Aliases for SEMA4B Gene

Aliases for SEMA4B Gene

  • Semaphorin 4B 2 3 5
  • Sema Domain, Immunoglobulin Domain (Ig), Transmembrane Domain (TM) And Short Cytoplasmic Domain, (Semaphorin) 4B 2 3
  • Semaphorin-4B 3 4
  • Semaphorin-C 3 4
  • KIAA1745 2 4
  • SEMAC 3 4
  • SemC 2 3
  • Sema Domain, Immunoglobulin Domain (Ig), Transmembrane Domain (TM) And Short Cytoplasmic Domain, 4B 3
  • MGC131831 2
  • SEMA4B 5

External Ids for SEMA4B Gene

Previous HGNC Symbols for SEMA4B Gene

  • SEMAC

Previous GeneCards Identifiers for SEMA4B Gene

  • GC15M087399
  • GC15P084251
  • GC15P088331
  • GC15P088474
  • GC15P088457
  • GC15P088529
  • GC15P090728
  • GC15P066843
  • GC15P090703

Summaries for SEMA4B Gene

GeneCards Summary for SEMA4B Gene

SEMA4B (Semaphorin 4B) is a Protein Coding gene. Diseases associated with SEMA4B include Kallmann Syndrome. Among its related pathways are Nanog in Mammalian ESC Pluripotency and Apoptotic Pathways in Synovial Fibroblasts. An important paralog of this gene is SEMA4D.

UniProtKB/Swiss-Prot Summary for SEMA4B Gene

  • Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons.

Gene Wiki entry for SEMA4B Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SEMA4B Gene

Genomics for SEMA4B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SEMA4B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SEMA4B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SEMA4B

Top Transcription factor binding sites by QIAGEN in the SEMA4B gene promoter:
  • c-Myc
  • GATA-2
  • HEN1
  • Max1
  • Pax-4a
  • Spz1

Genomic Locations for SEMA4B Gene

Latest Assembly
chr15:90,160,604-90,229,679
(GRCh38/hg38)
Size:
69,076 bases
Orientation:
Plus strand

Previous Assembly
chr15:90,728,152-90,772,911
(GRCh37/hg19 by Entrez Gene)
Size:
44,760 bases
Orientation:
Plus strand

chr15:90,703,836-90,772,911
(GRCh37/hg19 by Ensembl)
Size:
69,076 bases
Orientation:
Plus strand

Genomic View for SEMA4B Gene

Genes around SEMA4B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA4B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA4B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA4B Gene

Proteins for SEMA4B Gene

  • Protein details for SEMA4B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NPR2-SEM4B_HUMAN
    Recommended name:
    Semaphorin-4B
    Protein Accession:
    Q9NPR2
    Secondary Accessions:
    • J3KNP4
    • Q6UXE3
    • Q8WVP9
    • Q96FK5
    • Q9C0B8
    • Q9H691
    • Q9NPM8
    • Q9NPN0

    Protein attributes for SEMA4B Gene

    Size:
    837 amino acids
    Molecular mass:
    92766 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB15372.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB21836.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for SEMA4B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA4B Gene

Post-translational modifications for SEMA4B Gene

  • Glycosylation at Asn69, Asn96, Asn165, Asn410, Asn525, and Asn630
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • SEM4B_HUMAN (1975)

No data available for DME Specific Peptides for SEMA4B Gene

Domains & Families for SEMA4B Gene

Gene Families for SEMA4B Gene

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

Protein Domains for SEMA4B Gene

InterPro:
Blocks:
  • Semaphorin/CD100 antigen

Suggested Antigen Peptide Sequences for SEMA4B Gene

GenScript: Design optimal peptide antigens:
  • Sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (Semaphorin) 4B (Q2NL81_HUMAN)
  • SEMA4B protein (Q4VBY2_HUMAN)
  • Semaphorin-4B (SEM4B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NPR2

UniProtKB/Swiss-Prot:

SEM4B_HUMAN :
  • Belongs to the semaphorin family.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA4B: view

Function for SEMA4B Gene

Molecular function for SEMA4B Gene

UniProtKB/Swiss-Prot Function:
Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons.

Phenotypes From GWAS Catalog for SEMA4B Gene

Gene Ontology (GO) - Molecular Function for SEMA4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0030215 semaphorin receptor binding IEA,IBA 21873635
GO:0045499 chemorepellent activity IBA 21873635
genes like me logo Genes that share ontologies with SEMA4B: view
genes like me logo Genes that share phenotypes with SEMA4B: view

Animal Models for SEMA4B Gene

MGI Knock Outs for SEMA4B:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SEMA4B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SEMA4B Gene

Localization for SEMA4B Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA4B Gene

Membrane. Single-pass type I membrane protein.

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 SEMA4B gene
Compartment Confidence
plasma membrane 5
extracellular 4
cytoskeleton 2
nucleus 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for SEMA4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA 21873635
GO:0005886 plasma membrane IEA --
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 SEMA4B: view

Pathways & Interactions for SEMA4B Gene

PathCards logo

SuperPathways for SEMA4B Gene

SuperPathway Contained pathways
1 Apoptotic Pathways in Synovial Fibroblasts
.85
.85
.84
.84
.74
.72
.66
.65
.64
.62
.61
.60
.57
.57
2 GPCR Pathway
.73
.73
.62
.59
.58
.58
.55
3 ERK Signaling
.61
.61
.58
.51
.49
4 Nanog in Mammalian ESC Pluripotency
.61
.61
.59
.48
5 CREB Pathway
.68
.68
.63
.50
genes like me logo Genes that share pathways with SEMA4B: view

Pathways by source for SEMA4B Gene

1 KEGG pathway for SEMA4B Gene
54 Qiagen pathways for SEMA4B Gene
  • 14-3-3 Induced Intracellular Signaling
  • Actin-Based Motility by Rho Family GTPases
  • Activation of cAMP-Dependent PKA
  • Activation of PKA through GPCR
  • Activation of PKC through GPCR
2 Cell Signaling Technology pathways for SEMA4B Gene

Gene Ontology (GO) - Biological Process for SEMA4B 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 SEMA4B: view

No data available for SIGNOR curated interactions for SEMA4B Gene

Drugs & Compounds for SEMA4B Gene

No Compound Related Data Available

Transcripts for SEMA4B Gene

mRNA/cDNA for SEMA4B Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SEMA4B

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA4B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a · 15b ^ 16a · 16b ^ 17
SP1: - - - - -
SP2: - - - -
SP3: - - - -
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: -

Relevant External Links for SEMA4B Gene

GeneLoc Exon Structure for
SEMA4B

Expression for SEMA4B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SEMA4B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEMA4B Gene

This gene is overexpressed in Esophagus - Mucosa (x4.2).

Protein differential expression in normal tissues from HIPED for SEMA4B Gene

This gene is overexpressed in Serum (38.4) and Cervix (10.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SEMA4B Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SEMA4B

SOURCE GeneReport for Unigene cluster for SEMA4B Gene:

Hs.474935

Evidence on tissue expression from TISSUES for SEMA4B Gene

  • Nervous system(4.9)
  • Pancreas(4.8)
  • Intestine(4.5)
  • Bone marrow(4.4)
  • Kidney(2.9)
  • Lung(2.8)
  • Skin(2.7)
  • Heart(2.7)
  • Eye(2.5)
  • Blood(2.4)
  • Spleen(2.3)
  • Muscle(2.3)
  • Lymph node(2.2)
  • Liver(2.1)
  • Thyroid gland(2)
genes like me logo Genes that share expression patterns with SEMA4B: view

Primer products for research

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA4B Gene

Orthologs for SEMA4B Gene

This gene was present in the common ancestor of chordates.

Orthologs for SEMA4B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SEMA4B 29 30
  • 96.77 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SEMA4B 29 30
  • 86.81 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SEMA4B 29 30
  • 84.72 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sema4b 29 16 30
  • 83.19 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sema4b 29
  • 82.98 (n)
Oppossum
(Monodelphis domestica)
Mammalia SEMA4B 30
  • 72 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SEMA4B 30
  • 67 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SEMA4B 29 30
  • 70.14 (n)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sema4b 29
  • 60.94 (n)
Zebrafish
(Danio rerio)
Actinopterygii sema4ba 30
  • 50 (a)
OneToMany
SEMA4B (2 of 2) 30
  • 47 (a)
OneToMany
Species where no ortholog for SEMA4B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Lizard (Anolis carolinensis)
  • 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 Vase (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 SEMA4B Gene

ENSEMBL:
Gene Tree for SEMA4B (if available)
TreeFam:
Gene Tree for SEMA4B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SEMA4B: view image
Alliance of Genome Resources:
Additional Orthologs for SEMA4B

Paralogs for SEMA4B Gene

(20) SIMAP similar genes for SEMA4B Gene using alignment to 14 proteins:

  • SEM4B_HUMAN
  • H0YKP2_HUMAN
  • H0YKV7_HUMAN
  • H0YLN3_HUMAN
  • H0YM68_HUMAN
  • H0YMD6_HUMAN
  • H0YMR1_HUMAN
  • H0YMZ3_HUMAN
  • H0YN49_HUMAN
  • H0YNC4_HUMAN
  • H0YNM2_HUMAN
  • J3KNP4_HUMAN
  • Q2NL81_HUMAN
  • Q4VBY2_HUMAN
genes like me logo Genes that share paralogs with SEMA4B: view

Variants for SEMA4B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SEMA4B Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
rs3751655 -- p.Ser797Ala

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SEMA4B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SEMA4B Gene

Variant ID Type Subtype PubMed ID
dgv112e55 CNV gain 17911159
esv2760054 CNV gain 17122850
esv3637214 CNV gain 21293372
nsv1052652 CNV gain 25217958
nsv442384 CNV gain 18776908
nsv570390 CNV loss 21841781
nsv570391 CNV loss 21841781
nsv817707 CNV gain 17921354
nsv833087 CNV loss 17160897
nsv984107 CNV duplication 23825009

Variation tolerance for SEMA4B Gene

Residual Variation Intolerance Score: 47.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.07; 80.34% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SEMA4B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA4B
Leiden Open Variation Database (LOVD)
SEMA4B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA4B Gene

Disorders for SEMA4B Gene

MalaCards: The human disease database

(1) MalaCards diseases for SEMA4B Gene - From: COP

Disorder Aliases PubMed IDs
kallmann syndrome
  • familial hypogonadism with anosmia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SEMA4B

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SEMA4B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEMA4B Gene

Publications for SEMA4B Gene

  1. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 40
  2. CLCP1 interacts with semaphorin 4B and regulates motility of lung cancer cells. (PMID: 17213806) Nagai H … Osada H (Oncogene 2007) 3 22
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4
  4. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. (PMID: 16335952) Liu T … Smith RD (Journal of proteome research 2005) 3 4
  5. Semaphorin 4B interacts with the post-synaptic density protein PSD-95/SAP90 and is recruited to synapses through a C-terminal PDZ-binding motif. (PMID: 15978582) Burkhardt C … Püschel AW (FEBS letters 2005) 3 22

Products for SEMA4B Gene

Sources for SEMA4B Gene