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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
  • 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 (Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (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 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

Regulatory Elements for SEMA3D Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

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

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

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:

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).

Gene Ontology (GO) - Molecular Function for SEMA3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding --
GO:0030215 semaphorin receptor binding IBA --
GO:0038191 neuropilin binding IBA --
GO:0045499 chemorepellent activity IBA --
genes like me logo Genes that share ontologies with SEMA3D: view
genes like me logo Genes that share phenotypes with SEMA3D: view

Animal Models for SEMA3D Gene

MGI Knock Outs for SEMA3D:

Animal Model Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SEMA3D

In Situ Assay Products

Flow Cytometry 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
Jensen Localization Image for SEMA3D Gene COMPARTMENTS Subcellular localization image for SEMA3D gene
Compartment Confidence
extracellular 3

Gene Ontology (GO) - Cellular Components for SEMA3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region --
GO:0005615 extracellular space IBA --
genes like me logo Genes that share ontologies with SEMA3D: view

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:0001755 neural crest cell migration IBA --
GO:0007399 nervous system development --
GO:0030154 cell differentiation --
GO:0030335 positive regulation of cell migration IBA --
GO:0048843 negative regulation of axon extension involved in axon guidance 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:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SEMA3D

Flow Cytometry 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
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
cow
(Bos Taurus)
Mammalia SEMA3D 35
  • 92.53 (n)
  • 94.07 (a)
SEMA3D 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA3D 35
  • 92.41 (n)
  • 96.14 (a)
SEMA3D 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema3d 35
  • 89.15 (n)
  • 92.92 (a)
Sema3d 16
Sema3d 36
  • 93 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SEMA3D 35
  • 99.7 (n)
  • 99.74 (a)
SEMA3D 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sema3d 35
  • 88.46 (n)
  • 92.41 (a)
oppossum
(Monodelphis domestica)
Mammalia SEMA3D 36
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA3D 36
  • 90 (a)
OneToOne
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 35
  • 63.49 (n)
  • 64.37 (a)
sema3d 36
  • 63 (a)
OneToOne
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 MAF
rs764077 -- 85,135,078(-) ATTCT(C/T)ACCAT intron-variant
rs957055 -- 85,173,938(+) AAGGA(C/T)TCTGA intron-variant
rs993312 -- 85,118,528(+) AAGAT(A/C)ATTTC 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: 47.24% 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

(3) 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
ischemic bone disease
- elite association

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. Sema3D, Sema3F, and Sema5A are expressed in overlapping and distinct patterns in chick embryonic heart. (PMID: 16261621) Jin Z. … Bao Z.Z. (Dev. Dyn. 2006) 23 67
  2. Differential expression of mitochondrial and extramitochondrial proteins in lymphocytes of male broilers with low and high feed efficiency. (PMID: 17135683) Lassiter K. … Bottje W. (Poult. Sci. 2006) 23 67
  3. Semaphorin profiling of periodontal fibroblasts and osteoblasts. (PMID: 15329371) Lallier T.E. (J. Dent. Res. 2004) 23 67
  4. A 70 amino acid region within the semaphorin domain activates specific cellular response of semaphorin family members. (PMID: 9331346) Koppel A.M. … Raper J.A. (Neuron 1997) 23 67
  5. A family of molecules related to collapsin in the embryonic chick nervous system. (PMID: 7605628) Luo Y. … Raper J.A. (Neuron 1995) 23 67

Products for SEMA3D Gene

Sources for SEMA3D Gene

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