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SEMA6B semaphorin 6B [ Homo sapiens (human) ]

Gene ID: 10501, updated on 2-Nov-2024

Summary

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Official Symbol
SEMA6Bprovided by HGNC
Official Full Name
semaphorin 6Bprovided by HGNC
Primary source
HGNC:HGNC:10739
See related
Ensembl:ENSG00000167680 MIM:608873; AllianceGenome:HGNC:10739
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
EPM11; SEMAN; semaZ; SEMA-VIB; SEM-SEMA-Y; SEM-SEMA-Z
Summary
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]
Expression
Broad expression in brain (RPKM 18.7), spleen (RPKM 8.6) and 15 other tissues See more
Orthologs
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Genomic context

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See SEMA6B in Genome Data Viewer
Location:
19p13.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (4542593..4559684, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (4526261..4543368, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (4542605..4559696, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene perilipin 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4534387-4534942 Neighboring gene leucine rich alpha-2-glycoprotein 1 Neighboring gene Sharpr-MPRA regulatory region 7851 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4567569-4568069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:4575301-4575893 Neighboring gene uncharacterized LOC105372249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9894 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:4596181-4596372 Neighboring gene Sharpr-MPRA regulatory region 4167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4606740-4607298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:4607299-4607856 Neighboring gene MPRA-validated peak3284 silencer Neighboring gene ribosomal protein S10 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The role of axon guidance factor semaphorin 6B in the invasion and metastasis of gastric cancer. Ge C, et al. J Int Med Res, 2013 Apr. PMID 23781008
  2. C-nucleoside studies. Part III. Glycofuranosylethynes from 2,3:5,6-di-O-isopropylidene-D-mannose. Buchanan JG, et al. J Chem Soc Perkin 1, 1976. PMID 942725
  3. 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. Correa RG, et al. Genomics, 2001 May 1. PMID 11350127
  4. The human semaphorin 6B gene is down regulated by PPARs. Collet P, et al. Genomics, 2004 Jun. PMID 15177567
  5. Analysis of SEMA6B gene expression in breast cancer: identification of a new isoform. D'Apice L, et al. Biochim Biophys Acta, 2013 Oct. PMID 23665584

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Progressive myoclonus epilepsies due to SEMA6B mutations. New variants and appraisal of published phenotypes.
    Title: Progressive myoclonus epilepsies due to SEMA6B mutations. New variants and appraisal of published phenotypes.
  2. SEMA6B variants cause intellectual disability and alter dendritic spine density and axon guidance.
    Title: SEMA6B variants cause intellectual disability and alter dendritic spine density and axon guidance.
  3. Aberrant expression of semaphorin 6B affects cell phenotypes in thyroid carcinoma by activating the Notch signalling pathway.
    Title: Aberrant expression of semaphorin 6B affects cell phenotypes in thyroid carcinoma by activating the Notch signalling pathway.
  4. A Frameshift Variant in the SEMA6B Gene Causes Global Developmental Delay and Febrile Seizures.
    Title: A Frameshift Variant in the SEMA6B Gene Causes Global Developmental Delay and Febrile Seizures.
  5. Genome-Wide CRISPR Screen Identifies Semaphorin 6A and 6B as Receptors for Paeniclostridium sordellii Toxin TcsL.
    Title: Genome-Wide CRISPR Screen Identifies Semaphorin 6A and 6B as Receptors for Paeniclostridium sordellii Toxin TcsL.
  6. Heterozygous truncating variants in the NMD(+) region of SEMA6B are observed in general populations.
    Title: De Novo Truncating Variants in the Last Exon of SEMA6B Cause Progressive Myoclonic Epilepsy.
  7. Semaphorin 6B is related to tumour differentiation and metastasis in vivo, and tumour cell migration, adhesion and invasion in vitro.
    Title: The role of axon guidance factor semaphorin 6B in the invasion and metastasis of gastric cancer.
  8. states a clear relation among breast cancer and SEMA6B expression; moreover we describe for the first time the SEMA6Ba protein and report here the analysis of SEMA6Ba RNA messenger, the protein expression and the cellular localization
    Title: Analysis of SEMA6B gene expression in breast cancer: identification of a new isoform.
  9. Gene SEMA6B is strongly down regulated by peroxisome proliferator-activated receptors.
    Title: The human semaphorin 6B gene is down regulated by PPARs.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Epilepsy, progressive myoclonic, 11
MedGen: C5394362 OMIM: 618876 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables neuropilin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in central nervous system development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in hippocampus development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
semaphorin-6B
Names
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B
semaphorin VIB
semaphorin Z
semaphorin-6Ba

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_032108.4 → NP_115484.2  semaphorin-6B precursor

    See identical proteins and their annotated locations for NP_115484.2

    Status: REVIEWED

    Source sequence(s)
    BC142617, DA818632, DB257858
    Consensus CDS
    CCDS12131.1
    UniProtKB/Swiss-Prot
    A5PKU4, F6IB19, Q9H3T3, Q9NRK9
    Related
    ENSP00000467290.1, ENST00000586582.6
    Conserved Domains (2) summary
    cd11267
    Location:57 → 524
    Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
    pfam01437
    Location:525 → 554
    PSI; Plexin repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    4542593..4559684 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    4526261..4543368 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_020241.2: Suppressed sequence

    Description
    NM_020241.2: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.

  2. NM_133327.1: Suppressed sequence

    Description
    NM_133327.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H3T3.4 GenPept UniProtKB/Swiss-Prot:Q9H3T3

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