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Aliases for SEMA3D Gene

Aliases for SEMA3D Gene

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

External Ids for SEMA3D Gene

Summaries for SEMA3D Gene

GeneCards Summary for SEMA3D Gene

SEMA3D (Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3D) is a Protein Coding gene. Among its related pathways are Axon guidance. GO annotations related to this gene include receptor activity. An important paralog of this gene is SEMA4G.

UniProtKB/Swiss-Prot 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).

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA3D Gene

Genomics for SEMA3D Gene

Genomic Location for SEMA3D Gene

84,995,553 bp from pter
85,186,855 bp from pter
191,303 bases
Minus strand

Genomic View for SEMA3D Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SEMA3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA3D Gene

Regulatory Elements for SEMA3D Gene

Proteins for SEMA3D Gene

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

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A6NK46
    • Q6UW77
    • Q8NCQ1

    Protein attributes for SEMA3D Gene

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

neXtProt entry for SEMA3D Gene

Proteomics data for SEMA3D Gene at MOPED

Post-translational modifications for SEMA3D Gene

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

Other Protein References for SEMA3D Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SEMA3D Gene

Domains for SEMA3D Gene

Gene Families for SEMA3D Gene

  • VSET :Immunoglobulin superfamily / V-set domain containing
  • SEMA :Semaphorins


  • Strong binding to neuropilin is mediated by the carboxy third of the protein:
    • O95025
  • Contains 1 Ig-like C2-type (immunoglobulin-like) domain.:
    • O95025
  • Contains 1 PSI domain.:
    • O95025
  • Contains 1 Sema domain.:
    • O95025
  • Belongs to the semaphorin family.:
    • O95025
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).

Gene Ontology (GO) - Molecular Function for SEMA3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004872 receptor activity IEA --
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with SEMA3D: view

Phenotypes for SEMA3D Gene

MGI mutant phenotypes for SEMA3D:
inferred from 2 alleles
GenomeRNAi human phenotypes for SEMA3D:
genes like me logo Genes that share phenotypes with SEMA3D: view

Animal Models for SEMA3D Gene

MGI Knock Outs for SEMA3D:

miRNA for SEMA3D Gene

miRTarBase miRNAs that target SEMA3D

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

Localization for SEMA3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA3D Gene


Subcellular locations from

Jensen Localization Image for SEMA3D Gene COMPARTMENTS Subcellular localization image for SEMA3D gene
Compartment Confidence
extracellular 2
plasma membrane 2
cytosol 1
endoplasmic reticulum 1
golgi apparatus 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SEMA3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SEMA3D: view

Pathways for SEMA3D Gene

SuperPathways for SEMA3D Gene

Superpath 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

Interacting Proteins for SEMA3D Gene

Gene Ontology (GO) - Biological Process for SEMA3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organismal development --
GO:0007399 nervous system development IEA --
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with SEMA3D: view

Transcripts for SEMA3D Gene

Unigene Clusters for SEMA3D Gene

Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA3D Gene

No ASD Table

Relevant External Links for SEMA3D Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SEMA3D Gene

mRNA expression in normal human tissues 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 (8.6), Thyroid (7.8), and Artery - Aorta (4.2).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for SEMA3D Gene

SOURCE GeneReport for Unigene cluster for SEMA3D Gene Hs.201340

genes like me logo Genes that share expressions with SEMA3D: view

Orthologs for SEMA3D Gene

This gene was present in the common ancestor of chordates.

Orthologs for SEMA3D Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SEMA3D 36
  • 99.7 (n)
  • 99.74 (a)
  • 100 (a)
(Bos Taurus)
Mammalia SEMA3D 36
  • 92.53 (n)
  • 94.07 (a)
  • 94 (a)
(Canis familiaris)
Mammalia SEMA3D 36
  • 92.41 (n)
  • 96.14 (a)
  • 96 (a)
(Mus musculus)
Mammalia Sema3d 36
  • 89.15 (n)
  • 92.92 (a)
Sema3d 16
Sema3d 37
  • 93 (a)
(Monodelphis domestica)
Mammalia SEMA3D 37
  • 89 (a)
(Ornithorhynchus anatinus)
Mammalia SEMA3D 37
  • 90 (a)
(Rattus norvegicus)
Mammalia Sema3d 36
  • 88.46 (n)
  • 92.41 (a)
(Gallus gallus)
Aves SEMA3D 36
  • 80.09 (n)
  • 87.11 (a)
  • 85 (a)
(Anolis carolinensis)
Reptilia SEMA3D 37
  • 76 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3d 36
  • 71.8 (n)
  • 75.43 (a)
(Danio rerio)
Actinopterygii sema3d 36
  • 63.49 (n)
  • 64.37 (a)
sema3d 37
  • 63 (a)
Species with no ortholog for SEMA3D:
  • 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

Gene Tree for SEMA3D (if available)
Gene Tree for SEMA3D (if available)

Paralogs for SEMA3D Gene

Selected SIMAP similar genes for SEMA3D Gene using alignment to 2 proteins:

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

Variants for SEMA3D Gene

Sequence variations from dbSNP and Humsavar for SEMA3D Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type MAF
rs993312 -- 85,118,528(+) AAGAT(A/C)ATTTC intron-variant
rs1016027 -- 85,023,672(+) TCATG(A/C)CAAGG intron-variant
rs1017041 -- 85,082,898(+) GTGAT(C/G)AGCTA intron-variant
rs1029563 -- 85,109,179(+) TATTA(G/T)TTAAT intron-variant
rs1029564 -- 85,110,539(+) TAGCT(G/T)TCCTT intron-variant

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

Variant ID Type Subtype PubMed ID
nsv888633 CNV Gain 21882294
esv2422324 CNV Deletion 17116639
nsv519125 CNV Loss 19592680
nsv521507 CNV Loss 19592680
nsv888645 CNV Loss 21882294

Relevant External Links for SEMA3D Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

Disorders for SEMA3D Gene

(2) University of Copenhagen DISEASES for SEMA3D Gene

Relevant External Links for SEMA3D

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SEMA3D: view

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

Publications for SEMA3D Gene

  1. Semaphorin profiling of periodontal fibroblasts and osteoblasts. (PMID: 15329371) Lallier T.E. (J. Dent. Res. 2004) 3 23
  2. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier L.W. … Wilson R.K. (Nature 2003) 3 4
  3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  5. 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 49

Products for SEMA3D Gene

Sources for SEMA3D Gene

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