:
  • AML1a
  • AREB6
  • ATF-2
  • GCNF-1
  • Pax-3
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c

Genomic Locations for SEMA3C Gene

Genomic Locations for SEMA3C Gene
chr7:80,742,538-80,922,359
(GRCh38/hg38)
Size:
179,822 bases
Orientation:
Minus strand
chr7:80,371,854-80,551,675
(GRCh37/hg19)
Size:
179,822 bases
Orientation:
Minus strand

Genomic View for SEMA3C Gene

Genes around SEMA3C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA3C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA3C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA3C Gene

Proteins for SEMA3C Gene

  • Protein details for SEMA3C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q99985-SEM3C_HUMAN
    Recommended name:
    Semaphorin-3C
    Protein Accession:
    Q99985
    Secondary Accessions:
    • B4DRL8

    Protein attributes for SEMA3C Gene

    Size:
    751 amino acids
    Molecular mass:
    85207 Da
    Quaternary structure:
    • Interacts with PLXND1.

    Alternative splice isoforms for SEMA3C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA3C Gene

Post-translational modifications for SEMA3C Gene

  • Glycosylation at Asn81, Asn252, Asn268, Asn123, Asn465, Asn585, and Asn586
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • SEM3C_HUMAN (1730)

Other Protein References for SEMA3C Gene

No data available for DME Specific Peptides for SEMA3C Gene

Domains & Families for SEMA3C Gene

Gene Families for SEMA3C Gene

Protein Domains for SEMA3C Gene

Blocks:
  • Immunoglobulin subtype
  • Semaphorin/CD100 antigen
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SEMA3C Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ50181, highly similar to Semaphorin-3C (B4DRL8_HUMAN)
  • Semaphorin-E (SEM3C_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q99985

UniProtKB/Swiss-Prot:

SEM3C_HUMAN :
  • Belongs to the semaphorin family.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA3C: view

Function for SEMA3C Gene

Molecular function for SEMA3C Gene

UniProtKB/Swiss-Prot Function:
Binds to plexin family members and plays an important role in the regulation of developmental processes. Required for normal cardiovascular development during embryogenesis. Functions as attractant for growing axons, and thereby plays an important role in axon growth and axon guidance (By similarity).
GENATLAS Biochemistry:
semaphorin 3C,secreted in the developing nervous system,repellent of the nerve growth cone guidance

LifeMap Function Summary for SEMA3C Gene

During embryonic development, SEMA3C as signaling molecule is secreted from the following cells

Phenotypes From GWAS Catalog for SEMA3C Gene

Gene Ontology (GO) - Molecular Function for SEMA3C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0030215 semaphorin receptor binding IBA 21873635
GO:0045499 chemorepellent activity IBA 21873635
genes like me logo Genes that share ontologies with SEMA3C: view
genes like me logo Genes that share phenotypes with SEMA3C: view

Human Phenotype Ontology for SEMA3C Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SEMA3C Gene

MGI Knock Outs for SEMA3C:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA3C

CRISPR Products

miRNA for SEMA3C Gene

miRTarBase miRNAs that target SEMA3C

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SEMA3C Gene

Localization for SEMA3C Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA3C Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SEMA3C gene
Compartment Confidence
extracellular 5
plasma membrane 4
cytosol 3
golgi apparatus 3
cytoskeleton 2
nucleus 2
endoplasmic reticulum 2
mitochondrion 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SEMA3C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA 21873635
GO:0005887 integral component of plasma membrane IBA 21873635
GO:0070062 extracellular exosome HDA 23533145
genes like me logo Genes that share ontologies with SEMA3C: view

Pathways & Interactions for SEMA3C Gene

PathCards logo

SuperPathways for SEMA3C Gene

SuperPathway Contained pathways
1 Axon guidance
genes like me logo Genes that share pathways with SEMA3C: view

Pathways by source for SEMA3C Gene

1 KEGG pathway for SEMA3C Gene

SIGNOR curated interactions for SEMA3C Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for SEMA3C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001755 neural crest cell migration IBA 21873635
GO:0001756 somitogenesis IEA --
GO:0001974 blood vessel remodeling IEA --
GO:0003148 outflow tract septum morphogenesis ISS --
GO:0003151 outflow tract morphogenesis IEA --
genes like me logo Genes that share ontologies with SEMA3C: view

Drugs & Compounds for SEMA3C Gene

(2) Drugs for SEMA3C Gene - From: PharmGKB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Irinotecan Approved, Investigational Pharma Topoisomerase I inhibitor, TOPO I inhibitor, Topoisomerase 1 Inhibitors 1353
genes like me logo Genes that share compounds with SEMA3C: view

Transcripts for SEMA3C Gene

mRNA/cDNA for SEMA3C Gene

3 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA3C Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21
SP1: - - -
SP2: -
SP3: -
SP4:

Relevant External Links for SEMA3C Gene

GeneLoc Exon Structure for
SEMA3C

Expression for SEMA3C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SEMA3C Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SEMA3C Gene

This gene is overexpressed in Amniocyte (40.8), Lung (8.1), Liver, secretome (8.0), and Pancreas (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SEMA3C Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEMA3C

SOURCE GeneReport for Unigene cluster for SEMA3C Gene:

Hs.269109

mRNA Expression by UniProt/SwissProt for SEMA3C Gene:

Q99985-SEM3C_HUMAN
Tissue specificity: Expressed intensely in the heart, skeletal muscle, colon, small intestine, ovary, testis, and prostate. Faint expression ubiquitously among other organs, including brain.

Evidence on tissue expression from TISSUES for SEMA3C Gene

  • Nervous system(4.2)
  • Heart(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA3C Gene

Germ Layers:
  • ectoderm
  • endoderm
Systems:
  • digestive
  • immune
  • nervous
Regions:
Head and neck:
  • brain
  • head
Thorax:
  • esophagus
Abdomen:
  • duodenum
  • intestine
  • large intestine
  • small intestine
  • stomach
Pelvis:
  • rectum
genes like me logo Genes that share expression patterns with SEMA3C: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for SEMA3C Gene

Orthologs for SEMA3C Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA3C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA3C 31 30
  • 99.69 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA3C 31 30
  • 92.37 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA3C 31 30
  • 92.36 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SEMA3C 31
  • 92 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA3C 31
  • 91 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema3c 30
  • 88.46 (n)
mouse
(Mus musculus)
Mammalia Sema3c 17 31 30
  • 88.15 (n)
chicken
(Gallus gallus)
Aves SEMA3C 31 30
  • 81.45 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA3C 31
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3c 30
  • 76.43 (n)
Str.7048 30
zebrafish
(Danio rerio)
Actinopterygii sema3c 31 30
  • 67.23 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Sema-2a 32
  • 31 (a)
Species where no ortholog for SEMA3C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SEMA3C Gene

ENSEMBL:
Gene Tree for SEMA3C (if available)
TreeFam:
Gene Tree for SEMA3C (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEMA3C: view image

Paralogs for SEMA3C Gene

(18) SIMAP similar genes for SEMA3C Gene using alignment to 7 proteins:

  • SEM3C_HUMAN
  • B4DRL8_HUMAN
  • F2Z2Y0_HUMAN
  • F5H1Z7_HUMAN
  • F8WEP9_HUMAN
  • Q75L25_HUMAN
  • Q75MX0_HUMAN
genes like me logo Genes that share paralogs with SEMA3C: view

Variants for SEMA3C Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEMA3C Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
rs7779029 Drug Response: irinotecan response - Toxicity/ADR 80,902,796(-) T/C INTRON_VARIANT
rs906961857 Uncertain Significance: Severe Myopia 80,802,673(-) T/C MISSENSE_VARIANT
rs1527482 - p.Val337Met
rs35070362 - p.Phe302Ser

Additional dbSNP identifiers (rs#s) for SEMA3C Gene

Structural Variations from Database of Genomic Variants (DGV) for SEMA3C Gene

Variant ID Type Subtype PubMed ID
esv2434401 CNV deletion 19546169
esv2673014 CNV deletion 23128226
esv3305918 CNV mobile element insertion 20981092
esv3309942 CNV mobile element insertion 20981092
esv3340736 CNV insertion 20981092
esv3344655 CNV insertion 20981092
esv3446152 CNV insertion 20981092
esv3931 CNV loss 18987735
nsv1028776 CNV loss 25217958
nsv1034690 CNV gain 25217958
nsv1128346 CNV deletion 24896259
nsv474274 CNV novel sequence insertion 20440878
nsv477389 CNV novel sequence insertion 20440878
nsv478968 CNV novel sequence insertion 20440878

Variation tolerance for SEMA3C Gene

Residual Variation Intolerance Score: 7.58% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.14; 69.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEMA3C Gene

Human Gene Mutation Database (HGMD)
SEMA3C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA3C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA3C Gene

Disorders for SEMA3C Gene

MalaCards: The human disease database

(5) MalaCards diseases for SEMA3C Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hirschsprung disease 1
  • hirschsprung disease, susceptibility to, 1
posterior cortical atrophy
  • pca
cone-rod dystrophy 10
  • cord10
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
tetralogy of fallot
  • tof
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA3C

genes like me logo Genes that share disorders with SEMA3C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA3C Gene

Publications for SEMA3C Gene

  1. Identification of semaphorin E as a non-MDR drug resistance gene of human cancers. (PMID: 9405678) Yamada T … Hirohashi S (Proceedings of the National Academy of Sciences of the United States of America 1997) 3 4 23 54
  2. Identification of human semaphorin E gene expression in rheumatoid synovial cells by mRNA differential display. (PMID: 9168980) Mangasser-Stephan K … Hanselmann RG (Biochemical and biophysical research communications 1997) 2 3 23 54
  3. The cleavage of semaphorin 3C induced by ADAMTS1 promotes cell migration. (PMID: 19915008) Esselens C … Arribas J (The Journal of biological chemistry 2010) 3 23 54
  4. Genome-wide association meta-analysis for total serum bilirubin levels. (PMID: 19414484) Johnson AD … Witteman JC (Human molecular genetics 2009) 3 41 54
  5. GATA6 mutations cause human cardiac outflow tract defects by disrupting semaphorin-plexin signaling. (PMID: 19666519) Kodo K … Yamagishi H (Proceedings of the National Academy of Sciences of the United States of America 2009) 3 23 54

Products for SEMA3C Gene

Sources for SEMA3C Gene