SEMA3B semaphorin 3B [Homo sapiens (human)] - Gene

Summary

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

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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).
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC156606P2 (e-PCR)
- UniSTS:271409

D8S2279 (e-PCR)
- UniSTS:473907

D3S4347 (e-PCR)
- UniSTS:474094

RH41936 (e-PCR)
- UniSTS:17904

D1S466 (e-PCR), detects polymorphism
- UniSTS:25075

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 more info	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

NG_032938.1 RefSeqGene

Range

6540..14939

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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