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    SEMA6B semaphorin 6B [ Homo sapiens (human) ]

    Gene ID: 10501, updated on 28-Oct-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
    		Compare labs

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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