This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [pr... See more...

Aliases for SEMA3D Gene

Aliases for SEMA3D Gene

  • Semaphorin 3D 2 3 5
  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3D 2 3
  • Semaphorin-3D 3 4
  • Collapsin 2 3
  • Sema-Z2 3
  • Coll-2 3

External Ids for SEMA3D Gene

Previous GeneCards Identifiers for SEMA3D Gene

  • GC00U990482
  • GC07M083163
  • GC07M084226
  • GC07M084240
  • GC07M084236
  • GC07M084269
  • GC07M084462
  • GC07M084624
  • GC07M079234

Summaries for SEMA3D Gene

Entrez Gene Summary for SEMA3D Gene

  • This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]

GeneCards Summary for SEMA3D Gene

SEMA3D (Semaphorin 3D) is a Protein Coding gene. Diseases associated with SEMA3D include Hirschsprung Disease 1 and Meniere Disease. Among its related pathways are Axon guidance. An important paralog of this gene is SEMA3A.

UniProtKB/Swiss-Prot Summary for SEMA3D Gene

  • Induces the collapse and paralysis of neuronal growth cones. Could potentially act as repulsive cues toward specific neuronal populations. Binds to neuropilin (By similarity).

Additional gene information for SEMA3D Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEMA3D Gene

Genomics for SEMA3D Gene

GeneHancer (GH) Regulatory Elements for SEMA3D Gene

Promoters and enhancers for SEMA3D 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
GH07J085184 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.9 857 3.6 CTCF ZIC2 REST ZBTB10 ZBTB26 SAP30 RFX1 RAD21 MXI1 ZNF341 SEMA3D piR-32325-188
GH07J085554 Enhancer 0.8 Ensembl ENCODE 11.6 -367.6 -367622 1 CTCF REST RAD21 TRIM22 SMC3 FOXA2 CEBPB JUND ZNF654 RFX5 SEMA3D piR-38351-437 HSALNG0059328
GH07J085135 Enhancer 0.7 Ensembl ENCODE 11.3 +50.7 50747 1.8 JUND CEBPB JUN EZH2 FOS EP300 DPF2 GATA2 GATA3 POLR2A SEMA3D piR-32325-188 lnc-SEMA3A-2
GH07J085049 Enhancer 0.5 Ensembl 11.5 +137.2 137154 0.6 TCF7L2 ZNF843 PRDM6 FEZF1 ZNF133 CTBP1 PKNOX1 ZSCAN4 PRDM1 SEMA3D lnc-SEMA3A-2 HSPA8P16
GH07J085719 Enhancer 0.8 Ensembl ENCODE 7.7 -533.8 -533846 3.4 TCF12 JUND EP300 FOS FOSL2 CEBPB CHD2 JUN GTF2F1 MAX SEMA3D piR-44110-073 piR-55948-106
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA3D on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEMA3D

Top Transcription factor binding sites by QIAGEN in the SEMA3D gene promoter:
  • ATF-2
  • Cdc5
  • CUTL1
  • FOXL1
  • FOXO4
  • POU2F1
  • POU2F1a
  • RORalpha2
  • Sox5
  • SRY

Genomic Locations for SEMA3D Gene

Genomic Locations for SEMA3D Gene
chr7:84,995,192-85,186,855
(GRCh38/hg38)
Size:
191,664 bases
Orientation:
Minus strand
chr7:84,624,869-84,816,171
(GRCh37/hg19)
Size:
191,303 bases
Orientation:
Minus strand

Genomic View for SEMA3D Gene

Genes around SEMA3D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA3D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA3D Gene

Proteins for SEMA3D Gene

  • Protein details for SEMA3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95025-SEM3D_HUMAN
    Recommended name:
    Semaphorin-3D
    Protein Accession:
    O95025
    Secondary Accessions:
    • A6NK46
    • Q6UW77
    • Q8NCQ1

    Protein attributes for SEMA3D Gene

    Size:
    777 amino acids
    Molecular mass:
    89651 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH29590.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for SEMA3D Gene

Post-translational modifications for SEMA3D Gene

  • Glycosylation at Asn139, Asn607, and Asn724
  • Modification sites at PhosphoSitePlus

Other Protein References for SEMA3D Gene

No data available for DME Specific Peptides for SEMA3D Gene

Domains & Families for SEMA3D Gene

Gene Families for SEMA3D Gene

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

Protein Domains for SEMA3D Gene

Blocks:
  • Immunoglobulin subtype
  • Immunoglobulin V-set
  • Semaphorin/CD100 antigen
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SEMA3D Gene

GenScript: Design optimal peptide antigens:
  • Semaphorin-3D (SEM3D_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O95025

UniProtKB/Swiss-Prot:

SEM3D_HUMAN :
  • Strong binding to neuropilin is mediated by the carboxy third of the protein.
  • Belongs to the semaphorin family.
Domain:
  • Strong binding to neuropilin is mediated by the carboxy third of the protein.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA3D: view

Function for SEMA3D Gene

Molecular function for SEMA3D Gene

UniProtKB/Swiss-Prot Function:
Induces the collapse and paralysis of neuronal growth cones. Could potentially act as repulsive cues toward specific neuronal populations. Binds to neuropilin (By similarity).

Phenotypes From GWAS Catalog for SEMA3D Gene

Gene Ontology (GO) - Molecular Function for SEMA3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0030215 semaphorin receptor binding IBA,IEA 21873635
GO:0045499 chemorepellent activity IBA 21873635
genes like me logo Genes that share ontologies with SEMA3D: view
genes like me logo Genes that share phenotypes with SEMA3D: view

Human Phenotype Ontology for SEMA3D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SEMA3D Gene

MGI Knock Outs for SEMA3D:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA3D

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SEMA3D Gene

Localization for SEMA3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA3D 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 SEMA3D gene
Compartment Confidence
plasma membrane 4
extracellular 4
cytoskeleton 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for SEMA3D 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:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SEMA3D: view

Pathways & Interactions for SEMA3D Gene

PathCards logo

SuperPathways for SEMA3D Gene

SuperPathway Contained pathways
1 Axon guidance
genes like me logo Genes that share pathways with SEMA3D: view

Pathways by source for SEMA3D Gene

1 KEGG pathway for SEMA3D Gene

Gene Ontology (GO) - Biological Process for SEMA3D 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 SEMA3D: view

No data available for SIGNOR curated interactions for SEMA3D Gene

Drugs & Compounds for SEMA3D Gene

No Compound Related Data Available

Transcripts for SEMA3D Gene

mRNA/cDNA for SEMA3D Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
4 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 SEMA3D Gene

No ASD Table

Relevant External Links for SEMA3D Gene

GeneLoc Exon Structure for
SEMA3D

Expression for SEMA3D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SEMA3D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA3D Gene

This gene is overexpressed in Spleen (x8.6), Thyroid (x7.8), and Artery - Aorta (x4.2).

Protein differential expression in normal tissues from HIPED for SEMA3D Gene

This gene is overexpressed in Placenta (57.0) and Adipocyte (9.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SEMA3D Gene



Protein tissue co-expression partners for SEMA3D Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEMA3D

SOURCE GeneReport for Unigene cluster for SEMA3D Gene:

Hs.201340

Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA3D 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 SEMA3D: view

No data available for mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES for SEMA3D Gene

Orthologs for SEMA3D Gene

This gene was present in the common ancestor of chordates.

Orthologs for SEMA3D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA3D 31 30
  • 99.7 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA3D 31 30
  • 92.53 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA3D 31 30
  • 92.41 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA3D 31
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema3d 17 31 30
  • 89.15 (n)
oppossum
(Monodelphis domestica)
Mammalia SEMA3D 31
  • 89 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema3d 30
  • 88.46 (n)
chicken
(Gallus gallus)
Aves SEMA3D 31 30
  • 80.09 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA3D 31
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3d 30
  • 71.8 (n)
zebrafish
(Danio rerio)
Actinopterygii sema3d 31 30
  • 63.49 (n)
OneToOne
Species where no ortholog for SEMA3D 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)
  • fruit fly (Drosophila melanogaster)
  • 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 SEMA3D Gene

ENSEMBL:
Gene Tree for SEMA3D (if available)
TreeFam:
Gene Tree for SEMA3D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEMA3D: view image

Paralogs for SEMA3D Gene

(14) SIMAP similar genes for SEMA3D Gene using alignment to 2 proteins:

  • SEM3D_HUMAN
  • C9JYT6_HUMAN
genes like me logo Genes that share paralogs with SEMA3D: view

Variants for SEMA3D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEMA3D Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
709258 Likely Benign: not provided 85,065,425(-) A/G SYNONYMOUS_VARIANT
710331 Likely Benign: not provided 85,040,696(-) T/C SYNONYMOUS_VARIANT
716081 Benign: not provided 85,121,733(-) A/G INTRON_VARIANT
716955 Benign: not provided 85,097,974(-) A/G INTRON_VARIANT
719135 Likely Benign: not provided 85,042,223(-) C/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SEMA3D Gene

Structural Variations from Database of Genomic Variants (DGV) for SEMA3D Gene

Variant ID Type Subtype PubMed ID
esv2422324 CNV deletion 17116639
esv3613978 CNV loss 21293372
nsv1032610 CNV loss 25217958
nsv1034620 CNV loss 25217958
nsv1143187 CNV tandem duplication 24896259
nsv1161578 CNV deletion 26073780
nsv1161579 CNV deletion 26073780
nsv519125 CNV loss 19592680
nsv521507 CNV loss 19592680
nsv970547 CNV duplication 23825009

Variation tolerance for SEMA3D Gene

Residual Variation Intolerance Score: 47.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.06; 87.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEMA3D Gene

Human Gene Mutation Database (HGMD)
SEMA3D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA3D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA3D Gene

Disorders for SEMA3D Gene

MalaCards: The human disease database

(3) MalaCards diseases for SEMA3D Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hirschsprung disease 1
  • hirschsprung disease, susceptibility to, 1
meniere disease
  • meniere's disease
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA3D

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 SEMA3D: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA3D Gene

Publications for SEMA3D Gene

  1. 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
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  3. Semaphorin profiling of periodontal fibroblasts and osteoblasts. (PMID: 15329371) Lallier TE (Journal of dental research 2004) 3 23 54
  4. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier LW … Wilson RK (Nature 2003) 3 4 54
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 54

Products for SEMA3D Gene

Sources for SEMA3D Gene