This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010] See more...

Aliases for SEMA6C Gene

Aliases for SEMA6C Gene

  • Semaphorin 6C 2 3 5
  • Sema Domain, Transmembrane Domain (TM), And Cytoplasmic Domain, (Semaphorin) 6C 2 3
  • Semaphorin-6C 3 4
  • Semaphorin-Y 3 4
  • Sema Y 3 4
  • SEMAY 3 4
  • M-Sema Y2 2
  • M-SemaY2 3
  • KIAA1869 4
  • M-SemaY 3

External Ids for SEMA6C Gene

Previous GeneCards Identifiers for SEMA6C Gene

  • GC01M148946
  • GC01M146851
  • GC01M147879
  • GC01M148320
  • GC01M147918
  • GC01M149370
  • GC01M151104
  • GC01M122481

Summaries for SEMA6C Gene

Entrez Gene Summary for SEMA6C Gene

  • This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]

GeneCards Summary for SEMA6C Gene

SEMA6C (Semaphorin 6C) is a Protein Coding gene. Diseases associated with SEMA6C include Diversion Colitis. 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 SEMA6D.

UniProtKB/Swiss-Prot Summary for SEMA6C Gene

  • Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections.

Gene Wiki entry for SEMA6C Gene

Additional gene information for SEMA6C Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEMA6C Gene

Genomics for SEMA6C Gene

GeneHancer (GH) Regulatory Elements for SEMA6C Gene

Promoters and enhancers for SEMA6C Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA6C on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEMA6C

Top Transcription factor binding sites by QIAGEN in the SEMA6C gene promoter:
  • E47
  • MAZR
  • Nkx2-5
  • Olf-1
  • PPAR-alpha
  • RREB-1
  • Spz1
  • Tal-1
  • TGIF

Genomic Locations for SEMA6C Gene

Genomic Locations for SEMA6C Gene
chr1:151,131,685-151,146,664
(GRCh38/hg38)
Size:
14,980 bases
Orientation:
Minus strand
chr1:151,104,161-151,119,140
(GRCh37/hg19)
Size:
14,980 bases
Orientation:
Minus strand

Genomic View for SEMA6C Gene

Genes around SEMA6C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA6C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA6C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA6C Gene

Proteins for SEMA6C Gene

  • Protein details for SEMA6C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H3T2-SEM6C_HUMAN
    Recommended name:
    Semaphorin-6C
    Protein Accession:
    Q9H3T2
    Secondary Accessions:
    • D3DV15
    • Q5JR71
    • Q5JR72
    • Q5JR73
    • Q8WXT8
    • Q8WXT9
    • Q8WXU0
    • Q96JF8

    Protein attributes for SEMA6C Gene

    Size:
    930 amino acids
    Molecular mass:
    99686 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB47498.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for SEMA6C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA6C Gene

Post-translational modifications for SEMA6C Gene

  • Glycosylation at Asn70, Asn286, and Asn437
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEMA6C Gene

Domains & Families for SEMA6C Gene

Gene Families for SEMA6C Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SEMA6C Gene

Blocks:
  • Semaphorin/CD100 antigen
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SEMA6C Gene

GenScript: Design optimal peptide antigens:
  • SEMA6C protein (Q1RMY5_HUMAN)
  • SEMA6C protein (Q24JR3_HUMAN)
  • Semaphorin-Y (SEM6C_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H3T2

UniProtKB/Swiss-Prot:

SEM6C_HUMAN :
  • Belongs to the semaphorin family.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA6C: view

Function for SEMA6C Gene

Molecular function for SEMA6C Gene

UniProtKB/Swiss-Prot Function:
Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections.

Phenotypes From GWAS Catalog for SEMA6C Gene

Gene Ontology (GO) - Molecular Function for SEMA6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0030215 semaphorin receptor binding IEA,IBA 21873635
GO:0045499 chemorepellent activity IBA 21873635
genes like me logo Genes that share ontologies with SEMA6C: view
genes like me logo Genes that share phenotypes with SEMA6C: view

Animal Models for SEMA6C Gene

MGI Knock Outs for SEMA6C:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA6C

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SEMA6C

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for SEMA6C Gene

Localization for SEMA6C Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA6C Gene

Cell membrane; Single-pass type I membrane protein.

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 SEMA6C gene
Compartment Confidence
plasma membrane 5
extracellular 4
cytoskeleton 2
mitochondrion 2
nucleus 2
cytosol 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Cytosol (2)
  • Nucleoli fibrillar center (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SEMA6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SEMA6C: view

Pathways & Interactions for SEMA6C Gene

PathCards logo

SuperPathways for SEMA6C Gene

SuperPathway Contained pathways
1 Axon guidance
genes like me logo Genes that share pathways with SEMA6C: view

Pathways by source for SEMA6C Gene

1 KEGG pathway for SEMA6C Gene

Interacting Proteins for SEMA6C Gene

;

Gene Ontology (GO) - Biological Process for SEMA6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001755 neural crest cell migration IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0007411 axon guidance IBA 21873635
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with SEMA6C: view

No data available for SIGNOR curated interactions for SEMA6C Gene

Drugs & Compounds for SEMA6C Gene

No Compound Related Data Available

Transcripts for SEMA6C Gene

mRNA/cDNA for SEMA6C Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SEMA6C

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA6C Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^
SP1: - - - - - - -
SP2:
SP3: - - - - - - -
SP4: -
SP5:
SP6:
SP7: - - -
SP8: - - - - -
SP9:
SP10:
SP11:
SP12:

ExUns: 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21a · 21b
SP1:
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for SEMA6C Gene

GeneLoc Exon Structure for
SEMA6C

Expression for SEMA6C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SEMA6C Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA6C Gene

This gene is overexpressed in Muscle - Skeletal (x10.4).

Protein differential expression in normal tissues from HIPED for SEMA6C Gene

This gene is overexpressed in Esophagus (52.3) and Neutrophil (15.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SEMA6C Gene



Protein tissue co-expression partners for SEMA6C Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEMA6C

SOURCE GeneReport for Unigene cluster for SEMA6C Gene:

Hs.516316

mRNA Expression by UniProt/SwissProt for SEMA6C Gene:

Q9H3T2-SEM6C_HUMAN
Tissue specificity: In adult tissues, expressed only in skeletal muscle.

Evidence on tissue expression from TISSUES for SEMA6C Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with SEMA6C: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA6C Gene

Orthologs for SEMA6C Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA6C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA6C 31 30
  • 99.69 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA6C 31 30
  • 89.66 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA6C 31 30
  • 87.93 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema6c 30
  • 87.06 (n)
mouse
(Mus musculus)
Mammalia Sema6c 17 31 30
  • 86.34 (n)
oppossum
(Monodelphis domestica)
Mammalia SEMA6C 31
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 31 (a)
ManyToMany
-- 31
  • 24 (a)
ManyToMany
chicken
(Gallus gallus)
Aves LOC100859892 30
  • 59.94 (n)
SEMA6C 31
  • 52 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA6C 31
  • 66 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii sema6d 31
  • 43 (a)
OneToMany
sema6e 31
  • 41 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Sema-1b 32
  • 36 (a)
Sema-1a 32
  • 35 (a)
CG4383 32
  • 34 (a)
Sema-2a 31 32
  • 28 (a)
ManyToMany
Sema-2b 31
  • 24 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea mab-20 32
  • 28 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 31 (a)
OneToMany
Species where no ortholog for SEMA6C 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 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for SEMA6C Gene

ENSEMBL:
Gene Tree for SEMA6C (if available)
TreeFam:
Gene Tree for SEMA6C (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEMA6C: view image

Paralogs for SEMA6C Gene

(9) SIMAP similar genes for SEMA6C Gene using alignment to 3 proteins:

  • SEM6C_HUMAN
  • Q1RMY5_HUMAN
  • Q24JR3_HUMAN
genes like me logo Genes that share paralogs with SEMA6C: view

Variants for SEMA6C Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEMA6C Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
717809 Benign: not provided 151,135,315(-) G/A INTRON_VARIANT
767698 Benign: not provided 151,134,828(-) C/G MISSENSE_VARIANT
767699 Benign: not provided 151,136,850(-) T/G INTRON_VARIANT
770327 Benign: not provided 151,142,531(-) G/A MISSENSE_VARIANT
rs4971007 - p.Thr455Pro

Additional dbSNP identifiers (rs#s) for SEMA6C Gene

Structural Variations from Database of Genomic Variants (DGV) for SEMA6C Gene

Variant ID Type Subtype PubMed ID
dgv2n68 CNV loss 17160897
nsv522840 CNV gain 19592680

Variation tolerance for SEMA6C Gene

Residual Variation Intolerance Score: 65.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.77; 73.51% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEMA6C Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA6C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA6C Gene

Disorders for SEMA6C Gene

MalaCards: The human disease database

(1) MalaCards diseases for SEMA6C Gene - From: DISEASES

Disorder Aliases PubMed IDs
diversion colitis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA6C

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SEMA6C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA6C Gene

Publications for SEMA6C Gene

  1. Identification, characterization, and functional study of the two novel human members of the semaphorin gene family. (PMID: 12110693) Qu X … He F (The Journal of biological chemistry 2002) 2 3 4 54
  2. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. (PMID: 19054571) Gregório SP … Dias-Neto E (Psychiatry research 2009) 3 41 54
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 54
  4. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11347906) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 3 4 54
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 54

Products for SEMA6C Gene

Sources for SEMA6C Gene