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Aliases for SEMA6B Gene

Aliases for SEMA6B Gene

  • Semaphorin 6B 2 3 5
  • Sema Domain, Transmembrane Domain (TM), And Cytoplasmic Domain, (Semaphorin) 6B 2 3
  • Semaphorin VIB 2 3
  • Semaphorin Z 2 3
  • SemaZ 3 4
  • SEMAN 3 4
  • Semaphorin-6Ba 3
  • Semaphorin-6B 3
  • Semaphorin-Z 4
  • SEM-SEMA-Y 3
  • Sema VIb 2
  • SEMA-VIB 3
  • Sema Z 4

External Ids for SEMA6B Gene

Previous HGNC Symbols for SEMA6B Gene

  • SEMAN

Previous GeneCards Identifiers for SEMA6B Gene

  • GC19M004634
  • GC19M004482
  • GC19M004493
  • GC19M004304

Summaries for SEMA6B Gene

Entrez Gene Summary for SEMA6B Gene

  • This gene encodes a member of the semaphorin family, a group of proteins characterized by the presence of a conserved semaphorin (sema) domain. Whereas some semaphorins are transmembrane proteins, others are secreted. Semaphorins play a major role in axon guidance. The protein encoded by this gene may be involved in both peripheral and central nervous system development. [provided by RefSeq, Jul 2008]

GeneCards Summary for SEMA6B Gene

SEMA6B (Semaphorin 6B) is a Protein Coding gene. Among its related pathways are Axon guidance. GO annotations related to this gene include receptor activity and semaphorin receptor binding. An important paralog of this gene is SEMA6A.

UniProtKB/Swiss-Prot for SEMA6B Gene

  • May play a role in both peripheral and central nervous system development.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEMA6B Gene

Genomics for SEMA6B Gene

Regulatory Elements for SEMA6B Gene

Enhancers for SEMA6B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19G004367 2 FANTOM5 Ensembl ENCODE dbSUPER 33.6 +206.8 206782 14.8 CREB3L1 MLX AGO1 DMAP1 ZNF143 ZNF263 NFYC TBX21 MEF2D SSRP1 ENSG00000267769 SEMA6B CHAF1A SH3GL1 UBXN6 CACTIN ENSG00000267030 FSD1 TMIGD2 ENSG00000267980
GH19G004811 2 FANTOM5 Ensembl ENCODE dbSUPER 15.8 -232.7 -232747 5.9 HDGF FOXA2 PKNOX1 CREB3L1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 TICAM1 SEMA6B PLIN3 SAFB2 ENSG00000268536 ENSG00000269604
GH19G004056 1.8 FANTOM5 ENCODE dbSUPER 14.6 +518.4 518371 12.7 HNRNPUL1 PKNOX1 MLX AGO1 WRNIP1 ZFP64 ARID4B SIN3A DMAP1 YY1 SEMA6B CACTIN NFIC ZBTB7A PLIN5 UBXN6 SIRT6 ATCAY CCDC94 MATK
GH19G004567 1.8 FANTOM5 Ensembl ENCODE dbSUPER 14.3 +13.8 13801 0.8 HDGF HDAC1 CBX3 PTBP1 RB1 INSM2 KLF17 ZNF48 ZNF2 ZBTB7B SEMA6B TICAM1 KDM4B CCDC94 LOC105372249 GC19P004547
GH19G004632 1.7 FANTOM5 Ensembl ENCODE 13.7 -53.4 -53430 4.2 HDGF PKNOX1 ARNT SIN3A ARID4B FEZF1 ZNF2 ZBTB7B ZNF766 CBX5 TICAM1 SEMA6B TNFAIP8L1 CCDC94 ANKRD24 SH3GL1 LOC100287614
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEMA6B on UCSC Golden Path with GeneCards custom track

Genomic Location for SEMA6B Gene

Chromosome:
19
Start:
4,542,587 bp from pter
End:
4,581,602 bp from pter
Size:
39,016 bases
Orientation:
Minus strand

Genomic View for SEMA6B Gene

Genes around SEMA6B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEMA6B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEMA6B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEMA6B Gene

Proteins for SEMA6B Gene

  • Protein details for SEMA6B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H3T3-SEM6B_HUMAN
    Recommended name:
    Semaphorin-6B
    Protein Accession:
    Q9H3T3
    Secondary Accessions:
    • A5PKU4
    • F6IB19
    • Q9NRK9

    Protein attributes for SEMA6B Gene

    Size:
    888 amino acids
    Molecular mass:
    95285 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF87661.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};

    Alternative splice isoforms for SEMA6B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SEMA6B Gene

Post-translational modifications for SEMA6B Gene

  • Glycosylation at isoforms=374, Asn155, isoforms=3167, isoforms=3291, isoforms=3386, isoforms=3441, and Asn462
  • Modification sites at PhosphoSitePlus

Other Protein References for SEMA6B Gene

No data available for DME Specific Peptides for SEMA6B Gene

Domains & Families for SEMA6B Gene

Gene Families for SEMA6B Gene

Protein Domains for SEMA6B Gene

Suggested Antigen Peptide Sequences for SEMA6B Gene

Graphical View of Domain Structure for InterPro Entry

Q9H3T3

UniProtKB/Swiss-Prot:

SEM6B_HUMAN :
  • Belongs to the semaphorin family.
Family:
  • Belongs to the semaphorin family.
genes like me logo Genes that share domains with SEMA6B: view

Function for SEMA6B Gene

Molecular function for SEMA6B Gene

UniProtKB/Swiss-Prot Function:
May play a role in both peripheral and central nervous system development.

Gene Ontology (GO) - Molecular Function for SEMA6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030215 semaphorin receptor binding IEA --
genes like me logo Genes that share ontologies with SEMA6B: view

Phenotypes for SEMA6B Gene

MGI mutant phenotypes for SEMA6B:
inferred from 1 alleles
GenomeRNAi human phenotypes for SEMA6B:
genes like me logo Genes that share phenotypes with SEMA6B: view

Animal Models for SEMA6B Gene

MGI Knock Outs for SEMA6B:

Animal Model Products

  • Taconic Biosciences Mouse Models for SEMA6B

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SEMA6B Gene

Localization for SEMA6B Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEMA6B Gene

Cell 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 SEMA6B gene
Compartment Confidence
plasma membrane 5
extracellular 2
peroxisome 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SEMA6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SEMA6B: view

Pathways & Interactions for SEMA6B Gene

SuperPathways for SEMA6B Gene

SuperPathway Contained pathways
1 Axon guidance
genes like me logo Genes that share pathways with SEMA6B: view

Pathways by source for SEMA6B Gene

1 KEGG pathway for SEMA6B Gene

Interacting Proteins for SEMA6B Gene

Selected Interacting proteins: Q9H3T3-SEM6B_HUMAN for SEMA6B Gene via IID

Gene Ontology (GO) - Biological Process for SEMA6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with SEMA6B: view

No data available for SIGNOR curated interactions for SEMA6B Gene

Drugs & Compounds for SEMA6B Gene

(1) Additional Compounds for SEMA6B Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SEMA6B: view

Transcripts for SEMA6B Gene

Unigene Clusters for SEMA6B Gene

Sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEMA6B Gene

No ASD Table

Relevant External Links for SEMA6B Gene

GeneLoc Exon Structure for
SEMA6B
ECgene alternative splicing isoforms for
SEMA6B

Expression for SEMA6B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SEMA6B Gene

mRNA differential expression in normal tissues according to GTEx for SEMA6B Gene

This gene is overexpressed in Brain - Cortex (x4.1) and Brain - Hippocampus (x4.0).

Protein differential expression in normal tissues from HIPED for SEMA6B Gene

This gene is overexpressed in Liver, secretome (66.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SEMA6B Gene



Protein tissue co-expression partners for SEMA6B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SEMA6B Gene:

SEMA6B

SOURCE GeneReport for Unigene cluster for SEMA6B Gene:

Hs.465642

Evidence on tissue expression from TISSUES for SEMA6B Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with SEMA6B: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SEMA6B Gene

Orthologs for SEMA6B Gene

This gene was present in the common ancestor of animals.

Orthologs for SEMA6B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SEMA6B 34 35
  • 97.65 (n)
cow
(Bos Taurus)
Mammalia SEMA6B 34 35
  • 89.67 (n)
dog
(Canis familiaris)
Mammalia SEMA6B 35
  • 85 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sema6b 34 16 35
  • 82.79 (n)
rat
(Rattus norvegicus)
Mammalia Sema6b 34
  • 82.69 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 70 (a)
OneToMany
-- 35
  • 33 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia SEMA6B 35
  • 50 (a)
OneToOne
chicken
(Gallus gallus)
Aves SEMA6B 34 35
  • 72.36 (n)
lizard
(Anolis carolinensis)
Reptilia SEMA6B 35
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sema6b 34
  • 62.68 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100148883 34
  • 62.17 (n)
sema6bb 35
  • 62 (a)
OneToMany
sema6ba 35
  • 53 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Sema-1a 36
  • 39 (a)
CG4383 36
  • 37 (a)
Sema-1b 36
  • 36 (a)
Sema-2a 35
  • 28 (a)
ManyToMany
Sema-2b 35
  • 26 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea mab-20 36
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 28 (a)
OneToMany
Species where no ortholog for SEMA6B 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 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)

Evolution for SEMA6B Gene

ENSEMBL:
Gene Tree for SEMA6B (if available)
TreeFam:
Gene Tree for SEMA6B (if available)

Paralogs for SEMA6B Gene

Paralogs for SEMA6B Gene

(4) SIMAP similar genes for SEMA6B Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with SEMA6B: view

Variants for SEMA6B Gene

Sequence variations from dbSNP and Humsavar for SEMA6B Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs1000014149 -- 4,542,755(+) CTGGG(A/G)CCGTA utr-variant-3-prime
rs1000071870 -- 4,569,836(+) GCTCT(A/G)ACCCT intron-variant
rs1000074501 -- 4,578,103(+) GAGAG(G/T)TGATG intron-variant, upstream-variant-2KB
rs1000105664 -- 4,556,822(+) CCAGG(A/G)CTGAT intron-variant
rs1000153266 -- 4,542,935(+) CACCT(C/T)GGAGA utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for SEMA6B Gene

Variant ID Type Subtype PubMed ID
dgv614e199 CNV deletion 23128226
esv3643502 CNV loss 21293372
nsv1113961 CNV deletion 24896259
nsv1125667 CNV tandem duplication 24896259
nsv2394 CNV deletion 18451855
nsv428361 CNV loss 18775914
nsv578444 CNV gain 21841781
nsv828405 CNV gain 20364138
nsv953950 CNV deletion 24416366

Variation tolerance for SEMA6B Gene

Residual Variation Intolerance Score: 9.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.97; 36.45% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SEMA6B Gene

Human Gene Mutation Database (HGMD)
SEMA6B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEMA6B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEMA6B Gene

Disorders for SEMA6B Gene

Relevant External Links for SEMA6B

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEMA6B

No disorders were found for SEMA6B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SEMA6B Gene

Publications for SEMA6B Gene

  1. Human semaphorin 6b [(HSA)SEMA6B], a novel human class 6 semaphorin gene: alternative splicing and all-trans-retinoic acid-dependent downregulation in glioblastoma cell lines. (PMID: 11350127) Correa R.G. … Simpson A.J.G. (Genomics 2001) 3 4 22 64
  2. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PMID: 15340161) Zhang Z. … Henzel W.J. (Protein Sci. 2004) 3 4 64
  3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 3 4 64
  4. Analysis of SEMA6B gene expression in breast cancer: identification of a new isoform. (PMID: 23665584) D'Apice L. … De Berardinis P. (Biochim. Biophys. Acta 2013) 3 64
  5. The role of axon guidance factor semaphorin 6B in the invasion and metastasis of gastric cancer. (PMID: 23781008) Ge C. … Xu X. (J. Int. Med. Res. 2013) 3 64

Products for SEMA6B Gene

Sources for SEMA6B Gene

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