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Aliases for SEMA3D Gene

Aliases for SEMA3D Gene

  • Semaphorin 3D 2 3
  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3D 2 3 5
  • 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

GeneCards Summary for SEMA3D Gene

SEMA3D (Semaphorin 3D) is a Protein Coding gene. Diseases associated with SEMA3D include hirschsprung disease 1 and osteochondrosis. Among its related pathways are Axon guidance. GO annotations related to this gene include receptor activity. An important paralog of this gene is SEMA3F.

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

Regulatory Elements for SEMA3D Gene

Promoters for SEMA3D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SEMA3D on UCSC Golden Path with GeneCards custom track

Genomic Location for SEMA3D Gene

Chromosome:
7
Start:
84,995,192 bp from pter
End:
85,186,855 bp from pter
Size:
191,664 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

Proteomics data for SEMA3D Gene at MOPED

Post-translational modifications for SEMA3D Gene

  • Glycosylation at Asn 139, Asn 607, and Asn 724
  • Modification sites at PhosphoSitePlus

Other Protein References for SEMA3D Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for SEMA3D Gene

Domains & Families for SEMA3D Gene

Gene Families for SEMA3D Gene

Suggested Antigen Peptide Sequences for SEMA3D Gene

GenScript: Design optimal peptide antigens:

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.
  • Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
  • Contains 1 PSI domain.
  • Contains 1 Sema domain.
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).
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

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
Jensen Localization Image for SEMA3D Gene COMPARTMENTS Subcellular localization image for SEMA3D gene
Compartment Confidence
extracellular 4
plasma membrane 2
cytosol 1
endoplasmic reticulum 1
golgi apparatus 1
mitochondrion 1
nucleus 1
peroxisome 1

No data available for Gene Ontology (GO) - Cellular Components for SEMA3D Gene

Pathways & Interactions 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:0030335 positive regulation of cell migration IBA --
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

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
SEMA3D
ECgene alternative splicing isoforms for
SEMA3D

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 (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, PaxDb, and MOPED for SEMA3D Gene



SOURCE GeneReport for Unigene cluster for SEMA3D Gene Hs.201340

genes like me logo Genes that share expression patterns with SEMA3D: view

Protein tissue co-expression partners for SEMA3D Gene

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt 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 35
  • 99.7 (n)
  • 99.74 (a)
SEMA3D 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA3D 36
  • 94 (a)
OneToOne
SEMA3D 35
  • 92.53 (n)
  • 94.07 (a)
dog
(Canis familiaris)
Mammalia SEMA3D 35
  • 92.41 (n)
  • 96.14 (a)
SEMA3D 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema3d 16
Sema3d 36
  • 93 (a)
OneToOne
Sema3d 35
  • 89.15 (n)
  • 92.92 (a)
oppossum
(Monodelphis domestica)
Mammalia SEMA3D 36
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA3D 36
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema3d 35
  • 88.46 (n)
  • 92.41 (a)
chicken
(Gallus gallus)
Aves SEMA3D 35
  • 80.09 (n)
  • 87.11 (a)
SEMA3D 36
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA3D 36
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3d 35
  • 71.8 (n)
  • 75.43 (a)
zebrafish
(Danio rerio)
Actinopterygii sema3d 36
  • 63 (a)
OneToOne
sema3d 35
  • 63.49 (n)
  • 64.37 (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

ENSEMBL:
Gene Tree for SEMA3D (if available)
TreeFam:
Gene Tree for SEMA3D (if available)

Paralogs for SEMA3D Gene

(14) 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
rs7800072 - 84,999,673(+) GACCT(G/T)CCCCT reference, missense
rs993312 -- 85,118,528(+) AAGAT(A/C)ATTTC intron-variant
rs1017041 -- 85,082,898(+) GTGAT(C/G)AGCTA intron-variant
rs1003292 -- 85,187,200(-) ATCCA(C/T)GCTGC upstream-variant-2KB
rs1003293 -- 85,187,184(-) GCCTC(C/G)GCGCA upstream-variant-2KB

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

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)

Relevant External Links for SEMA3D Gene

HapMap Linkage Disequilibrium report
SEMA3D
Human Gene Mutation Database (HGMD)
SEMA3D

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

Disorders for SEMA3D Gene

MalaCards: The human disease database

(2) MalaCards diseases for SEMA3D Gene - From: Orphanet and DISEASES

Disorder Aliases PubMed IDs
hirschsprung disease 1
  • hirschsprung's disease
osteochondrosis
  • juvenile osteochondrosis of tibial tubercle
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SEMA3D

Genetic Association Database (GAD)
SEMA3D
Human Genome Epidemiology (HuGE) Navigator
SEMA3D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEMA3D
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) GregA^rio S.P. … Dias-Neto E. (Psychiatry Res 2009) 3 48 67
  2. Semaphorin profiling of periodontal fibroblasts and osteoblasts. (PMID: 15329371) Lallier T.E. (J. Dent. Res. 2004) 3 23
  3. Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability. (PMID: 25839327) Jiang Q. … Chakravarti A. (Am. J. Hum. Genet. 2015) 3
  4. Semaphorin 3d and semaphorin 3e direct endothelial motility through distinct molecular signaling pathways. (PMID: 24825896) Aghajanian H. … Epstein J.A. (J. Biol. Chem. 2014) 3
  5. Semaphorin 3d signaling defects are associated with anomalous pulmonary venous connections. (PMID: 23685842) Degenhardt K. … Epstein J.A. (Nat. Med. 2013) 3

Products for SEMA3D Gene

Sources for SEMA3D Gene

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