SEMA4B

gene
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Also known as SemCKIAA1745MGC131831

Summary

SEMA4B (semaphorin 4B, HGNC:10730) is a protein-coding gene on chromosome 15q26.1, encoding Semaphorin-4B (Q9NPR2). Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons.

Predicted to enable chemorepellent activity; neuropilin binding 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.

Source: NCBI Gene 10509 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 166 total
  • MANE Select transcript: NM_198925

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10730
Approved symbolSEMA4B
Namesemaphorin 4B
Location15q26.1
Locus typegene with protein product
StatusApproved
AliasesSemC, KIAA1745, MGC131831
Ensembl geneENSG00000185033
Ensembl biotypeprotein_coding
OMIM617029
Entrez10509

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 17 protein_coding, 7 retained_intron, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000332496, ENST00000411539, ENST00000558051, ENST00000558065, ENST00000558848, ENST00000558895, ENST00000558975, ENST00000559074, ENST00000559247, ENST00000559300, ENST00000559322, ENST00000559792, ENST00000559983, ENST00000560003, ENST00000560089, ENST00000560263, ENST00000560993, ENST00000561085, ENST00000561252, ENST00000561321, ENST00000864015, ENST00000864016, ENST00000864017, ENST00000864018, ENST00000864019, ENST00000928644, ENST00000928645, ENST00000947039

RefSeq mRNA: 8 — MANE Select: NM_198925 NM_001324029, NM_001324030, NM_001324031, NM_001324032, NM_001324034, NM_001393916, NM_020210, NM_198925

CCDS: CCDS45347

Canonical transcript exons

ENST00000411539 — 14 exons

ExonStartEnd
ENSE000017009239020133090201735
ENSE000025467419022790490229660
ENSE000034621549022098290221093
ENSE000034724059022566190225827
ENSE000034768419022528290225397
ENSE000034835369022496890225178
ENSE000035503519022383890223988
ENSE000035611359022161490221765
ENSE000035775389022355990223740
ENSE000036133529021776790217829
ENSE000036355559022136790221480
ENSE000036490089022755790227642
ENSE000036661949021979390219891
ENSE000037294539021743990217602

Expression profiles

Bgee: expression breadth ubiquitous, 212 present calls, max score 98.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.9921 / max 559.4280, expressed in 1766 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
14841410.71501485
1484179.09551666
1484186.6964985
1484150.4852180

Top tissues by expression

241 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
ileal mucosaUBERON:000033198.02gold quality
esophagus mucosaUBERON:000246997.63gold quality
lower esophagus mucosaUBERON:003583497.39gold quality
secondary oocyteCL:000065597.08gold quality
esophagusUBERON:000104395.52gold quality
muscle layer of sigmoid colonUBERON:003580595.07gold quality
olfactory segment of nasal mucosaUBERON:000538694.69gold quality
gingivaUBERON:000182894.34gold quality
vaginaUBERON:000099694.24gold quality
transverse colonUBERON:000115794.14gold quality
gingival epitheliumUBERON:000194994.12silver quality
right lobe of thyroid glandUBERON:000111994.03gold quality
skin of abdomenUBERON:000141694.02gold quality
left lobe of thyroid glandUBERON:000112093.97gold quality
skin of legUBERON:000151193.81gold quality
mucosa of transverse colonUBERON:000499193.79gold quality
minor salivary glandUBERON:000183093.72gold quality
mouth mucosaUBERON:000372993.52gold quality
left adrenal glandUBERON:000123493.30gold quality
sural nerveUBERON:001548893.28gold quality
tibial nerveUBERON:000132393.27gold quality
small intestine Peyer’s patchUBERON:000345493.27gold quality
lower esophagusUBERON:001347393.25gold quality
lower esophagus muscularis layerUBERON:003583393.23gold quality
oocyteCL:000002393.22gold quality
colonUBERON:000115593.19gold quality
thyroid glandUBERON:000204693.13gold quality
left adrenal gland cortexUBERON:003582593.11gold quality
large intestineUBERON:000005992.76gold quality
zone of skinUBERON:000001492.67gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-75688yes590.12
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

71 targeting SEMA4B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-453499.9966.581907
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-7152-3P99.9767.47849
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-6499-3P99.9066.381212
HSA-MIR-17-5P99.8973.832665
HSA-MIR-345-3P99.8970.231421
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-93-5P99.8873.982606
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-1211999.8768.351653
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-431999.7669.832586
HSA-MIR-674599.7465.331321

Literature-anchored findings (GeneRIF, showing 5)

  • showed that HIF-1alpha recognized a hypoxia-responsive element (HRE) of SEMA4B gene, which is required for HIF-1-repressed SEMA4B expression (PMID:24474252)
  • Decrease in SEMA4b levels are associated with metastasis of non-small cell lung cancer. (PMID:25095981)
  • 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. (PMID:25746385)
  • Semaphorin 4B promotes tumor progression and associates with immune infiltrates in lung adenocarcinoma. (PMID:35676688)
  • CircSEMA4B inhibits the progression of breast cancer by encoding a novel protein SEMA4B-211aa and regulating AKT phosphorylation. (PMID:36115854)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosema4baENSDARG00000074414
danio_reriosema4bbENSDARG00000076104
mus_musculusSema4bENSMUSG00000030539
rattus_norvegicusSema4bENSRNOG00000025167

Paralogs (19): SEMA3F (ENSG00000001617), SEMA3G (ENSG00000010319), SEMA3B (ENSG00000012171), SEMA3A (ENSG00000075213), SEMA3C (ENSG00000075223), SEMA5B (ENSG00000082684), SEMA6A (ENSG00000092421), SEMA4G (ENSG00000095539), SEMA5A (ENSG00000112902), SEMA4F (ENSG00000135622), SEMA6D (ENSG00000137872), SEMA7A (ENSG00000138623), SEMA6C (ENSG00000143434), SEMA3D (ENSG00000153993), SEMA6B (ENSG00000167680), SEMA4C (ENSG00000168758), SEMA3E (ENSG00000170381), SEMA4D (ENSG00000187764), SEMA4A (ENSG00000196189)

Protein

Protein identifiers

Semaphorin-4BQ9NPR2 (reviewed: Q9NPR2)

Alternative names: Semaphorin-C

All UniProt accessions (10): Q9NPR2, H0YKV7, H0YLN3, H0YM68, H0YMD6, H0YMR1, H0YMZ3, H0YN49, H0YNC4, H0YNM2

UniProt curated annotations — full annotation on UniProt →

Function. Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons.

Subcellular location. Membrane.

Similarity. Belongs to the semaphorin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9NPR2-11yes
Q9NPR2-22

RefSeq proteins (8): NP_001310958, NP_001310959, NP_001310960, NP_001310961, NP_001310963, NP_001380845, NP_064595, NP_945119* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001627Semap_domDomain
IPR002165Plexin_repeatRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR016201PSIDomain
IPR027231SemaphorinFamily
IPR036352Semap_dom_sfHomologous_superfamily

Pfam: PF01403, PF01437

UniProt features (28 total): glycosylation site 6, disulfide bond 6, modified residue 3, domain 3, topological domain 2, sequence conflict 2, signal peptide 1, chain 1, splice variant 1, sequence variant 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NPR2-F182.140.64

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 818, 830, 793

Disulfide bonds (6): 120–131, 149–158, 286–399, 310–359, 526–543, 611–656

Glycosylation sites (6): 69, 96, 165, 410, 525, 630

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 238 (showing top): TGCACTT_MIR519C_MIR519B_MIR519A, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_NEUROGENESIS, GOBP_AMEBOIDAL_TYPE_CELL_MIGRATION, BILD_HRAS_ONCOGENIC_SIGNATURE, GOBP_TAXIS, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GOBP_MESENCHYMAL_CELL_DIFFERENTIATION, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, TGCTGAY_UNKNOWN, MARTIN_VIRAL_GPCR_SIGNALING_UP, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, BASAKI_YBX1_TARGETS_DN, GOBP_MESENCHYME_DEVELOPMENT, RFX1_02

GO Biological Process (7): neural crest cell migration (GO:0001755), axon guidance (GO:0007411), positive regulation of cell migration (GO:0030335), negative chemotaxis (GO:0050919), semaphorin-plexin signaling pathway (GO:0071526), nervous system development (GO:0007399), cell differentiation (GO:0030154)

GO Molecular Function (4): semaphorin receptor binding (GO:0030215), neuropilin binding (GO:0038191), chemorepellent activity (GO:0045499), protein binding (GO:0005515)

GO Cellular Component (5): plasma membrane (GO:0005886), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), membrane (GO:0016020), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
signaling receptor binding2
neural crest cell development1
mesenchymal cell migration1
axonogenesis1
neuron projection guidance1
cell migration1
regulation of cell migration1
positive regulation of cell motility1
chemotaxis1
cell surface receptor signaling pathway1
system development1
cellular developmental process1
receptor ligand activity1
negative chemotaxis1
binding1
membrane1
cell periphery1
postsynaptic density1
postsynaptic membrane1
postsynaptic specialization membrane1
synapse1
cellular anatomical structure1
cell junction1

Protein interactions and networks

STRING

542 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SEMA4BDCBLD2Q96PD2874
SEMA4BGNAT1P11488691
SEMA4BPLXNB2O15031594
SEMA4BGNAI2P04899590
SEMA4BGTPBP4Q9BZE4589
SEMA4BPLXNA1Q9UIW2536
SEMA4BDLG4P78352491
SEMA4BNRP2O60462462
SEMA4BSNX33Q8WV41459
SEMA4BSNX18Q96RF0449
SEMA4BSYT1P21579422
SEMA4BEZH2Q15910414
SEMA4BNCDNQ9UBB6409
SEMA4BABATP80404396
SEMA4BPPATQ06203388

IntAct

33 interactions, top by confidence:

ABTypeScore
SEMA4Bpsi-mi:“MI:0915”(physical association)0.660
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
C1orf54EXTL3psi-mi:“MI:0914”(association)0.530
TDRD9SEMA4Bpsi-mi:“MI:0915”(physical association)0.400
SEMA4Bpsi-mi:“MI:0915”(physical association)0.370
SHTN1psi-mi:“MI:0914”(association)0.350
TMEM223psi-mi:“MI:0914”(association)0.350
FAM171A2psi-mi:“MI:0914”(association)0.350
PDCD2PRMT3psi-mi:“MI:0914”(association)0.350
SEMA4ATMEM192psi-mi:“MI:0914”(association)0.350
SEMA4BNLGN1psi-mi:“MI:0914”(association)0.350
TMEM106ATMEM131Lpsi-mi:“MI:0914”(association)0.350
SFTPCTMEM131Lpsi-mi:“MI:0914”(association)0.350
BRICD5TMEM131Lpsi-mi:“MI:0914”(association)0.350
HLA-DQA1TMEM131Lpsi-mi:“MI:0914”(association)0.350
PTCH1TMEM131Lpsi-mi:“MI:0914”(association)0.350
NCR3POTEFpsi-mi:“MI:0914”(association)0.350
LYPD4POTEFpsi-mi:“MI:0914”(association)0.350
DNAJB9POTEFpsi-mi:“MI:0914”(association)0.350
CFC1POTEFpsi-mi:“MI:0914”(association)0.350
EDN3POTEFpsi-mi:“MI:0914”(association)0.350
DPEP2QSOX1psi-mi:“MI:0914”(association)0.350
PDGFRAQSOX1psi-mi:“MI:0914”(association)0.350
ELSPBP1QSOX1psi-mi:“MI:0914”(association)0.350
PRG2QSOX1psi-mi:“MI:0914”(association)0.350
CST9LQSOX1psi-mi:“MI:0914”(association)0.350
SDF2L1MANBApsi-mi:“MI:0914”(association)0.350
LYZL1MAN2B1psi-mi:“MI:0914”(association)0.350
FIBINMAN2B1psi-mi:“MI:0914”(association)0.350

ESM2 similar proteins: A0JND9, D3YTS9, O19058, O35795, O55026, O75173, P08648, P11117, P17405, P20611, P21217, P24638, P29376, P56433, Q04519, Q0P5F0, Q0V8G3, Q0VD19, Q11128, Q11131, Q32M88, Q4R5N9, Q4R942, Q5MY95, Q5NVF6, Q5RFQ8, Q62994, Q63148, Q6IY74, Q8BH73, Q8HYJ3, Q8HYJ4, Q8HYJ5, Q8HYJ7, Q8HZR3, Q8K1S1, Q8N135, Q923W9, Q9BZG2, Q9H3T2

Diamond homologs: A7MB70, D3ZTD8, O08665, O09126, O15041, O35464, O42236, O42237, O88632, O95025, O95754, P70275, Q13214, Q13275, Q13591, Q14563, Q17330, Q24322, Q24323, Q26473, Q26972, Q4LFA9, Q5EA85, Q5R7F5, Q5RE75, Q60519, Q62177, Q62178, Q62179, Q62181, Q62217, Q63548, Q64151, Q76KF0, Q8BH34, Q8NFY4, Q90607, Q90663, Q90665, Q92854

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

166 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance140
Likely benign10
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2814 predictions. Top by Δscore:

VariantEffectΔscore
15:90217434:CCCA:Cacceptor_loss1.0000
15:90217435:CCAG:Cacceptor_loss1.0000
15:90217436:CA:Cacceptor_loss1.0000
15:90217437:A:AGacceptor_gain1.0000
15:90217437:AGGCT:Aacceptor_loss1.0000
15:90217438:G:Aacceptor_loss1.0000
15:90217438:G:GAacceptor_gain1.0000
15:90217598:AGGAG:Adonor_loss1.0000
15:90217599:GGAG:Gdonor_gain1.0000
15:90217600:G:GTdonor_gain1.0000
15:90217600:GAGGT:Gdonor_loss1.0000
15:90217603:GTGA:Gdonor_loss1.0000
15:90217604:T:Gdonor_loss1.0000
15:90217765:A:AGacceptor_gain1.0000
15:90217766:G:GGacceptor_gain1.0000
15:90219788:CCCA:Cacceptor_loss1.0000
15:90219789:CCA:Cacceptor_loss1.0000
15:90219791:A:AGacceptor_gain1.0000
15:90219791:AGC:Aacceptor_gain1.0000
15:90219791:AGCGC:Aacceptor_gain1.0000
15:90219792:G:Aacceptor_loss1.0000
15:90219792:G:GTacceptor_gain1.0000
15:90219792:GC:Gacceptor_gain1.0000
15:90219792:GCG:Gacceptor_gain1.0000
15:90219792:GCGC:Gacceptor_gain1.0000
15:90219792:GCGCG:Gacceptor_gain1.0000
15:90219888:CATC:Cdonor_gain1.0000
15:90219889:ATC:Adonor_gain1.0000
15:90219890:TC:Tdonor_gain1.0000
15:90219890:TCGT:Tdonor_loss1.0000

AlphaMissense

5436 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:90223595:T:AW300R0.999
15:90223595:T:CW300R0.999
15:90217803:T:AC120S0.998
15:90217804:G:CC120S0.998
15:90219799:T:AC131S0.998
15:90219800:G:CC131S0.998
15:90219868:T:CF154L0.998
15:90219870:C:AF154L0.998
15:90219870:C:GF154L0.998
15:90221746:G:CR281P0.998
15:90221760:T:AC286S0.998
15:90221761:G:CC286S0.998
15:90223612:G:CK305N0.998
15:90223612:G:TK305N0.998
15:90219800:G:AC131Y0.997
15:90219801:T:GC131W0.997
15:90219807:C:AN133K0.997
15:90219807:C:GN133K0.997
15:90221400:T:GF210C0.997
15:90221623:T:GF240C0.997
15:90221752:C:AA283D0.997
15:90221761:G:AC286Y0.997
15:90223597:G:CW300C0.997
15:90223597:G:TW300C0.997
15:90217803:T:CC120R0.996
15:90217805:C:GC120W0.996
15:90219854:G:AC149Y0.996
15:90219855:T:GC149W0.996
15:90219875:C:AP156H0.996
15:90221751:G:CA283P0.996

dbSNP variants (sampled 300 via entrez): RS1000082982 (15:90185387 A>C,G,T), RS1000145295 (15:90193314 A>G), RS1000146032 (15:90208981 T>C), RS1000147064 (15:90185109 G>A), RS1000229027 (15:90188767 A>T), RS1000306011 (15:90229326 G>A), RS1000341834 (15:90203930 G>A), RS1000408421 (15:90193694 G>A), RS1000486838 (15:90184677 G>A), RS1000516913 (15:90213349 A>G), RS1000589671 (15:90215482 CTTG>C), RS1000606883 (15:90224441 C>T), RS1000620613 (15:90215713 G>A), RS1000664071 (15:90214337 A>C), RS1000692069 (15:90184326 C>T)

Disease associations

OMIM: gene MIM:617029 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

StudyTraitp-value
GCST007096_28Pulse pressure4.000000e-08
GCST007234_18Acne (severe)6.000000e-15
GCST007234_19Acne (severe)7.000000e-08
GCST007713_4Frontal fibrosing alopecia8.000000e-10
GCST90011900_119Serum alkaline phosphatase levels4.000000e-13
GCST90013406_285Liver enzyme levels (alkaline phosphatase)1.000000e-16
GCST90013407_11Liver enzyme levels (gamma-glutamyl transferase)7.000000e-12

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0005763pulse pressure measurement
EFO:0009855frontal fibrosing alopecia
EFO:0004533alkaline phosphatase measurement
EFO:0004532serum gamma-glutamyl transferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

52 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects splicing, decreases expression, increases expression3
Air Pollutantsaffects expression, increases abundance, decreases expression, increases expression3
Particulate Matterincreases abundance, increases expression, affects cotreatment, decreases expression3
Acetaminophendecreases expression2
Calcitriolincreases expression2
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphateaffects expression, affects response to substance1
tris(2-butoxyethyl) phosphateaffects expression1
beta-lapachoneincreases expression1
butyraldehydedecreases expression1
ferrous chloridedecreases expression1
beta-methylcholineaffects expression1
azoxystrobindecreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
deguelindecreases expression1
fenpyroximatedecreases expression1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamidedecreases expression1
pyrimidifendecreases expression1
abrinedecreases expression1
pyrachlostrobindecreases expression1
darinaparsindecreases expression1
bisphenol Sdecreases methylation1
jinfukangincreases expression1
picoxystrobindecreases expression1
PCI 5002affects cotreatment, increases expression1
Temozolomidedecreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): acne