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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-Y 3 4
  • Sema Y 3 4
  • SEMAY 3 4
  • Semaphorin-6C 3
  • 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. Among its related pathways are Axon guidance. GO annotations related to this gene include receptor activity and semaphorin receptor binding. An important paralog of this gene is SEMA6D.

UniProtKB/Swiss-Prot 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA6C Gene

Genomics for SEMA6C Gene

Regulatory Elements for SEMA6C Gene

Enhancers for SEMA6C Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F151142 1 Ensembl ENCODE 17.2 +1.5 1456 6.1 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF48 ZNF2 YY1 ZNF121 BNIPL GABPB2 SEMA6C PRUNE1 TMOD4 VPS72 PIP5K1A RNU6-884P LYSMD1 C1orf56
GH01F151130 0.5 ENCODE 17 +14.9 14900 1.8 PKNOX1 ZMYM3 BMI1 SP1 ZNF366 POLR2A EGR1 NFYB ZNF512 KDM1A BNIPL SEMA6C GABPB2 CTSS ENSG00000261168
GH01F151156 0.7 ENCODE 16.8 -11.9 -11919 4.9 HDGF PKNOX1 WRNIP1 ARID4B BMI1 ZBTB40 RAD21 YY1 RFX5 ZNF366 SEMA6C BNIPL SCNM1 LYSMD1
GH01F151010 0.8 Ensembl ENCODE 14.4 +134.0 133970 4.6 PKNOX1 ATF1 MLX ARID4B FEZF1 DMAP1 ZNF48 YY1 FOS PPARG SEMA6C PSMD4 HORMAD1 PRUNE1 GC01M151022 RNU6-884P
GH01F151133 0.5 ENCODE 13.1 +13.0 12963 0.8 CTCF ZFHX2 KDM1A EGR2 EZH2 BNIPL SEMA6C ENSG00000261168
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SEMA6C on UCSC Golden Path with GeneCards custom track

Promoters for SEMA6C Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001524698 364 1801 HDGF PKNOX1 ZFP64 ARID4B SIN3A DMAP1 ZNF48 ZNF2 YY1 GLIS2

Genomic Location for SEMA6C Gene

Chromosome:
1
Start:
151,131,685 bp from pter
End:
151,146,664 bp from pter
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=Translation N-terminally shortened.; 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 Asn 70, Asn 286, and Asn 437
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SEMA6C Gene

Domains & Families for SEMA6C Gene

Gene Families for SEMA6C Gene

Protein Domains for SEMA6C Gene

Suggested Antigen Peptide Sequences for SEMA6C Gene

Graphical View of Domain Structure for InterPro Entry

Q9H3T2

UniProtKB/Swiss-Prot:

SEM6C_HUMAN :
  • Contains 1 PSI domain.
  • Belongs to the semaphorin family.
Domain:
  • Contains 1 PSI domain.
  • Contains 1 Sema domain.
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.

Gene Ontology (GO) - Molecular Function for SEMA6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030215 semaphorin receptor binding IBA --
GO:0045499 chemorepellent activity IBA --
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

Flow Cytometry 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
Jensen Localization Image for SEMA6C Gene COMPARTMENTS Subcellular localization image for SEMA6C gene
Compartment Confidence
plasma membrane 5
extracellular 3
cytosol 1
lysosome 1
mitochondrion 1
vacuole 1

Gene Ontology (GO) - Cellular Components for SEMA6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IBA --
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

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 --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0007411 axon guidance IEA --
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

Transcripts for SEMA6C Gene

Unigene Clusters for SEMA6C Gene

Sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C:
Representative Sequences:

Flow Cytometry 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
ECgene alternative splicing isoforms 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, PaxDb, and MOPED for SEMA6C Gene



Protein tissue co-expression partners for SEMA6C Gene

NURSA nuclear receptor signaling pathways regulating expression of SEMA6C Gene:

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.
genes like me logo Genes that share expression patterns with SEMA6C: view

Primer Products

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 34 35
  • 99.69 (n)
cow
(Bos Taurus)
Mammalia SEMA6C 34 35
  • 89.66 (n)
dog
(Canis familiaris)
Mammalia SEMA6C 34 35
  • 87.93 (n)
rat
(Rattus norvegicus)
Mammalia Sema6c 34
  • 87.06 (n)
mouse
(Mus musculus)
Mammalia Sema6c 34 16 35
  • 86.34 (n)
oppossum
(Monodelphis domestica)
Mammalia SEMA6C 35
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 31 (a)
ManyToMany
-- 35
  • 24 (a)
ManyToMany
chicken
(Gallus gallus)
Aves LOC100859892 34
  • 59.94 (n)
SEMA6C 35
  • 52 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA6C 35
  • 66 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii sema6d 35
  • 43 (a)
OneToMany
sema6e 35
  • 41 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Sema-1b 36
  • 36 (a)
Sema-1a 36
  • 35 (a)
CG4383 36
  • 34 (a)
Sema-2a 36 35
  • 33 (a)
Sema-2b 35
  • 24 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea mab-20 36
  • 28 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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)

Paralogs for SEMA6C Gene

Paralogs for SEMA6C Gene

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

genes like me logo Genes that share paralogs with SEMA6C: view

Variants for SEMA6C Gene

Sequence variations from dbSNP and Humsavar for SEMA6C Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs10788800 -- 151,132,474(+) CGTGG(A/G)CCGCT utr-variant-3-prime
rs10888405 -- 151,139,051(+) TCGTG(C/T)CATTG intron-variant, upstream-variant-2KB
rs111518157 -- 151,133,465(+) AGGAG(C/G/T)GGGAT reference, synonymous-codon
rs111640977 -- 151,140,936(+) GAGCT(C/T)GCAGT intron-variant
rs11204781 -- 151,131,818(+) GCTCC(A/G)AGGGC downstream-variant-500B, utr-variant-3-prime

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)

Relevant External Links 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

Relevant External Links for SEMA6C

Genetic Association Database (GAD)
SEMA6C
Human Genome Epidemiology (HuGE) Navigator
SEMA6C
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEMA6C

No disorders were found for SEMA6C Gene.

No data available for MalaCards , 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. (J. Biol. Chem. 2002) 2 3 4 64
  2. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. (PMID: 19054571) GregA^rio S.P. … Dias-Neto E. (Psychiatry Res 2009) 3 46 64
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64
  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 Res. 2001) 3 4 64
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K. … Sugano S. (Genome Res. 2006) 3 64

Products for SEMA6C Gene

Sources for SEMA6C Gene

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