FOXJ3

gene
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Also known as KIAA1041

Summary

FOXJ3 (forkhead box J3, HGNC:29178) is a protein-coding gene on chromosome 1p34.2, encoding Forkhead box protein J3 (Q9UPW0). Transcriptional activator of MEF2C involved in the regulation of adult muscle fiber type identity and skeletal muscle regeneration.

Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin. Predicted to be active in nucleus.

Source: NCBI Gene 22887 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 110 total
  • MANE Select transcript: NM_014947

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29178
Approved symbolFOXJ3
Nameforkhead box J3
Location1p34.2
Locus typegene with protein product
StatusApproved
AliasesKIAA1041
Ensembl geneENSG00000198815
Ensembl biotypeprotein_coding
OMIM616035
Entrez22887

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 14 protein_coding

ENST00000361346, ENST00000361776, ENST00000372571, ENST00000372572, ENST00000372573, ENST00000422278, ENST00000445886, ENST00000454417, ENST00000545068, ENST00000861681, ENST00000861682, ENST00000940310, ENST00000940311, ENST00000959443

RefSeq mRNA: 4 — MANE Select: NM_014947 NM_001198850, NM_001198851, NM_001198852, NM_014947

CCDS: CCDS30689, CCDS55594

Canonical transcript exons

ENST00000361346 — 13 exons

ExonStartEnd
ENSE000014183094233505942335235
ENSE000038426934217654842179825
ENSE000038893474226511542265189
ENSE000038901084231105042311110
ENSE000038909644227834842278672
ENSE000038915754222788342227966
ENSE000038916514219130342191719
ENSE000038918384220576242205863
ENSE000038927154219489042195064
ENSE000038928014218930342189404
ENSE000038944034218873742188928
ENSE000038950144218191742182024
ENSE000038953554219910242199230

Expression profiles

Bgee: expression breadth ubiquitous, 294 present calls, max score 97.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.3955 / max 449.1848, expressed in 1820 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1198633.00211820
119851.8272986
119841.1654695
119830.5272310
119880.5159214
119810.3577160

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
middle temporal gyrusUBERON:000277197.73gold quality
endothelial cellCL:000011597.32gold quality
Brodmann (1909) area 23UBERON:001355497.15gold quality
tibiaUBERON:000097996.42gold quality
germinal epithelium of ovaryUBERON:000130496.19gold quality
visceral pleuraUBERON:000240195.86gold quality
parietal pleuraUBERON:000240095.81gold quality
cerebellar vermisUBERON:000472095.81gold quality
pleuraUBERON:000097795.60gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451195.07gold quality
deltoidUBERON:000147694.89gold quality
cervix squamous epitheliumUBERON:000692294.80silver quality
colonic epitheliumUBERON:000039794.79gold quality
vastus lateralisUBERON:000137994.61gold quality
paraflocculusUBERON:000535194.61gold quality
quadriceps femorisUBERON:000137794.60gold quality
squamous epitheliumUBERON:000691494.49gold quality
esophagus squamous epitheliumUBERON:000692094.43gold quality
cartilage tissueUBERON:000241894.40gold quality
gingival epitheliumUBERON:000194994.33gold quality
skin of hipUBERON:000155494.26gold quality
secondary oocyteCL:000065594.06gold quality
gluteal muscleUBERON:000200094.05gold quality
synovial jointUBERON:000221794.05gold quality
triceps brachiiUBERON:000150994.02gold quality
parotid glandUBERON:000183194.01gold quality
hair follicleUBERON:000207393.97gold quality
penisUBERON:000098993.83gold quality
Brodmann (1909) area 10UBERON:001354193.74gold quality
skeletal muscle tissueUBERON:000113493.69gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.40
E-MTAB-6678yes6.38

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

TargetRegulation
E2F1Activation
MEF2CActivation

miRNA regulators (miRDB)

204 targeting FOXJ3, 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-8485100.0077.574731
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4481100.0066.421669
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-4668-3P100.0068.742635
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-480399.9871.993117
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-548P99.9872.253784
HSA-MIR-806899.9873.852376
HSA-MIR-4745-5P99.9865.951028
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-60799.9773.625593
HSA-MIR-314899.9775.066478
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-493-5P99.9672.472382
HSA-MIR-548AJ-3P99.9673.385345

Literature-anchored findings (GeneRIF, showing 8)

  • FOXJ3 is identified as a novel cell cycle reguulator that may regulate a network of zinc finger proteins. (PMID:22740631)
  • FOXJ3 may be associated with the development of rheumatoid arthritis. (PMID:23933633)
  • This study demonstrated that miR-517a-3p promoted lung cancer cell proliferation and invasion by targeting of FOXJ3 expression (PMID:24846831)
  • FOXO3-dependent gene regulation is generally mediated not through uniquely bound regions but through regions occupied by both FOXK2 and FOXO3 where both factors play a regulatory role. (PMID:26578569)
  • The found the stimulation effects of miR-425-5p on prostate cancer (PCa) cell behaviors were fulfilled through directly regulating the expression of FOXJ3, which validated FOXJ3 as a functional target of miR-425-5p in PCa. (PMID:30720162)
  • Integrin Subunit Alpha 5 (ITGA5) Gene Circular RNA Sponges microRNA-107 in Colorectal Carcinoma Cells and Tissues and Regulates the Expression of the Forkhead Box J3 (FOXJ3) Gene. (PMID:32305992)
  • Circular RNA circSLC8A1 inhibits the proliferation and invasion of non-small cell lung cancer cells through targeting the miR-106b-5p /FOXJ3 axis. (PMID:34724864)
  • FOXJ3 Regulates Cell Proliferation and Motility Through Modulating Snail Expression in Breast Cancer Cells. (PMID:37351974)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusFoxj3ENSMUSG00000032998
rattus_norvegicusFoxj3ENSRNOG00000061851

Paralogs (41): FOXP3 (ENSG00000049768), FOXC1 (ENSG00000054598), FOXJ2 (ENSG00000065970), FOXF1 (ENSG00000103241), FOXN1 (ENSG00000109101), FOXM1 (ENSG00000111206), FOXP1 (ENSG00000114861), FOXO3 (ENSG00000118689), FOXA2 (ENSG00000125798), FOXA1 (ENSG00000129514), FOXJ1 (ENSG00000129654), FOXK2 (ENSG00000141568), FOXO1 (ENSG00000150907), FOXH1 (ENSG00000160973), FOXQ1 (ENSG00000164379), FOXK1 (ENSG00000164916), FOXD4 (ENSG00000170122), FOXA3 (ENSG00000170608), FOXB1 (ENSG00000171956), FOXR1 (ENSG00000176302), FOXL1 (ENSG00000176678), FOXC2 (ENSG00000176692), FOXE1 (ENSG00000178919), FOXS1 (ENSG00000179772), FOXL2 (ENSG00000183770), FOXO4 (ENSG00000184481), FOXD4L1 (ENSG00000184492), FOXD4L4 (ENSG00000184659), FOXD2 (ENSG00000186564), FOXI2 (ENSG00000186766), FOXE3 (ENSG00000186790), FOXD3 (ENSG00000187140), FOXD4L3 (ENSG00000187559), FOXR2 (ENSG00000189299), FOXO6 (ENSG00000204060), FOXB2 (ENSG00000204612), FOXD4L5 (ENSG00000204779), FOXI3 (ENSG00000214336), FOXL3 (ENSG00000248767), FOXD1 (ENSG00000251493)

Protein

Protein identifiers

Forkhead box protein J3Q9UPW0 (reviewed: Q9UPW0)

All UniProt accessions (5): C9JVP0, C9JXI1, Q9UPW0, F6VXT0, H7C1Y6

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional activator of MEF2C involved in the regulation of adult muscle fiber type identity and skeletal muscle regeneration. Plays an important role in spermatogenesis. Required for the survival of spermatogonia and participates in spermatocyte meiosis.

Subcellular location. Nucleus.

Isoforms (2)

UniProt IDNamesCanonical?
Q9UPW0-11yes
Q9UPW0-22

RefSeq proteins (4): NP_001185779, NP_001185780, NP_001185781, NP_055762* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001766Fork_head_domDomain
IPR018122TF_fork_head_CS_1Conserved_site
IPR030456TF_fork_head_CS_2Conserved_site
IPR036388WH-like_DNA-bd_sfHomologous_superfamily
IPR036390WH_DNA-bd_sfHomologous_superfamily
IPR045912FOXJ2/3-likeFamily

Pfam: PF00250

UniProt features (18 total): compositionally biased region 5, modified residue 4, region of interest 3, sequence variant 2, chain 1, DNA-binding region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UPW0-F154.240.11

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 (4): 223, 295, 489, 606

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 271 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, RNGTGGGC_UNKNOWN, LOPEZ_MESOTHELIOMA_SURVIVAL_DN, HNF3ALPHA_Q6, TGCACTT_MIR519C_MIR519B_MIR519A, MORF_UBE2I, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GENTILE_RESPONSE_CLUSTER_D3, GOBP_MALE_GAMETE_GENERATION, AATGGAG_MIR136, MORF_TERF1, MORF_RAF1, GOBP_ORGANELLE_FISSION, MYCMAX_01

GO Biological Process (7): regulation of transcription by RNA polymerase II (GO:0006357), male meiosis I (GO:0007141), spermatogenesis (GO:0007283), cell differentiation (GO:0030154), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of DNA-templated transcription (GO:0006355), meiotic cell cycle (GO:0051321)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), sequence-specific DNA binding (GO:0043565), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
regulation of DNA-templated transcription2
transcription by RNA polymerase II2
male gamete generation2
regulation of transcription by RNA polymerase II2
meiosis I1
male meiotic nuclear division1
meiotic cell cycle1
developmental process involved in reproduction1
cellular developmental process1
positive regulation of DNA-templated transcription1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cell cycle1
sexual reproduction1
reproductive process1
meiotic nuclear division1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
DNA binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
transcription cis-regulatory region binding1
transcription regulator activity1
binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1486 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FOXJ3SOX6P35712644
FOXJ3HES5Q5TA89521
FOXJ3PAX6P26367445
FOXJ3PDGFRAP16234431
FOXJ3ZBTB18Q99592430
FOXJ3MTF1Q14872396
FOXJ3DICER1Q9UPY3387
FOXJ3RARGP13631378
FOXJ3RCVRNP35243375
FOXJ3ESRRAP11474375
FOXJ3TFAMQ00059374
FOXJ3RPGRIP1LQ68CZ1373
FOXJ3PDCD10Q9BUL8371
FOXJ3TCF7P36402359
FOXJ3NF1P21359349

IntAct

15 interactions, top by confidence:

ABTypeScore
NEK6FOXJ3psi-mi:“MI:0915”(physical association)0.560
NEDD4FOXJ3psi-mi:“MI:0407”(direct interaction)0.440
YAP1FOXJ3psi-mi:“MI:0407”(direct interaction)0.440
MED23FOXJ3psi-mi:“MI:0915”(physical association)0.370
FOXJ3SMARCA5psi-mi:“MI:0914”(association)0.350
FOXJ3RPA2psi-mi:“MI:0914”(association)0.350
TBK1FMNL1psi-mi:“MI:0914”(association)0.350
TBK1UBR5psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
ENGIGKV2-28psi-mi:“MI:0914”(association)0.350
FOXJ3SERPINB7psi-mi:“MI:0914”(association)0.350
NEK6FOXJ3psi-mi:“MI:0915”(physical association)0.000

BioGRID (43): ALB (Affinity Capture-MS), TP53 (Affinity Capture-MS), RANGAP1 (Affinity Capture-MS), SMARCA5 (Affinity Capture-MS), UBR2 (Affinity Capture-MS), ZBTB10 (Affinity Capture-MS), RPA2 (Affinity Capture-MS), USP11 (Affinity Capture-MS), FOXJ1 (Affinity Capture-MS), PSMB4 (Affinity Capture-MS), ZBTB2 (Affinity Capture-MS), FOXJ3 (Affinity Capture-RNA), FOXJ3 (Affinity Capture-RNA), FOXJ3 (Affinity Capture-MS), FOXJ3 (Affinity Capture-RNA)

ESM2 similar proteins: A0A096MJY4, A0A486WWJ9, A2ICN5, A2VDZ3, A4UTP7, A8WL06, B7ZR65, H2LBU8, O89038, P10071, P40791, P55197, P55879, Q02078, Q03413, Q03414, Q06413, Q0VGT2, Q14814, Q2KIA0, Q2MJT0, Q32NP8, Q4VYR7, Q5IS56, Q5R444, Q5REW7, Q5U4X3, Q60929, Q61602, Q63943, Q6DFF5, Q6DIF3, Q6F2E7, Q7ZY13, Q8BUR3, Q8CFN5, Q91660, Q91661, Q9DE25, Q9EPK5

Diamond homologs: A0A078BQN7, A0A1W2PRP0, A0A8V0YY16, A1L1S5, A3KNJ3, A8MTJ6, A8XJN7, B5RHS5, D3Z120, F1R8Z9, O00358, O17617, O43638, O54743, O60129, O88470, P32027, P32028, P32030, P32315, P42128, P55316, P56260, P58012, P79772, P85037, P91278, Q00939, Q01167, Q02360, Q12946, Q12947, Q12948, Q12950, Q12951, Q12952, Q13461, Q19802, Q1A1A1, Q1A1A2

SIGNOR signaling

1 interactions.

AEffectBMechanism
FOXJ3“up-regulates quantity by expression”MEF2C“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance87
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2834 predictions. Top by Δscore:

VariantEffectΔscore
1:42189298:CTCA:Cdonor_loss1.0000
1:42189299:TCAC:Tdonor_loss1.0000
1:42189300:CA:Cdonor_loss1.0000
1:42194885:CTCA:Cdonor_loss1.0000
1:42194886:TCAC:Tdonor_loss1.0000
1:42194887:CA:Cdonor_loss1.0000
1:42194888:A:ACdonor_gain1.0000
1:42194889:C:CCdonor_gain1.0000
1:42194889:C:Gdonor_loss1.0000
1:42195062:CAC:Cacceptor_gain1.0000
1:42195065:C:CCacceptor_gain1.0000
1:42199095:GACTT:Gdonor_loss1.0000
1:42199096:ACTT:Adonor_loss1.0000
1:42199097:CT:Cdonor_loss1.0000
1:42199098:TTA:Tdonor_loss1.0000
1:42199099:TA:Tdonor_loss1.0000
1:42199100:A:ACdonor_gain1.0000
1:42199100:ACC:Adonor_loss1.0000
1:42199101:C:CCdonor_gain1.0000
1:42205760:A:ACdonor_gain1.0000
1:42205761:C:CCdonor_gain1.0000
1:42205769:G:Cdonor_gain1.0000
1:42227881:AC:Adonor_gain1.0000
1:42227882:CC:Cdonor_gain1.0000
1:42227964:CCC:Cacceptor_gain1.0000
1:42227965:CC:Cacceptor_gain1.0000
1:42227965:CCC:Cacceptor_gain1.0000
1:42227966:CC:Cacceptor_gain1.0000
1:42227967:C:CCacceptor_gain1.0000
1:42265109:TCCTA:Tdonor_loss1.0000

AlphaMissense

4136 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:42179725:C:AW618C1.000
1:42179725:C:GW618C1.000
1:42179726:C:GW618S1.000
1:42179727:A:GW618R1.000
1:42179727:A:TW618R1.000
1:42179731:A:CF616L1.000
1:42179731:A:TF616L1.000
1:42179732:A:CF616C1.000
1:42179732:A:GF616S1.000
1:42179733:A:GF616L1.000
1:42188838:A:GF515S1.000
1:42188847:A:GL512P1.000
1:42188859:A:GL508P1.000
1:42188890:A:GW498R1.000
1:42188890:A:TW498R1.000
1:42188905:C:GA493P1.000
1:42188925:A:GL486P1.000
1:42189333:A:GW475R1.000
1:42189333:A:TW475R1.000
1:42189347:G:TA470D1.000
1:42189368:A:GL463P1.000
1:42194928:A:GL299P1.000
1:42194937:A:GF296S1.000
1:42227954:C:GA153P1.000
1:42227955:C:AW152C1.000
1:42227955:C:GW152C1.000
1:42227956:C:GW152S1.000
1:42227957:A:CW152G1.000
1:42227957:A:GW152R1.000
1:42227957:A:TW152R1.000

dbSNP variants (sampled 300 via entrez): RS1000000261 (1:42265511 G>C), RS1000005230 (1:42263492 T>C), RS1000006415 (1:42290127 T>C), RS1000071445 (1:42218778 C>A), RS1000072289 (1:42313369 T>C), RS1000113606 (1:42271334 T>C), RS1000119354 (1:42326021 G>A,C), RS1000160560 (1:42282535 C>T), RS1000184202 (1:42239633 T>A), RS1000188194 (1:42198320 C>G), RS1000240923 (1:42307330 T>C), RS1000294137 (1:42217992 T>G), RS1000297521 (1:42225378 C>A), RS1000316545 (1:42289149 T>C), RS1000324471 (1:42295359 C>T)

Disease associations

OMIM: gene MIM:616035 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects methylation, decreases expression2
Valproic Acidaffects expression, decreases expression2
Cadmium Chloridedecreases expression, increases abundance2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
FR900359increases phosphorylation1
geraniolincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteincreases abundance, increases expression1
aflatoxin B2increases methylation1
coumarindecreases phosphorylation1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
deguelinincreases expression1
jinfukangdecreases expression1
Sunitinibincreases expression1
Leflunomideincreases expression1
Arsenicincreases abundance, increases expression1
Vehicle Emissionsaffects expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Cadmiumdecreases expression, increases abundance1
Doxorubicindecreases expression1
Estradioldecreases expression1
Methotrexatedecreases expression1
Phenobarbitalaffects expression1
Silicon Dioxidedecreases expression1
Tretinoindecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Cyclosporineincreases expression1
Aflatoxin B1decreases methylation1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.