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Aliases for FAM53A Gene

Aliases for FAM53A Gene

  • Family With Sequence Similarity 53 Member A 2 3 5
  • Dorsal Neural-Tube Nuclear Protein 3 4
  • Family With Sequence Similarity 53, Member A 2
  • Protein FAM53A 3
  • DNTNP 3

External Ids for FAM53A Gene

Summaries for FAM53A Gene

GeneCards Summary for FAM53A Gene

FAM53A (Family With Sequence Similarity 53 Member A) is a Protein Coding gene. An important paralog of this gene is FAM53B.

UniProtKB/Swiss-Prot for FAM53A Gene

  • May play an important role in neural development; the dorsomedial roof of the third ventricle.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FAM53A Gene

Genomics for FAM53A Gene

Regulatory Elements for FAM53A Gene

Enhancers for FAM53A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04F001682 0.4 ENCODE 34.5 -0.1 -114 3.1 TBP ATF1 CREB3L1 ZNF48 ZNF121 GLIS2 ZNF143 ZNF207 KLF13 HDAC8 FAM53A SLBP TMEM129 GC04P001691
GH04F001694 0.5 ENCODE 31.3 -11.7 -11705 2.3 SMARCA4 POLR2A TMEM129 FAM53A TACC3 GC04M001697 GC04P001691
GH04F001710 0.6 FANTOM5 ENCODE 30.4 -29.1 -29111 5.7 HDGF PKNOX1 MLX CREB3L1 ZFP64 ARID4B SIN3A DMAP1 YY1 SLC30A9 FAM53A HAUS3 TMEM129 CTBP1-AS2 SLBP NSD2 ENSG00000270195 PIR44595
GH04F001719 0.6 ENCODE 30.3 -38.0 -37959 5.4 HDGF PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143 FAM53A TMEM129 TACC3 SLBP CRIPAK ENSG00000233799 GC04P001740
GH04F001725 0.6 ENCODE 30.3 -42.8 -42828 3.8 HDGF TBL1XR1 ARID4B SIN3A ZNF48 ZNF2 RAD21 GLIS2 ZNF143 ZNF207 FAM53A TMEM129 CTBP1-AS2 SLBP HAUS3 TACC3 GC04P001740
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around FAM53A on UCSC Golden Path with GeneCards custom track

Promoters for FAM53A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001234662 13 1801 TBP ATF1 CREB3L1 ZNF48 ZNF121 GLIS2 ZNF143 ZNF207 KLF13 HDAC8

Genomic Location for FAM53A Gene

1,574,062 bp from pter
1,684,313 bp from pter
110,252 bases
Minus strand

Genomic View for FAM53A Gene

Genes around FAM53A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FAM53A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FAM53A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FAM53A Gene

Proteins for FAM53A Gene

  • Protein details for FAM53A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein FAM53A
    Protein Accession:
    Secondary Accessions:
    • Q6ZUL5

    Protein attributes for FAM53A Gene

    398 amino acids
    Molecular mass:
    42585 Da
    Quaternary structure:
    No Data Available

neXtProt entry for FAM53A Gene

Post-translational modifications for FAM53A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for FAM53A Gene

Domains & Families for FAM53A Gene

Protein Domains for FAM53A Gene


Suggested Antigen Peptide Sequences for FAM53A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the FAM53 family.
  • Belongs to the FAM53 family.
genes like me logo Genes that share domains with FAM53A: view

No data available for Gene Families for FAM53A Gene

Function for FAM53A Gene

Molecular function for FAM53A Gene

UniProtKB/Swiss-Prot Function:
May play an important role in neural development; the dorsomedial roof of the third ventricle.
genes like me logo Genes that share phenotypes with FAM53A: view

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for FAM53A Gene

Localization for FAM53A Gene

Subcellular locations from UniProtKB/Swiss-Prot for FAM53A Gene

Nucleus. Note=Subnuclear distribution. {ECO:0000250}.

Subcellular locations from

Jensen Localization Image for FAM53A Gene COMPARTMENTS Subcellular localization image for FAM53A gene
Compartment Confidence
nucleus 5
cytoskeleton 2
cytosol 2

Gene Ontology (GO) - Cellular Components for FAM53A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with FAM53A: view

Pathways & Interactions for FAM53A Gene

SuperPathways for FAM53A Gene

No Data Available

Interacting Proteins for FAM53A Gene

Selected Interacting proteins: Q6NSI3-FA53A_HUMAN for FAM53A Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for FAM53A Gene


No data available for Pathways by source and SIGNOR curated interactions for FAM53A Gene

Transcripts for FAM53A Gene

Unigene Clusters for FAM53A Gene

Family with sequence similarity 53, member A:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for FAM53A Gene

No ASD Table

Relevant External Links for FAM53A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FAM53A Gene

mRNA expression in normal human tissues for FAM53A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FAM53A Gene

This gene is overexpressed in Testis (x12.0).

Protein differential expression in normal tissues from HIPED for FAM53A Gene

This gene is overexpressed in Fetal testis (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for FAM53A Gene

Protein tissue co-expression partners for FAM53A Gene

NURSA nuclear receptor signaling pathways regulating expression of FAM53A Gene:


SOURCE GeneReport for Unigene cluster for FAM53A Gene:

genes like me logo Genes that share expression patterns with FAM53A: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for FAM53A Gene

Orthologs for FAM53A Gene

This gene was present in the common ancestor of chordates.

Orthologs for FAM53A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FAM53A 34 35
  • 97.74 (n)
(Mus musculus)
Mammalia Fam53a 34 16 35
  • 75.49 (n)
(Rattus norvegicus)
Mammalia Fam53a 34
  • 75.24 (n)
(Canis familiaris)
Mammalia FAM53A 35
  • 57 (a)
(Ornithorhynchus anatinus)
Mammalia FAM53A 35
  • 52 (a)
(Monodelphis domestica)
Mammalia FAM53A 35
  • 51 (a)
(Gallus gallus)
Aves FAM53A 34 35
  • 62.53 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia fam53a 34
  • 60.6 (n)
Species where no ortholog for FAM53A 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)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • 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)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for FAM53A Gene

Gene Tree for FAM53A (if available)
Gene Tree for FAM53A (if available)

Paralogs for FAM53A Gene

Paralogs for FAM53A Gene

genes like me logo Genes that share paralogs with FAM53A: view

Variants for FAM53A Gene

Sequence variations from dbSNP and Humsavar for FAM53A Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs10003193 -- 1,621,657(+) CAGCC(C/T)CTCCC intron-variant
rs10003680 -- 1,587,250(+) atact(C/T)ccaat intron-variant
rs10004444 -- 1,585,274(+) tctct(C/T)ttttt intron-variant
rs10004445 -- 1,585,283(+) tcttt(C/T)ttttt intron-variant
rs10007990 -- 1,603,072(+) CTCTC(A/G)CCACC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for FAM53A Gene

Variant ID Type Subtype PubMed ID
dgv5081n100 CNV gain 25217958
dgv8901n54 CNV loss 21841781
esv1210969 CNV insertion 17803354
esv1444353 CNV insertion 17803354
esv1465412 CNV insertion 17803354
esv1776644 CNV insertion 17803354
esv23460 CNV loss 19812545
esv2726825 CNV deletion 23290073
esv2726826 CNV deletion 23290073
esv2726827 CNV deletion 23290073
esv2726828 CNV deletion 23290073
esv2726830 CNV deletion 23290073
esv2726831 CNV deletion 23290073
esv2759218 CNV gain 17122850
esv3396266 CNV duplication 20981092
esv3563245 CNV deletion 23714750
esv3563246 CNV deletion 23714750
esv3575670 CNV gain 25503493
nsv1074668 CNV deletion 25765185
nsv1117052 CNV deletion 24896259
nsv1118993 CNV deletion 24896259
nsv1123739 CNV deletion 24896259
nsv1129711 CNV tandem duplication 24896259
nsv1142598 CNV deletion 24896259
nsv428434 CNV gain 18775914
nsv470000 CNV loss 18288195
nsv508989 CNV insertion 20534489
nsv593316 CNV gain 21841781
nsv593320 CNV loss 21841781
nsv593334 CNV loss 21841781
nsv949754 CNV deletion 24416366
nsv949755 CNV deletion 24416366

Variation tolerance for FAM53A Gene

Residual Variation Intolerance Score: 96.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.87; 79.44% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for FAM53A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FAM53A Gene

Disorders for FAM53A Gene

Relevant External Links for FAM53A

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for FAM53A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for FAM53A Gene

Publications for FAM53A Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  3. Toward a comprehensive characterization of a human cancer cell phosphoproteome. (PMID: 23186163) Zhou H. … Mohammed S. (J. Proteome Res. 2013) 4 64
  4. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PMID: 21832049) OlA!h J. … OvA!di J. (J. Biol. Chem. 2011) 3 64
  5. A germline-specific class of small RNAs binds mammalian Piwi proteins. (PMID: 16751776) Girard A. … Carmell M.A. (Nature 2006) 3 64

Products for FAM53A Gene

Sources for FAM53A Gene

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