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SEMA5B semaphorin 5B [ Homo sapiens (human) ]

Gene ID: 54437, updated on 11-Apr-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
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Genomic context

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Location:
3q21.1
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (122909082..123028605, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (125628273..125748681, complement)
105.20220307 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: 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 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)

Genotypes

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
    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_2023_10

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
    Related
    ENSP00000497595.1, ENST00000648990.1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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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