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

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. Among its related pathways are ERK Signaling and Akt Signaling. An important paralog of this gene is SEMA4C.

UniProtKB/Swiss-Prot for SEMA4B Gene

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

Gene Wiki entry for SEMA4B Gene

Additional gene information for SEMA4B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA4B Gene

Genomics for SEMA4B Gene

GeneHancer (GH) Regulatory Elements for SEMA4B Gene

Promoters and enhancers for SEMA4B 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
GH15J090182 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 663 +24.1 24120 3.9 CLOCK IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 MEF2D SSRP1 ZNF610 SEMA4B PIR44533 UNC45A POLG RCCD1 RPL36AP43 NIFKP5 ENSG00000259314 ENSG00000270322 CRTC3
GH15J090200 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 662.5 +41.4 41360 3.9 HDGF SIN3A GLIS2 ATF7 SP3 SP5 SMARCB1 GLIS1 CTCF BACH1 SEMA4B VPS33B ENSG00000259314 CIB1 ENSG00000228998 TTLL13P RPS12P26 GC15M090188
GH15J090209 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 26.7 +51.9 51882 5.9 HDAC1 SMAD1 SIN3A FEZF1 BATF IRF4 RAD21 TCF12 SCRT2 ZNF143 SEMA4B CIB1 GDPGP1 IDH2 NGRN IQGAP1 ENSG00000228998 TTLL13P RPS12P26 PIR48569
GH15J090186 Enhancer 1.4 Ensembl ENCODE dbSUPER 22.1 +30.7 30731 8.7 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A YY1 POLR2B E2F8 SEMA4B CIB1 FANCI GDPGP1 NGRN PRC1 IDH2 LOC105370969 TTLL13P GC15M090188
GH15J090157 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 13 +2.9 2938 12.2 CLOCK MLX DMAP1 YBX1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 UNC45A ENSG00000259314 POLG CIB1 RCCD1 SEMA4B CRTC3 LOC100631255 RPL36AP43 GDPGP1
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for SEMA4B Gene

Genomic Locations for SEMA4B Gene
chr15:90,160,604-90,229,679
(GRCh38/hg38)
Size:
69,076 bases
Orientation:
Plus strand
chr15:90,703,836-90,772,911
(GRCh37/hg19)
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:
    • Q6UXE3
    • Q8WVP9
    • Q96FK5
    • Q9C0B8
    • Q9H691
    • Q9NPM8
    • Q9NPN0

    Protein attributes for SEMA4B Gene

    Size:
    832 amino acids
    Molecular mass:
    92193 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAQ88758.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=AAR15707.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAB15372.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB21836.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; 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 posLast=625625, posLast=520520, posLast=405405, posLast=160160, isoforms=291, and posLast=6464
  • Modification sites at PhosphoSitePlus

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
  • Predicted secreted proteins

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.

Gene Ontology (GO) - Molecular Function for SEMA4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030215 semaphorin receptor binding IBA --
GO:0038191 NOT neuropilin binding IBA --
GO:0045499 chemorepellent activity IBA --
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 Model Products

CRISPR Products

Inhibitory RNA Products

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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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
extracellular 4
plasma membrane 3
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for SEMA4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IBA --
GO:0005886 plasma membrane IEA,IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0045202 synapse IEA --
genes like me logo Genes that share ontologies with SEMA4B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SEMA4B Gene

Pathways & Interactions for SEMA4B Gene

genes like me logo Genes that share pathways with SEMA4B: view

Pathways by source 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 --
GO:0007399 nervous system development IEA --
GO:0030154 cell differentiation IEA --
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 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

Unigene Clusters for SEMA4B Gene

Sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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
ECgene alternative splicing isoforms for
SEMA4B

Expression for SEMA4B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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



NURSA nuclear receptor signaling pathways regulating expression of SEMA4B Gene:

SEMA4B

SOURCE GeneReport for Unigene cluster for SEMA4B Gene:

Hs.474935

Evidence on tissue expression from TISSUES for SEMA4B Gene

  • Nervous system(4.8)
  • Pancreas(4.7)
  • Intestine(4.3)
  • Bone marrow(4.1)
  • Lung(2.3)
genes like me logo Genes that share expression patterns with SEMA4B: view

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 34 33
  • 96.77 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SEMA4B 34 33
  • 86.81 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SEMA4B 34 33
  • 84.72 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Sema4b 16 34 33
  • 83.19 (n)
rat
(Rattus norvegicus)
Mammalia Sema4b 33
  • 82.98 (n)
oppossum
(Monodelphis domestica)
Mammalia SEMA4B 34
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SEMA4B 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves SEMA4B 34 33
  • 70.14 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema4b 33
  • 60.94 (n)
zebrafish
(Danio rerio)
Actinopterygii sema4ba 34
  • 50 (a)
OneToMany
SEMA4B (2 of 2) 34
  • 47 (a)
OneToMany
Species where no ortholog for SEMA4B 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)
  • 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 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 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

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 from dbSNP and Humsavar for SEMA4B Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1000082982 -- 90,185,387(+) A/C/G genic_upstream_transcript_variant, intron_variant
rs1000145295 -- 90,193,314(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000146032 -- 90,208,981(+) T/C intron_variant
rs1000147064 -- 90,185,109(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000229027 -- 90,188,767(+) A/T genic_upstream_transcript_variant, intron_variant

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

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

Disorders for SEMA4B Gene

Additional Disease Information for SEMA4B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for SEMA4B Gene.

No data available for MalaCards , 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 44 58
  2. CLCP1 interacts with semaphorin 4B and regulates motility of lung cancer cells. (PMID: 17213806) Nagai H … Osada H (Oncogene 2007) 3 22 58
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  4. 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 58
  5. 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 58

Products for SEMA4B Gene

Sources for SEMA4B Gene

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