Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, a... See more...

Aliases for SEMA3E Gene

Aliases for SEMA3E Gene

  • Semaphorin 3E 2 3 5
  • Sema Domain, Immunoglobulin Domain (Ig), Short Basic Domain, Secreted, (Semaphorin) 3E 2 3
  • Semaphorin-3E 3 4
  • SEMAH 3 4
  • KIAA0331 4
  • M-Sema H 2
  • M-SEMAH 3
  • M-SemaK 3
  • Coll-5 3

External Ids for SEMA3E Gene

Previous HGNC Symbols for SEMA3E Gene

  • SEMAH

Previous GeneCards Identifiers for SEMA3E Gene

  • GC07M081528
  • GC07M082591
  • GC07M082605
  • GC07M082637
  • GC07M082831
  • GC07M082993
  • GC07M077595

Summaries for SEMA3E Gene

Entrez Gene Summary for SEMA3E Gene

  • Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. This gene encodes a class 4 semaphorin. This gene encodes a class 3 semaphorin. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]

GeneCards Summary for SEMA3E Gene

SEMA3E (Semaphorin 3E) is a Protein Coding gene. Diseases associated with SEMA3E include Charge Syndrome and Hypogonadotropic Hypogonadism 7 With Or Without Anosmia. Among its related pathways are Developmental Biology and Semaphorin interactions. Gene Ontology (GO) annotations related to this gene include semaphorin receptor binding. An important paralog of this gene is SEMA3G.

UniProtKB/Swiss-Prot Summary for SEMA3E Gene

  • Plays an important role in signaling via the cell surface receptor PLXND1. Mediates reorganization of the actin cytoskeleton, leading to the retraction of cell projections. Promotes focal adhesion disassembly and inhibits adhesion of endothelial cells to the extracellular matrix. Regulates angiogenesis, both during embryogenesis and after birth. Can down-regulate sprouting angiogenesis. Required for normal vascular patterning during embryogenesis. Plays an important role in ensuring the specificity of synapse formation (By similarity).

Additional gene information for SEMA3E Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEMA3E Gene

Genomics for SEMA3E Gene

GeneHancer (GH) Regulatory Elements for SEMA3E Gene

Promoters and enhancers for SEMA3E 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
GH07J083648 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE CraniofacialAtlas 512 +0.5 520 1.5 USF1 CTCF ZIC2 ZNF341 SIN3A MYC ZNF263 REST ZNF335 IKZF3 SEMA3E piR-61240-265
GH07J083677 Enhancer 1 Ensembl ENCODE 10.9 -28.4 -28437 1.6 ZNF217 TCF12 JUND FOS ZNF639 ZIC2 FOXA1 ZNF423 TRIM28 KLF7 SEMA3E piR-49400-085 RF00017-6417
GH07J083684 Enhancer 0.9 Ensembl ENCODE 10 -36.2 -36160 1.4 ZNF217 TEAD4 HDAC2 CTBP1 ESRRA RXRA POLR2A NR3C1 YY1 NANOG SEMA3E RF00017-6417 piR-49400-085
GH07J083588 Enhancer 0.5 Ensembl 15 +60.3 60262 0.6 GATA3 REST RCOR1 TAF1 CHD2 YY1 GATA2 FOS MZF1 POLR2A SEMA3E L13714-427 piR-61240-265
GH07J083691 Enhancer 0.6 Ensembl ENCODE 10.8 -41.8 -41838 0.8 TEAD4 HDAC2 TCF12 SEMA3E RF00017-6417 piR-49400-085
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA3E on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEMA3E

Top Transcription factor binding sites by QIAGEN in the SEMA3E gene promoter:
  • Brachyury
  • CUTL1
  • Evi-1
  • HEN1
  • Pbx1a
  • Sox9
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT2

Genomic Locations for SEMA3E Gene

Genomic Locations for SEMA3E Gene
chr7:83,363,238-83,649,163
(GRCh38/hg38)
Size:
285,926 bases
Orientation:
Minus strand
chr7:82,993,222-83,278,479
(GRCh37/hg19)
Size:
285,258 bases
Orientation:
Minus strand

Genomic View for SEMA3E Gene

Genes around SEMA3E on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA3E Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA3E Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA3E Gene

Proteins for SEMA3E Gene

  • Protein details for SEMA3E Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15041-SEM3E_HUMAN
    Recommended name:
    Semaphorin-3E
    Protein Accession:
    O15041
    Secondary Accessions:
    • B4E1P1
    • Q75M94
    • Q75M97

    Protein attributes for SEMA3E Gene

    Size:
    775 amino acids
    Molecular mass:
    89228 Da
    Quaternary structure:
    • Interacts with PLXND1.
    SequenceCaution:
    • Sequence=BAA20789.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SEMA3E Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA3E Gene

Post-translational modifications for SEMA3E Gene

  • Glycosylation at Asn44, Asn126, Asn330, Asn595, and Asn596
  • Modification sites at PhosphoSitePlus

Other Protein References for SEMA3E Gene

No data available for DME Specific Peptides for SEMA3E Gene

Domains & Families for SEMA3E Gene

Gene Families for SEMA3E Gene

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

Protein Domains for SEMA3E Gene

Blocks:
  • Immunoglobulin subtype
  • Semaphorin/CD100 antigen
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SEMA3E Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ51451, highly similar to Semaphorin-3E (B4E1P1_HUMAN)
  • Semaphorin-3E (SEM3E_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O15041

UniProtKB/Swiss-Prot:

SEM3E_HUMAN :
  • Belongs to the semaphorin family.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA3E: view

Function for SEMA3E Gene

Molecular function for SEMA3E Gene

UniProtKB/Swiss-Prot Function:
Plays an important role in signaling via the cell surface receptor PLXND1. Mediates reorganization of the actin cytoskeleton, leading to the retraction of cell projections. Promotes focal adhesion disassembly and inhibits adhesion of endothelial cells to the extracellular matrix. Regulates angiogenesis, both during embryogenesis and after birth. Can down-regulate sprouting angiogenesis. Required for normal vascular patterning during embryogenesis. Plays an important role in ensuring the specificity of synapse formation (By similarity).

LifeMap Function Summary for SEMA3E Gene

It affects the following cells:

Phenotypes From GWAS Catalog for SEMA3E Gene

Gene Ontology (GO) - Molecular Function for SEMA3E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA,IPI 17318185
GO:0030215 semaphorin receptor binding IBA 21873635
GO:0045499 chemorepellent activity IBA 21873635
genes like me logo Genes that share ontologies with SEMA3E: view
genes like me logo Genes that share phenotypes with SEMA3E: view

Human Phenotype Ontology for SEMA3E Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SEMA3E Gene

MGI Knock Outs for SEMA3E:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA3E

miRNA for SEMA3E Gene

miRTarBase miRNAs that target SEMA3E

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SEMA3E Gene

Localization for SEMA3E Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA3E 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 SEMA3E gene
Compartment Confidence
extracellular 5
plasma membrane 4
cytoskeleton 2
mitochondrion 2
nucleus 2
cytosol 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SEMA3E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space TAS,IBA 21873635
GO:0005887 integral component of plasma membrane IBA 21873635
genes like me logo Genes that share ontologies with SEMA3E: view

Pathways & Interactions for SEMA3E Gene

genes like me logo Genes that share pathways with SEMA3E: view

Pathways by source for SEMA3E Gene

1 KEGG pathway for SEMA3E Gene

Gene Ontology (GO) - Biological Process for SEMA3E Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001569 branching involved in blood vessel morphogenesis ISS --
GO:0001755 neural crest cell migration IBA 21873635
GO:0001953 negative regulation of cell-matrix adhesion ISS --
GO:0002040 sprouting angiogenesis ISS --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with SEMA3E: view

No data available for SIGNOR curated interactions for SEMA3E Gene

Drugs & Compounds for SEMA3E Gene

No Compound Related Data Available

Transcripts for SEMA3E Gene

mRNA/cDNA for SEMA3E Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA3E Gene

No ASD Table

Relevant External Links for SEMA3E Gene

GeneLoc Exon Structure for
SEMA3E

Expression for SEMA3E Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SEMA3E Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA3E Gene

This gene is overexpressed in Esophagus - Muscularis (x4.4) and Esophagus - Gastroesophageal Junction (x4.3).

Protein differential expression in normal tissues from HIPED for SEMA3E Gene

This gene is overexpressed in Islet of Langerhans (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SEMA3E Gene



Protein tissue co-expression partners for SEMA3E Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEMA3E

SOURCE GeneReport for Unigene cluster for SEMA3E Gene:

Hs.528721

Evidence on tissue expression from TISSUES for SEMA3E Gene

  • Nervous system(4.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA3E Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • hypothalamus
  • inner ear
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • olfactory bulb
  • outer ear
  • parathyroid
  • pharynx
  • pituitary gland
  • sinus
  • skull
  • thyroid
  • tooth
Thorax:
  • aorta
  • breast
  • esophagus
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • thymus
Abdomen:
  • abdominal wall
  • biliary tract
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • stomach
Pelvis:
  • fallopian tube
  • ovary
  • pelvis
  • penis
  • placenta
  • prostate
  • testicle
  • ureter
  • uterus
  • vagina
  • vas deferens
  • vulva
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with SEMA3E: view

No data available for mRNA Expression by UniProt/SwissProt for SEMA3E Gene

Orthologs for SEMA3E Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA3E Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA3E 31 30
  • 99.57 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA3E 31 30
  • 90.32 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA3E 31 30
  • 89.27 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SEMA3E 31
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema3e 17 31 30
  • 85.16 (n)
rat
(Rattus norvegicus)
Mammalia Sema3e 30
  • 84.77 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA3E 31
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves SEMA3E 31 30
  • 77.63 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SEMA3E 31
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema3e 30
  • 73.78 (n)
zebrafish
(Danio rerio)
Actinopterygii sema3e 31 30
  • 62.4 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Sema-2a 32
  • 32 (a)
Sema-1b 32
  • 32 (a)
CG4383 32
  • 31 (a)
Species where no ortholog for SEMA3E 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 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 SEMA3E Gene

ENSEMBL:
Gene Tree for SEMA3E (if available)
TreeFam:
Gene Tree for SEMA3E (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEMA3E: view image

Paralogs for SEMA3E Gene

(13) SIMAP similar genes for SEMA3E Gene using alignment to 3 proteins:

  • SEM3E_HUMAN
  • C9JVH5_HUMAN
  • F8WCZ5_HUMAN

Pseudogenes.org Pseudogenes for SEMA3E Gene

genes like me logo Genes that share paralogs with SEMA3E: view

Variants for SEMA3E Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEMA3E Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
641084 Uncertain Significance: CHARGE association 83,402,732(-) C/T MISSENSE_VARIANT
641315 Uncertain Significance: CHARGE association 83,396,667(-) C/T MISSENSE_VARIANT
642340 Uncertain Significance: CHARGE association 83,367,996(-) G/A MISSENSE_VARIANT
643841 Uncertain Significance: CHARGE association 83,407,192(-) C/A MISSENSE_VARIANT
644003 Uncertain Significance: CHARGE association 83,418,429(-) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SEMA3E Gene

Structural Variations from Database of Genomic Variants (DGV) for SEMA3E Gene

Variant ID Type Subtype PubMed ID
dgv1120n67 CNV gain 20364138
dgv196n73 CNV deletion 24416366
dgv3605n106 CNV deletion 24896259
dgv6517n100 CNV loss 25217958
esv1184566 CNV insertion 17803354
esv2519932 CNV deletion 19546169
esv2673845 CNV deletion 23128226
esv2674112 CNV deletion 23128226
esv2678160 CNV deletion 23128226
esv27343 CNV loss 19812545
esv2734754 CNV deletion 23290073
esv2734755 CNV deletion 23290073
esv2734756 CNV deletion 23290073
esv2734757 CNV deletion 23290073
esv2734758 CNV deletion 23290073
esv33579 CNV loss 17666407
esv3450305 CNV insertion 20981092
esv3542008 CNV deletion 23714750
esv3542009 CNV deletion 23714750
esv3576399 CNV gain 25503493
esv3613932 CNV loss 21293372
esv3613933 CNV loss 21293372
esv3613935 CNV loss 21293372
esv3613936 CNV loss 21293372
esv3613937 CNV loss 21293372
esv3613938 CNV loss 21293372
esv3613939 CNV loss 21293372
esv3613940 CNV loss 21293372
esv3613941 CNV loss 21293372
esv3891157 CNV loss 25118596
nsv1017248 CNV loss 25217958
nsv1018662 CNV loss 25217958
nsv1023612 CNV loss 25217958
nsv1074135 CNV deletion 25765185
nsv1110807 CNV insertion 24896259
nsv1114980 CNV deletion 24896259
nsv1148608 CNV insertion 26484159
nsv1149101 CNV insertion 26484159
nsv483120 CNV loss 15286789
nsv511976 CNV loss 21212237
nsv526178 CNV loss 19592680
nsv607706 CNV loss 21841781
nsv818531 CNV gain 17921354
nsv821148 CNV deletion 20802225
nsv824189 CNV gain 20364138
nsv824191 CNV gain 20364138
nsv824195 CNV loss 20364138

Variation tolerance for SEMA3E Gene

Residual Variation Intolerance Score: 14.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.22; 76.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEMA3E Gene

Human Gene Mutation Database (HGMD)
SEMA3E
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA3E

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA3E Gene

Disorders for SEMA3E Gene

MalaCards: The human disease database

(4) MalaCards diseases for SEMA3E Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
charge syndrome
  • hhs
hypogonadotropic hypogonadism 7 with or without anosmia
  • hh7
cone-rod dystrophy 10
  • cord10
kallmann syndrome
  • hypogonadotropic hypogonadism and anosmia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA3E

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 SEMA3E: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA3E Gene

Publications for SEMA3E Gene

  1. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9205841) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4 54
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  3. Semaphorin 3E expression correlates inversely with Plexin D1 during tumor progression. (PMID: 18974298) Roodink I … Leenders W (The American journal of pathology 2008) 3 23 54
  4. SEMA3E mutation in a patient with CHARGE syndrome. (PMID: 15235037) Lalani SR … Belmont JW (Journal of medical genetics 2004) 3 4 54
  5. The DNA sequence of human chromosome 7. (PMID: 12853948) Hillier LW … Wilson RK (Nature 2003) 3 4 54

Products for SEMA3E Gene

Sources for SEMA3E Gene