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    SEMA5B semaphorin 5B [ Homo sapiens (human) ]

    Gene ID: 54437, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SEMA5Bprovided by HGNC
    Official Full Name
    semaphorin 5Bprovided by HGNC
    Primary source
    HGNC:HGNC:10737
    See related
    Ensembl:ENSG00000082684 MIM:609298; AllianceGenome:HGNC:10737
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SemG; SEMAG
    Summary
    This gene encodes a member of the semaphorin protein family which regulates axon growth during development of the nervous system. The encoded protein has a characteristic Sema domain near the N-terminus, through which semaphorins bind to plexin, and five thrombospondin type 1 repeats in the C-terminal region of the protein. The protein product may be cleaved and exist as a secreted molecule (PMID: 19463192). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
    Expression
    Broad expression in brain (RPKM 2.8), heart (RPKM 1.3) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SEMA5B in Genome Data Viewer
    Location:
    3q21.1
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (122909082..123028605, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (125628273..125748681, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (122627929..122747452, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14645 Neighboring gene solute carrier family 49 member 4 Neighboring gene MPRA-validated peak4798 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20387 Neighboring gene long intergenic non-protein coding RNA 2035 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122632187-122632687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122645367-122645867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:122693322-122694086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:122694087-122694852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122701773-122702273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122739281-122739946 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:122739947-122740611 Neighboring gene NANOG hESC enhancer GRCh37_chr3:122747214-122747721 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:122752890-122753444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14646 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:122803094-122803728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122803729-122804364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:122817925-122818646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122829483-122829983 Neighboring gene protein disulfide isomerase family A member 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:122872975-122873475 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:122875517-122876016 Neighboring gene microRNA 7110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20391 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20392 Neighboring gene MPRA-validated peak4799 silencer Neighboring gene SEC22 homolog A, vesicle trafficking protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Semaphorin 5B mediates synapse elimination in hippocampal neurons. O'Connor TP, et al. Neural Dev, 2009 May 23. PMID 19463192, Free PMC Article
    2. Driver Gene and Novel Mutations in Asbestos-Exposed Lung Adenocarcinoma and Malignant Mesothelioma Detected by Exome Sequencing. Mäki-Nevala S, et al. Lung, 2016 Feb. PMID 26463840
    3. A novel class of murine semaphorins with homology to thrombospondin is differentially expressed during early embryogenesis. Adams RH, et al. Mech Dev, 1996 Jun. PMID 8817451
    4. Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations. Wu C, et al. Nat Genet, 2011 Jun 5. PMID 21642993
    5. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SEMA5B could possibly serve as a candidate gene for alterations associated with asbestos exposure.
      Title: Driver Gene and Novel Mutations in Asbestos-Exposed Lung Adenocarcinoma and Malignant Mesothelioma Detected by Exome Sequencing.
    2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. Sema5B regulates the development and maintenance of synapse size and number in hippocampal neurons.
      Title: Semaphorin 5B mediates synapse elimination in hippocampal neurons.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of sema domain, 5B (SEMA5B) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10372, KIAA1445

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in axon extension IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in detection of light stimulus involved in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative chemotaxis IEA
    Inferred from Electronic Annotation
    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-5B
    Names
    sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B

    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_001031702.4 → NP_001026872.2  semaphorin-5B isoform 1

      See identical proteins and their annotated locations for NP_001026872.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 2 encode the same protein (isoform 1).
      Source sequence(s)
      AB040878, AC078794, AK091481, BC002776, BC077726, DA115188, DA797213
      Consensus CDS
      CCDS35491.1
      UniProtKB/Swiss-Prot
      A8K5U2, B7Z393, F8W9U8, Q6DD89, Q6UY12, Q9NW17, Q9P283
      UniProtKB/TrEMBL
      B5ME80
      Related
      ENSP00000350215.3, ENST00000357599.8
      Conserved Domains (4) summary
      cd11264
      Location:118 → 554
      Sema_5B; The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B)
      smart00209
      Location:856 → 908
      TSP1; Thrombospondin type 1 repeats
      pfam00090
      Location:969 → 1010
      TSP_1; Thrombospondin type 1 domain
      pfam01437
      Location:555 → 602
      PSI; Plexin repeat

    2. NM_001256346.2 → NP_001243275.1  semaphorin-5B isoform 1

      See identical proteins and their annotated locations for NP_001243275.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein (isoform 1).
      Source sequence(s)
      AC078794, AC109130, AK091481
      Consensus CDS
      CCDS35491.1
      UniProtKB/Swiss-Prot
      A8K5U2, B7Z393, F8W9U8, Q6DD89, Q6UY12, Q9NW17, Q9P283
      UniProtKB/TrEMBL
      B5ME80
      Related
      ENSP00000479602.1, ENST00000616742.4
      Conserved Domains (4) summary
      cd11264
      Location:118 → 554
      Sema_5B; The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B)
      smart00209
      Location:856 → 908
      TSP1; Thrombospondin type 1 repeats
      pfam00090
      Location:969 → 1010
      TSP_1; Thrombospondin type 1 domain
      pfam01437
      Location:555 → 602
      PSI; Plexin repeat

    3. NM_001256347.1 → NP_001243276.1  semaphorin-5B isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding region and uses an alternate start codon compared to variant 1. The resulting protein (isoform 2) has a longer N-terminus compared to isoform 1.
      Source sequence(s)
      AC078794, AC109130, AK295619
      Consensus CDS
      CCDS58848.1
      UniProtKB/TrEMBL
      B5ME80
      Related
      ENSP00000389588.2, ENST00000451055.6
      Conserved Domains (4) summary
      cd11264
      Location:172 → 608
      Sema_5B; The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B)
      smart00209
      Location:910 → 962
      TSP1; Thrombospondin type 1 repeats
      pfam00090
      Location:1023 → 1064
      TSP_1; Thrombospondin type 1 domain
      pfam01437
      Location:609 → 656
      PSI; Plexin repeat

    4. NM_001256348.2 → NP_001243277.1  semaphorin-5B isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, uses a downstream start codon and uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The resulting protein (isoform 3) is shorter and has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AC078794, AC083797, AK294528
      Consensus CDS
      CCDS74995.1
      UniProtKB/TrEMBL
      B7Z2B3, C9JKR3
      Related
      ENSP00000195173.5, ENST00000195173.8
      Conserved Domains (4) summary
      cd11264
      Location:60 → 496
      Sema_5B; The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B)
      smart00209
      Location:798 → 850
      TSP1; Thrombospondin type 1 repeats
      pfam00090
      Location:875 → 916
      TSP_1; Thrombospondin type 1 domain
      pfam01437
      Location:497 → 544
      PSI; Plexin repeat

    5. NM_001410801.1 → NP_001397730.1  semaphorin-5B isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      AC078794, AC083797
      Consensus CDS
      CCDS93351.1
      UniProtKB/TrEMBL
      A0A3B3IRP9, B7Z2B3
      Related
      ENSP00000496878.1, ENST00000650207.1

    RNA

    1. NR_046079.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) has an alternate 5' exon and uses an alternate splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC078794, AY358124

    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
      122909082..123028605 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448353.1 → XP_047304309.1  semaphorin-5B isoform X9

      UniProtKB/TrEMBL
      A0A3B3IT43, B7Z2B3
      Related
      ENSP00000497595.1, ENST00000648990.1

    2. XM_047448354.1 → XP_047304310.1  semaphorin-5B isoform X10

      UniProtKB/TrEMBL
      B7Z2B3

    3. XM_047448355.1 → XP_047304311.1  semaphorin-5B isoform X11

      UniProtKB/TrEMBL
      B7Z2B3

    4. XM_047448352.1 → XP_047304308.1  semaphorin-5B isoform X8

      UniProtKB/TrEMBL
      B7Z2B3

    5. XM_047448347.1 → XP_047304303.1  semaphorin-5B isoform X4

      UniProtKB/TrEMBL
      B5ME80

    6. XM_047448348.1 → XP_047304304.1  semaphorin-5B isoform X5

      UniProtKB/TrEMBL
      B5ME80

    7. XM_047448349.1 → XP_047304305.1  semaphorin-5B isoform X6

      UniProtKB/TrEMBL
      B5ME80

    8. XM_047448346.1 → XP_047304302.1  semaphorin-5B isoform X3

      UniProtKB/TrEMBL
      B5ME80

    9. XM_047448345.1 → XP_047304301.1  semaphorin-5B isoform X2

      UniProtKB/TrEMBL
      B5ME80

    10. XM_047448344.1 → XP_047304300.1  semaphorin-5B isoform X1

      UniProtKB/TrEMBL
      B5ME80

    11. XM_047448351.1 → XP_047304307.1  semaphorin-5B isoform X7

      UniProtKB/TrEMBL
      F8WAT5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      125628273..125748681 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346925.1 → XP_054202900.1  semaphorin-5B isoform X9

      UniProtKB/TrEMBL
      B7Z2B3

    2. XM_054346926.1 → XP_054202901.1  semaphorin-5B isoform X10

      UniProtKB/TrEMBL
      B7Z2B3

    3. XM_054346927.1 → XP_054202902.1  semaphorin-5B isoform X11

      UniProtKB/TrEMBL
      B7Z2B3

    4. XM_054346924.1 → XP_054202899.1  semaphorin-5B isoform X8

      UniProtKB/TrEMBL
      B7Z2B3

    5. XM_054346920.1 → XP_054202895.1  semaphorin-5B isoform X4

      UniProtKB/TrEMBL
      B5ME80

    6. XM_054346921.1 → XP_054202896.1  semaphorin-5B isoform X5

      UniProtKB/TrEMBL
      B5ME80

    7. XM_054346922.1 → XP_054202897.1  semaphorin-5B isoform X6

      UniProtKB/TrEMBL
      B5ME80

    8. XM_054346919.1 → XP_054202894.1  semaphorin-5B isoform X3

      UniProtKB/TrEMBL
      B5ME80

    9. XM_054346918.1 → XP_054202893.1  semaphorin-5B isoform X2

      UniProtKB/TrEMBL
      B5ME80

    10. XM_054346917.1 → XP_054202892.1  semaphorin-5B isoform X1

      UniProtKB/TrEMBL
      B5ME80

    11. XM_054346923.1 → XP_054202898.1  semaphorin-5B isoform X7

      UniProtKB/TrEMBL
      F8WAT5

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_018987.1: Suppressed sequence

      Description
      NM_018987.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate and has no publication or homolog support.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P283.4 GenPept UniProtKB/Swiss-Prot:Q9P283

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