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    SEMA3B semaphorin 3B [ Homo sapiens (human) ]

    Gene ID: 7869, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SEMA3Bprovided by HGNC
    Official Full Name
    semaphorin 3Bprovided by HGNC
    Primary source
    HGNC:HGNC:10724
    See related
    Ensembl:ENSG00000012171 MIM:601281; AllianceGenome:HGNC:10724
    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
    SemA; SEMA5; SEMAA; semaV; LUCA-1
    Summary
    The protein encoded by this gene belongs to the class-3 semaphorin/collapsin family, whose members function in growth cone guidance during neuronal development. This family member inhibits axonal extension and has been shown to act as a tumor suppressor by inducing apoptosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014]
    Expression
    Broad expression in placenta (RPKM 31.6), small intestine (RPKM 29.6) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SEMA3B in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (50267652..50277546)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (50296986..50306895)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50305084..50314977)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19890 Neighboring gene microRNA 5787 Neighboring gene G protein subunit alpha i2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50272293-50272903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50272904-50273514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50275957-50276566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19892 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50280231-50280841 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50280842-50281451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50283071-50283786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50283787-50284502 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14388 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50297648-50298153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50298661-50299165 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50301209-50301784 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:50301785-50302358 and GRCh37_chr3:50302359-50302934 Neighboring gene SEMA3B antisense RNA 1 (head to head) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19897 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:50310784-50311307 Neighboring gene microRNA 6872 Neighboring gene leucine rich single-pass membrane protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:50330739-50331294 Neighboring gene interferon related developmental regulator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19899 Neighboring gene hyaluronidase 3 Neighboring gene N-alpha-acetyltransferase 80, NatH catalytic subunit

    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. Semaphorin 3B-associated membranous nephropathy is a distinct type of disease predominantly present in pediatric patients. Sethi S, et al. Kidney Int, 2020 Nov. PMID 32534052
    2. [Alteration of SEMA3B gene expression levels in epithelial tumors]. Pronina IV, et al. Mol Biol (Mosk), 2009 May-Jun. PMID 19548530
    3. Semaphorin-3B is an angiogenesis inhibitor that is inactivated by furin-like pro-protein convertases. Varshavsky A, et al. Cancer Res, 2008 Sep 1. PMID 18757406
    4. Promoter hypermethylation-mediated downregulation of tumor suppressor gene SEMA3B and lncRNA SEMA3B-AS1 correlates with progression and prognosis of esophageal squamous cell carcinoma. Dong Z, et al. Clin Exp Metastasis, 2019 Jun. PMID 30915595
    5. Mechanism of SEMA3B gene silencing and clinical significance in glioma. Pang CH, et al. Genet Mol Res, 2016 Mar 18. PMID 27050958

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SEMA3B inhibits TGFbeta-induced extracellular matrix protein production and its reduced levels are associated with a decline in lung function in IPF.
      Title: SEMA3B inhibits TGFβ-induced extracellular matrix protein production and its reduced levels are associated with a decline in lung function in IPF.
    2. Semaphorin3B promotes an anti-inflammatory and pro-resolving phenotype in macrophages from rheumatoid arthritis patients in a MerTK-dependent manner.
      Title: Semaphorin3B promotes an anti-inflammatory and pro-resolving phenotype in macrophages from rheumatoid arthritis patients in a MerTK-dependent manner.
    3. Central Role of Semaphorin 3B in a Serum-Induced Arthritis Model and Reduced Levels in Patients With Rheumatoid Arthritis.
      Title: Central Role of Semaphorin 3B in a Serum-Induced Arthritis Model and Reduced Levels in Patients With Rheumatoid Arthritis.
    4. Semaphorin 3B-associated membranous nephropathy is a distinct type of disease predominantly present in pediatric patients.
      Title: Semaphorin 3B-associated membranous nephropathy is a distinct type of disease predominantly present in pediatric patients.
    5. our research revealed the regulation of EFEMP1 on cell proliferation and apoptosis in HCC. EFEMP1 may suppress the growth of HCC cells by promoting SEMA3B.
      Title: Epidermal growth factor-containing fibulin-like extracellular matrix protein 1 (EFEMP1) suppressed the growth of hepatocellular carcinoma cells by promoting Semaphorin 3B(SEMA3B).
    6. the findings suggest that SEMA3B and SEMA3B-AS1 may act as tumor suppressors and may serve as potential targets for antitumor therapy.
      Title: Promoter hypermethylation-mediated downregulation of tumor suppressor gene SEMA3B and lncRNA SEMA3B-AS1 correlates with progression and prognosis of esophageal squamous cell carcinoma.
    7. Analysis of the SEMA3B expression profile shows the complexity of neoplastic transformation, which confirms the different expression of SEMA3B in endometrial cancer cells and endothelial cells.
      Title: Expression of Semaphorin 3B (SEMA3B) in Various Grades of Endometrial Cancer.
    8. Low SEMA3B expression is associated with gastric cardia adenocarcinoma.
      Title: MiR-6872 host gene SEMA3B and its antisense lncRNA SEMA3B-AS1 function synergistically to suppress gastric cardia adenocarcinoma progression.
    9. miR-374b promotes glioma process in vitro through suppressing SEMA3B via targeting GATA3
      Title: MiR-374b targets GATA3 to promote progression and development of glioblastoma via regulating SEMA3B.
    10. Advanced peri-implantitis lesions showed higher levels of gene expression for Sem3A and Sem4D and lower levels of Sem4A in comparison to tissues obtained from a healthy dental implant.
      Title: Expression Levels of Semaphorins 3A, 3B, 4A, and 4D on Human Peri-implantitis.
    Submit: New GeneRIF Correction See all GeneRIFs (38)

    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

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34863

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chemorepellent activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    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 cell-cell signaling TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in chemorepulsion of axon TAS
    Traceable Author Statement
    more info
    		 PubMed 
    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
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    semaphorin-3B
    Names
    sema A(V)
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B
    semaphorin A
    semaphorin-V

    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.

    Genomic

    1. NG_032938.1 RefSeqGene

      Range
      6540..14939
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001005914.3 → NP_001005914.1  semaphorin-3B isoform 2 precursor

      See identical proteins and their annotated locations for NP_001005914.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (2) that is 1 aa shorter than isoform 1. The 5' terminal exon of this variant is inferred based on tiled partial transcript alignments.
      Source sequence(s)
      AI309508, BC009113, BC013975, HY146744, U90094
      Consensus CDS
      CCDS77744.1
      UniProtKB/TrEMBL
      A0A1S5UZH6
      Related
      ENSP00000485281.1, ENST00000433753.4
      Conserved Domains (3) summary
      cd05871
      Location:574 → 664
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      smart00423
      Location:514 → 550
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl15693
      Location:46 → 515
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. NM_001290060.2 → NP_001276989.1  semaphorin-3B isoform 1 precursor

      See identical proteins and their annotated locations for NP_001276989.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode isoform 1.
      Source sequence(s)
      AI309508, BC009113, U28369, U90094
      Consensus CDS
      CCDS74941.1
      UniProtKB/Swiss-Prot
      Q13214, Q6GU46, Q8TB71, Q8TDV7, Q93018, Q96GX0
      UniProtKB/TrEMBL
      A0A1S5UZH6
      Related
      ENSP00000484146.1, ENST00000616701.5
      Conserved Domains (3) summary
      cd05871
      Location:575 → 665
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11250
      Location:46 → 516
      Sema_3B; The Sema domain, a protein interacting module, of semaphorin 3B (Sema3B)
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins

    3. NM_001290061.1 → NP_001276990.1  semaphorin-3B isoform 3 precursor

      See identical proteins and their annotated locations for NP_001276990.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (3) is longer than isoform 1.
      Source sequence(s)
      AB083186, AI309508, BC009113, HY146744
      Consensus CDS
      CCDS77743.1
      UniProtKB/TrEMBL
      A0A0C4DGV8, A0A1S5UZH6
      Related
      ENSP00000480680.1, ENST00000611067.4
      Conserved Domains (3) summary
      cd05871
      Location:580 → 670
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      smart00423
      Location:520 → 556
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl15693
      Location:46 → 521
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    4. NM_001290062.2 → NP_001276991.1  semaphorin-3B isoform 4

      See identical proteins and their annotated locations for NP_001276991.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several 5' exons but contains alternate 5' exon structure, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 6 encode isoform 4.
      Source sequence(s)
      AI309508, AK293678, BC009113, BC044602, DC330072, U90094
      Consensus CDS
      CCDS77745.1
      UniProtKB/TrEMBL
      B4DEK9, Q59FY7
      Related
      ENSP00000485646.1, ENST00000456560.6
      Conserved Domains (4) summary
      smart00423
      Location:172 → 208
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:231 → 237
      Ig; Ig strand A [structural motif]
      cl11960
      Location:231 → 322
      Ig; Immunoglobulin domain
      cl15693
      Location:1 → 173
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    5. NM_001290063.2 → NP_001276992.1  semaphorin-3B isoform 4

      See identical proteins and their annotated locations for NP_001276992.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks several 5' exons but contains alternate 5' exon structure, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 6 encode isoform 4.
      Source sequence(s)
      AI309508, AK293678, BC009113, DC330072, U90094
      Consensus CDS
      CCDS77745.1
      UniProtKB/TrEMBL
      B4DEK9, Q59FY7
      Related
      ENSP00000485173.1, ENST00000418576.3
      Conserved Domains (4) summary
      smart00423
      Location:172 → 208
      PSI; domain found in Plexins, Semaphorins and Integrins
      cd00096
      Location:231 → 237
      Ig; Ig strand A [structural motif]
      cl11960
      Location:231 → 322
      Ig; Immunoglobulin domain
      cl15693
      Location:1 → 173
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    6. NM_004636.4 → NP_004627.1  semaphorin-3B isoform 1 precursor

      See identical proteins and their annotated locations for NP_004627.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1. Both variants 1 and 3 encode isoform 1. The 5' terminal exon of this variant is inferred based on tiled partial transcript alignments.
      Source sequence(s)
      AI309508, BC009113, HY146744, U28369, U90094
      Consensus CDS
      CCDS74941.1
      UniProtKB/Swiss-Prot
      Q13214, Q6GU46, Q8TB71, Q8TDV7, Q93018, Q96GX0
      UniProtKB/TrEMBL
      A0A1S5UZH6
      Related
      ENSP00000481957.1, ENST00000618865.4
      Conserved Domains (3) summary
      cd05871
      Location:575 → 665
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11250
      Location:46 → 516
      Sema_3B; The Sema domain, a protein interacting module, of semaphorin 3B (Sema3B)
      smart00423
      Location:515 → 551
      PSI; domain found in Plexins, Semaphorins and Integrins

    RNA

    1. NR_110697.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AI309508, AK092182, BC009113, DC330072
      Related
      ENST00000456210.5

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      50267652..50277546
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      50296986..50306895
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q13214.1 GenPept UniProtKB/Swiss-Prot:Q13214

    Gene LinkOut

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