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Aliases for FNDC3A Gene

Aliases for FNDC3A Gene

  • Fibronectin Type III Domain Containing 3A 2 3 5
  • Human Gene Expressed In Odontoblasts 3 4
  • FNDC3 3 4
  • HUGO 3 4
  • Fibronectin Type-III Domain-Containing Protein 3A 3
  • Fibronectin Type III Domain Containing 3 2
  • BA203I16.1 3
  • BA203I16.5 3
  • KIAA0970 4

External Ids for FNDC3A Gene

Previous HGNC Symbols for FNDC3A Gene

  • FNDC3

Previous GeneCards Identifiers for FNDC3A Gene

  • GC13P048449
  • GC13P049550
  • GC13P030344

Summaries for FNDC3A Gene

GeneCards Summary for FNDC3A Gene

FNDC3A (Fibronectin Type III Domain Containing 3A) is a Protein Coding gene. Diseases associated with FNDC3A include Holoprosencephaly 3. An important paralog of this gene is FNDC3B.

UniProtKB/Swiss-Prot for FNDC3A Gene

  • Mediates spermatid-Sertoli adhesion during spermatogenesis.

Gene Wiki entry for FNDC3A Gene

Additional gene information for FNDC3A Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FNDC3A Gene

Genomics for FNDC3A Gene

GeneHancer (GH) Regulatory Elements for FNDC3A Gene

Promoters and enhancers for FNDC3A 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
GH13J048974 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 656.6 +1.8 1790 6.2 HDGF PKNOX1 ARID4B SIN3A FEZF1 ZNF2 IRF4 YY1 POLR2B ZNF213 FNDC3A GC13M048972 ENSG00000275202 SETDB2 MED4 CDADC1 GC13P048988
GH13J049109 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.1 +134.7 134731 1.9 ATF1 MLX ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 FOS FNDC3A SETDB2 PPP1R26P1 RNY3P2 COX7CP1
GH13J048890 Enhancer 1.2 FANTOM5 Ensembl ENCODE 21.3 -83.9 -83926 2.5 JUN BATF FOSL1 POLR2A EED NFE2 FOSL2 ETV6 FOS MAFK FNDC3A RCBTB2 GC13P048866 GC13M048972
GH13J048883 Enhancer 1 FANTOM5 Ensembl ENCODE 21.2 -91.4 -91378 1.3 MEF2D MEIS2 JUNB ATF2 FNDC3A RCBTB2 GC13P048866 GC13M048972
GH13J048858 Enhancer 1.2 FANTOM5 Ensembl ENCODE 17.6 -116.4 -116371 2.5 PKNOX1 FEZF1 BMI1 BATF HIC1 ZFHX2 PATZ1 EGR2 RFX1 ZNF189 FNDC3A EBPL RCBTB2 GC13P048866 GC13P048772
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FNDC3A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FNDC3A gene promoter:
  • Nkx2-5
  • ATF
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • FOXC1
  • AP-1

Genomic Locations for FNDC3A Gene

Genomic Locations for FNDC3A Gene
233,868 bases
Plus strand
233,868 bases
Plus strand

Genomic View for FNDC3A Gene

Genes around FNDC3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FNDC3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FNDC3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FNDC3A Gene

Proteins for FNDC3A Gene

  • Protein details for FNDC3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Fibronectin type-III domain-containing protein 3A
    Protein Accession:
    Secondary Accessions:
    • B4DYG1
    • Q5HYC9
    • Q5JVF8
    • Q5JVF9
    • Q6EVH3
    • Q6EVH4
    • Q6N020
    • Q6P9D5
    • Q6ZME4
    • Q9H1W1

    Protein attributes for FNDC3A Gene

    1198 amino acids
    Molecular mass:
    131852 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA76814.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAD18784.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for FNDC3A Gene

    Alternative splice isoforms for FNDC3A Gene


neXtProt entry for FNDC3A Gene

Post-translational modifications for FNDC3A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for FNDC3A Gene

Domains & Families for FNDC3A Gene

Gene Families for FNDC3A Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for FNDC3A Gene

Suggested Antigen Peptide Sequences for FNDC3A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the FNDC3 family.
  • Belongs to the FNDC3 family.
genes like me logo Genes that share domains with FNDC3A: view

Function for FNDC3A Gene

Molecular function for FNDC3A Gene

UniProtKB/Swiss-Prot Function:
Mediates spermatid-Sertoli adhesion during spermatogenesis.

Phenotypes From GWAS Catalog for FNDC3A Gene

Gene Ontology (GO) - Molecular Function for FNDC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with FNDC3A: view
genes like me logo Genes that share phenotypes with FNDC3A: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for FNDC3A Gene

Localization for FNDC3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for FNDC3A Gene

Golgi apparatus membrane; Single-pass membrane protein.

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 FNDC3A gene
Compartment Confidence
golgi apparatus 5
plasma membrane 3
endoplasmic reticulum 3
cytosol 3
mitochondrion 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FNDC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0001669 acrosomal vesicle IEA --
GO:0005794 Golgi apparatus IEA,IDA 18218838
GO:0005829 cytosol IEA --
GO:0012506 vesicle membrane IEA --
genes like me logo Genes that share ontologies with FNDC3A: view

Pathways & Interactions for FNDC3A Gene

SuperPathways for FNDC3A Gene

No Data Available

Gene Ontology (GO) - Biological Process for FNDC3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007286 spermatid development IEA --
GO:0009566 fertilization IEA --
GO:0060009 Sertoli cell development IEA --
GO:0098609 cell-cell adhesion IEA --
genes like me logo Genes that share ontologies with FNDC3A: view

No data available for Pathways by source and SIGNOR curated interactions for FNDC3A Gene

Drugs & Compounds for FNDC3A Gene

No Compound Related Data Available

Transcripts for FNDC3A Gene

Unigene Clusters for FNDC3A Gene

Fibronectin type III domain containing 3A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FNDC3A Gene

No ASD Table

Relevant External Links for FNDC3A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FNDC3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FNDC3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for FNDC3A Gene

This gene is overexpressed in Placenta (18.8) and Stomach (8.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for FNDC3A Gene

Protein tissue co-expression partners for FNDC3A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of FNDC3A Gene:


SOURCE GeneReport for Unigene cluster for FNDC3A Gene:


mRNA Expression by UniProt/SwissProt for FNDC3A Gene:

Tissue specificity: Expressed in the odontoblast and nerves in the dental pulp. Also expressed in trachea and to a lesser extent in the brain, liver, lung and kidney.

Evidence on tissue expression from TISSUES for FNDC3A Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Kidney(2.1)
  • Pancreas(2.1)
  • Lung(2)
genes like me logo Genes that share expression patterns with FNDC3A: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for FNDC3A Gene

Orthologs for FNDC3A Gene

This gene was present in the common ancestor of animals.

Orthologs for FNDC3A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FNDC3A 34 33
  • 99.81 (n)
(Canis familiaris)
Mammalia FNDC3A 34 33
  • 93.91 (n)
(Bos Taurus)
Mammalia FNDC3A 34 33
  • 92.79 (n)
(Mus musculus)
Mammalia Fndc3a 16 34 33
  • 88.45 (n)
(Rattus norvegicus)
Mammalia Fndc3a 33
  • 87.88 (n)
(Monodelphis domestica)
Mammalia FNDC3A 34
  • 86 (a)
(Ornithorhynchus anatinus)
Mammalia FNDC3A 34
  • 86 (a)
(Gallus gallus)
Aves FNDC3A 34 33
  • 80.37 (n)
(Anolis carolinensis)
Reptilia FNDC3A 34
  • 56 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492173 33
  • 73.95 (n)
Str.15243 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.21668 33
(Danio rerio)
Actinopterygii FNDC3A 34
  • 52 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG42389 34 33
  • 44.57 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009522 33
  • 25.26 (n)
(Caenorhabditis elegans)
Secernentea let-805 34
  • 7 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 38 (a)
Species where no ortholog for FNDC3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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 FNDC3A Gene

Gene Tree for FNDC3A (if available)
Gene Tree for FNDC3A (if available)
Evolutionary constrained regions (ECRs) for FNDC3A: view image

Paralogs for FNDC3A Gene

Paralogs for FNDC3A Gene

(2) SIMAP similar genes for FNDC3A Gene using alignment to 3 proteins:

  • G5E9X3_HUMAN
  • H7C507_HUMAN Pseudogenes for FNDC3A Gene

genes like me logo Genes that share paralogs with FNDC3A: view

Variants for FNDC3A Gene

Sequence variations from dbSNP and Humsavar for FNDC3A Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs1000002133 -- 49,141,984(+) C/T intron_variant
rs1000002524 -- 49,053,130(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000010205 -- 49,117,012(+) G/T intron_variant
rs1000018539 -- 49,116,256(+) G/A intron_variant
rs1000058265 -- 48,983,429(+) T/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for FNDC3A Gene

Variant ID Type Subtype PubMed ID
nsv1034 CNV deletion 18451855
nsv1035 CNV deletion 18451855
nsv1036 CNV insertion 18451855
nsv1052168 CNV gain 25217958
nsv1069751 CNV deletion 25765185
nsv1126342 CNV deletion 24896259
nsv455882 CNV loss 19166990
nsv561593 CNV loss 21841781
nsv832607 CNV loss 17160897
nsv951081 CNV duplication 24416366

Variation tolerance for FNDC3A Gene

Residual Variation Intolerance Score: 5.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.04; 60.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FNDC3A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FNDC3A Gene

Disorders for FNDC3A Gene

MalaCards: The human disease database

(1) MalaCards diseases for FNDC3A Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
holoprosencephaly 3
  • hpe3
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for FNDC3A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with FNDC3A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FNDC3A Gene

Publications for FNDC3A Gene

  1. HUGO (FNDC3A): a new gene overexpressed in human odontoblasts. (PMID: 18218838) Carrouel F … Bleicher F (Journal of dental research 2008) 3 4 58
  2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A … Ross MT (Nature 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for FNDC3A Gene

Sources for FNDC3A Gene

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