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SEMA4B semaphorin 4B [ Homo sapiens (human) ]

Gene ID: 10509, updated on 2-Nov-2024

Summary

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Official Symbol
SEMA4Bprovided by HGNC
Official Full Name
semaphorin 4Bprovided by HGNC
Primary source
HGNC:HGNC:10730
See related
Ensembl:ENSG00000185033 MIM:617029; AllianceGenome:HGNC:10730
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
SemC; SEMAC
Summary
Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including axon guidance; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be located in membrane and synapse. Predicted to be active in glutamatergic synapse and postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in esophagus (RPKM 24.0), skin (RPKM 20.0) and 25 other tissues See more
Orthologs
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Genomic context

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See SEMA4B in Genome Data Viewer
Location:
15q26.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (90184920..90229661)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (87940946..87985668)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (90728152..90772893)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90644982-90645836 Neighboring gene isocitrate dehydrogenase (NADP(+)) 2 Neighboring gene IDH2 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90664819-90665318 Neighboring gene Sharpr-MPRA regulatory region 4454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90686773-90687307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90701094-90701611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90701612-90702128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90704142-90704734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90704735-90705327 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:90707039-90707194 Neighboring gene RNA, 7SL, cytoplasmic 346, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90717667-90718167 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90721295-90722200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:90727462-90728195 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90744110-90745081 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10068 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:90754487-90755686 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:90755750-90755924 Neighboring gene Sharpr-MPRA regulatory region 13535 Neighboring gene ribosomal protein S12 pseudogene 26 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90764595-90765433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6818 Neighboring gene GDP-D-glucose phosphorylase 1 Neighboring gene calcium and integrin binding 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10070 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:90807916-90808887 Neighboring gene tubulin tyrosine ligase like 13

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. CircSEMA4B inhibits the progression of breast cancer by encoding a novel protein SEMA4B-211aa and regulating AKT phosphorylation. Wang X, et al. Cell Death Dis, 2022 Sep 17. PMID 36115854, Free PMC Article
  2. Semaphorin 4B promotes tumor progression and associates with immune infiltrates in lung adenocarcinoma. Jiang J, et al. BMC Cancer, 2022 Jun 8. PMID 35676688, Free PMC Article
  3. SEMA4B inhibits growth of non-small cell lung cancer in vitro and in vivo. Jian H, et al. Cell Signal, 2015 Jun. PMID 25746385
  4. CLCP1 interacts with semaphorin 4B and regulates motility of lung cancer cells. Nagai H, et al. Oncogene, 2007 Jun 7. PMID 17213806
  5. Hypoxia and hypoxia-inducible factor 1 repress SEMA4B expression to promote non-small cell lung cancer invasion. Jian H, et al. Tumour Biol, 2014 May. PMID 24474252

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CircSEMA4B inhibits the progression of breast cancer by encoding a novel protein SEMA4B-211aa and regulating AKT phosphorylation.
    Title: CircSEMA4B inhibits the progression of breast cancer by encoding a novel protein SEMA4B-211aa and regulating AKT phosphorylation.
  2. Semaphorin 4B promotes tumor progression and associates with immune infiltrates in lung adenocarcinoma.
    Title: Semaphorin 4B promotes tumor progression and associates with immune infiltrates in lung adenocarcinoma.
  3. SEMA4B may induce FoxO1 nuclear retention through suppressing PI3K/Akt signaling pathway, which subsequently inhibited cell growth through the direct nuclear target of FoxO1, p21.
    Title: SEMA4B inhibits growth of non-small cell lung cancer in vitro and in vivo.
  4. Decrease in SEMA4b levels are associated with metastasis of non-small cell lung cancer.
    Title: SEMA4b inhibits MMP9 to prevent metastasis of non-small cell lung cancer.
  5. showed that HIF-1alpha recognized a hypoxia-responsive element (HRE) of SEMA4B gene, which is required for HIF-1-repressed SEMA4B expression
    Title: Hypoxia and hypoxia-inducible factor 1 repress SEMA4B expression to promote non-small cell lung cancer invasion.
  6. 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.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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

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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Markers

Homology

Clone Names

  • KIAA1745, MGC131831

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 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 glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
semaphorin-4B
Names
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, 4B
semaphorin-C

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_001324029.3 → NP_001310958.1  semaphorin-4B isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC091167

  2. NM_001324030.3 → NP_001310959.1  semaphorin-4B isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC091167
    UniProtKB/TrEMBL
    Q7Z3N1
    Conserved Domains (3) summary
    cd05872
    Location:438 → 521
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
    pfam01437
    Location:369 → 415
    PSI; Plexin repeat
    cl15693
    Location:1 → 368
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  3. NM_001324031.4 → NP_001310960.2  semaphorin-4B isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AC091167
    Consensus CDS
    CCDS45347.1
    UniProtKB/Swiss-Prot
    J3KNP4, Q6UXE3, Q8WVP9, Q96FK5, Q9C0B8, Q9H691, Q9NPM8, Q9NPN0, Q9NPR2
    UniProtKB/TrEMBL
    Q7Z3N1
    Conserved Domains (3) summary
    cd11257
    Location:61 → 524
    Sema_4B; The Sema domain, a protein interacting module, of semaphorin 4B (Sema4B)
    pfam01437
    Location:525 → 571
    PSI; Plexin repeat
    cd05872
    Location:594 → 677
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B

  4. NM_001324032.3 → NP_001310961.1  semaphorin-4B isoform 5 precursor

    Status: VALIDATED

    Source sequence(s)
    AC091167
    Conserved Domains (2) summary
    cd11257
    Location:61 → 524
    Sema_4B; The Sema domain, a protein interacting module, of semaphorin 4B (Sema4B)
    pfam01437
    Location:525 → 556
    PSI; Plexin repeat

  5. NM_001324034.3 → NP_001310963.1  semaphorin-4B isoform 6 precursor

    Status: VALIDATED

    Source sequence(s)
    AC091167
    UniProtKB/TrEMBL
    Q7Z3N1

  6. NM_001393916.1 → NP_001380845.1  semaphorin-4B isoform 5 precursor

    Status: VALIDATED

    Source sequence(s)
    AC091167
    Conserved Domains (2) summary
    cd11257
    Location:61 → 524
    Sema_4B; The Sema domain, a protein interacting module, of semaphorin 4B (Sema4B)
    pfam01437
    Location:525 → 556
    PSI; Plexin repeat

  7. NM_020210.5 → NP_064595.2  semaphorin-4B isoform 1 precursor

    See identical proteins and their annotated locations for NP_064595.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 are predicted to encode the same protein which is annotated as the largest open reading frame. Translation may intitiate at either of the first two AUG sites.
    Source sequence(s)
    AC091167
    Consensus CDS
    CCDS45347.1
    UniProtKB/Swiss-Prot
    J3KNP4, Q6UXE3, Q8WVP9, Q96FK5, Q9C0B8, Q9H691, Q9NPM8, Q9NPN0, Q9NPR2
    UniProtKB/TrEMBL
    Q7Z3N1
    Related
    ENSP00000332204.6, ENST00000332496.10
    Conserved Domains (3) summary
    cd11257
    Location:61 → 524
    Sema_4B; The Sema domain, a protein interacting module, of semaphorin 4B (Sema4B)
    pfam01437
    Location:525 → 571
    PSI; Plexin repeat
    cd05872
    Location:594 → 677
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B

  8. NM_198925.4 → NP_945119.1  semaphorin-4B isoform 1 precursor

    See identical proteins and their annotated locations for NP_945119.1

    Status: VALIDATED

    Source sequence(s)
    AC091167
    Consensus CDS
    CCDS45347.1
    UniProtKB/Swiss-Prot
    J3KNP4, Q6UXE3, Q8WVP9, Q96FK5, Q9C0B8, Q9H691, Q9NPM8, Q9NPN0, Q9NPR2
    UniProtKB/TrEMBL
    Q7Z3N1
    Related
    ENSP00000394720.2, ENST00000411539.7
    Conserved Domains (3) summary
    cd11257
    Location:61 → 524
    Sema_4B; The Sema domain, a protein interacting module, of semaphorin 4B (Sema4B)
    pfam01437
    Location:525 → 571
    PSI; Plexin repeat
    cd05872
    Location:594 → 677
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B

RNA

  1. NR_172049.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC091167

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    90184920..90229661
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    87940946..87985668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NPR2.4 GenPept UniProtKB/Swiss-Prot:Q9NPR2

Gene LinkOut

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

Chemical Information
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