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Aliases for FHL3 Gene

Aliases for FHL3 Gene

  • Four And A Half LIM Domains 3 2 3 5
  • Skeletal Muscle LIM-Protein 2 3 4
  • SLIM-2 3 4
  • FHL-3 3 4
  • SLIM2 3 4
  • Four And A Half LIM Domains Protein 3 3
  • LIM-Only Protein FHL3 3

External Ids for FHL3 Gene

Previous GeneCards Identifiers for FHL3 Gene

  • GC01P038251
  • GC01U900008
  • GC01M037875
  • GC01M038131
  • GC01M038235
  • GC01M038462
  • GC01M036580

Summaries for FHL3 Gene

Entrez Gene Summary for FHL3 Gene

  • The protein encoded by this gene is a member of a family of proteins containing a four-and-a-half LIM domain, which is a highly conserved double zinc finger motif. The encoded protein has been shown to interact with the cancer developmental regulators SMAD2, SMAD3, and SMAD4, the skeletal muscle myogenesis protein MyoD, and the high-affinity IgE beta chain regulator MZF-1. This protein may be involved in tumor suppression, repression of MyoD expression, and repression of IgE receptor expression. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

GeneCards Summary for FHL3 Gene

FHL3 (Four And A Half LIM Domains 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include actin binding. An important paralog of this gene is FHL2.

Gene Wiki entry for FHL3 Gene

Additional gene information for FHL3 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FHL3 Gene

Genomics for FHL3 Gene

GeneHancer (GH) Regulatory Elements for FHL3 Gene

Promoters and enhancers for FHL3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J037994 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 699.5 +4.3 4268 13.7 HDGF SMAD1 ARNT ARID4B SIN3A ZNF2 YY1 POLR2B ZNF766 E2F8 FHL3 SF3A3 SNIP1 MYCBP C1orf109 FTH1P1 GNL2 MEAF6 UTP11 MTF1
GH01J037988 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 33.5 +15.8 15819 2.4 ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 SF3A3 RNU6-510P GC01P037993 C1orf109 GNL2 MYCBP FTH1P1 INPP5B FHL3 RSPO1
GH01J037944 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 22.7 +59.0 59020 3.2 HDGF PKNOX1 ARNT ARID4B SIN3A ZNF2 YY1 SLC30A9 POLR2B ZNF766 INPP5B FHL3 SF3A3 MYCBP GNL2 LOC105378651
GH01J037930 Promoter/Enhancer 1.5 Ensembl ENCODE 11.5 +73.9 73891 3.2 HDGF PKNOX1 ATF1 ZFP64 ARID4B SIN3A YY1 TCF12 GLIS2 E2F8 LOC105378651 SF3A3 SNIP1 C1orf109 GNL2 FHL3 UTP11 INPP5B RNU6-584P
GH01J037900 Enhancer 0.9 Ensembl ENCODE 16.8 +104.0 104047 2 PKNOX1 BACH1 EBF1 BATF RELA NFATC1 EED ATF7 ETV6 IKZF2 INPP5B FHL3 ENSG00000230955 MTF1 UTP11 RNU6-584P LOC105378651
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FHL3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FHL3 gene promoter:
  • MyoD
  • STAT1beta
  • STAT1alpha
  • STAT1
  • E2F-5
  • E2F-4
  • E2F-3a
  • E2F-2
  • E2F-1

Genomic Locations for FHL3 Gene

Genomic Locations for FHL3 Gene
8,837 bases
Minus strand
8,837 bases
Minus strand

Genomic View for FHL3 Gene

Genes around FHL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FHL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FHL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FHL3 Gene

Proteins for FHL3 Gene

  • Protein details for FHL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Four and a half LIM domains protein 3
    Protein Accession:
    Secondary Accessions:
    • D3DPT6
    • Q6I9T0
    • Q9BVA2

    Protein attributes for FHL3 Gene

    280 amino acids
    Molecular mass:
    31192 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for FHL3 Gene

neXtProt entry for FHL3 Gene

Post-translational modifications for FHL3 Gene

  • Ubiquitination at Lys235 and isoforms=167
  • Modification sites at PhosphoSitePlus

Other Protein References for FHL3 Gene

No data available for DME Specific Peptides for FHL3 Gene

Domains & Families for FHL3 Gene

Gene Families for FHL3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for FHL3 Gene


Suggested Antigen Peptide Sequences for FHL3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with FHL3: view

No data available for UniProtKB/Swiss-Prot for FHL3 Gene

Function for FHL3 Gene

Molecular function for FHL3 Gene

GENATLAS Biochemistry:
four and a half LIM domain protein 3,skeletal muscle specific

Phenotypes From GWAS Catalog for FHL3 Gene

Gene Ontology (GO) - Molecular Function for FHL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003712 transcription coregulator activity IBA --
GO:0003779 actin binding IEA --
GO:0005515 protein binding IPI 11135358
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with FHL3: view
genes like me logo Genes that share phenotypes with FHL3: view

Animal Model Products

CRISPR Products

miRNA for FHL3 Gene

miRTarBase miRNAs that target FHL3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FHL3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for FHL3 Gene

Localization for FHL3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FHL3 gene
Compartment Confidence
nucleus 4
cytosol 3
cytoskeleton 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for FHL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001725 stress fiber IEA --
GO:0005634 nucleus IEA --
GO:0005925 focal adhesion HDA 21423176
GO:0030018 Z disc IEA --
genes like me logo Genes that share ontologies with FHL3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for FHL3 Gene

Pathways & Interactions for FHL3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for FHL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007517 muscle organ development TAS 10049693
GO:0030036 actin cytoskeleton organization IEA --
genes like me logo Genes that share ontologies with FHL3: view

No data available for Pathways by source and SIGNOR curated interactions for FHL3 Gene

Drugs & Compounds for FHL3 Gene

(1) Drugs for FHL3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with FHL3: view

Transcripts for FHL3 Gene

Unigene Clusters for FHL3 Gene

Four and a half LIM domains 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for FHL3

Alternative Splicing Database (ASD) splice patterns (SP) for FHL3 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c
SP2: - - -
SP3: - -
SP4: -
SP6: - - - -
SP7: - - - -
SP8: - -

Relevant External Links for FHL3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FHL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FHL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FHL3 Gene

This gene is overexpressed in Muscle - Skeletal (x29.8).

Protein differential expression in normal tissues from HIPED for FHL3 Gene

This gene is overexpressed in Uterus (7.2), Breast (7.0), and Esophagus (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for FHL3 Gene

Protein tissue co-expression partners for FHL3 Gene

NURSA nuclear receptor signaling pathways regulating expression of FHL3 Gene:


SOURCE GeneReport for Unigene cluster for FHL3 Gene:


mRNA Expression by UniProt/SwissProt for FHL3 Gene:

Tissue specificity: Expressed only in skeletal muscle.

Evidence on tissue expression from TISSUES for FHL3 Gene

  • Muscle(4.7)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with FHL3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for FHL3 Gene

Orthologs for FHL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for FHL3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FHL3 34 33
  • 99.05 (n)
(Canis familiaris)
Mammalia FHL3 34 33
  • 92.38 (n)
(Monodelphis domestica)
Mammalia FHL3 34
  • 92 (a)
(Bos Taurus)
Mammalia FHL3 34 33
  • 91.67 (n)
(Mus musculus)
Mammalia Fhl3 16 34 33
  • 89.52 (n)
(Rattus norvegicus)
Mammalia Fhl3 33
  • 89.52 (n)
(Ornithorhynchus anatinus)
Mammalia FHL3 34
  • 73 (a)
(Gallus gallus)
Aves FHL3 34 33
  • 74.61 (n)
(Anolis carolinensis)
Reptilia FHL3 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia fhl3 33
  • 68.96 (n)
(Danio rerio)
Actinopterygii fhl3a 34 33
  • 67.75 (n)
fhl3b 34
  • 62 (a)
wufb09g09 33
fruit fly
(Drosophila melanogaster)
Insecta Lmpt 35
  • 50 (a)
(Caenorhabditis elegans)
Secernentea F25H5.1a 35
  • 47 (a)
F25H5.1b 35
  • 46 (a)
pin-2 34
  • 20 (a)
Species where no ortholog for FHL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for FHL3 Gene

Gene Tree for FHL3 (if available)
Gene Tree for FHL3 (if available)
Evolutionary constrained regions (ECRs) for FHL3: view image

Paralogs for FHL3 Gene

(10) SIMAP similar genes for FHL3 Gene using alignment to 3 proteins:

  • Q96C98_HUMAN
  • Q9P100_HUMAN
genes like me logo Genes that share paralogs with FHL3: view

Variants for FHL3 Gene

Sequence variations from dbSNP and Humsavar for FHL3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000272678 -- 38,002,008(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000307184 -- 37,997,322(-) A/G 3_prime_UTR_variant
rs1000402425 -- 37,996,698(-) T/G downstream_transcript_variant
rs1000454231 -- 38,001,356(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000600703 -- 37,997,197(-) G/C 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for FHL3 Gene

Variant ID Type Subtype PubMed ID
nsv1075438 CNV deletion 25765185
nsv1130955 CNV deletion 24896259
nsv950632 CNV deletion 24416366

Variation tolerance for FHL3 Gene

Residual Variation Intolerance Score: 58.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.15; 51.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FHL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FHL3 Gene

Disorders for FHL3 Gene

Additional Disease Information for FHL3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for FHL3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for FHL3 Gene

Publications for FHL3 Gene

  1. The LIM proteins FHL1 and FHL3 are expressed differently in skeletal muscle. (PMID: 10049693) Morgan MJ … Madgwick AJ (Biochemical and biophysical research communications 1999) 3 4 22 58
  2. Chromosomal mapping of a skeletal muscle specific LIM-only protein FHL3 to the distal end of the short arm of human chromosome 1. (PMID: 10226657) Lee SM … Lee CY (Somatic cell and molecular genetics 1998) 2 3 22 58
  3. Slim defines a novel family of LIM-proteins expressed in skeletal muscle. (PMID: 8753811) Morgan MJ … Madgwick AJ (Biochemical and biophysical research communications 1996) 2 3 4 58
  4. Human four-and-a-half LIM family members suppress tumor cell growth through a TGF-beta-like signaling pathway. (PMID: 19139564) Ding L … Ye Q (The Journal of clinical investigation 2009) 3 22 58
  5. FHL3 negatively regulates human high-affinity IgE receptor beta-chain gene expression by acting as a transcriptional co-repressor of MZF-1. (PMID: 15453830) Takahashi K … Ra C (The Biochemical journal 2005) 3 22 58

Products for FHL3 Gene

Sources for FHL3 Gene

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