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Aliases for ZNF540 Gene

Aliases for ZNF540 Gene

  • Zinc Finger Protein 540 2 3 5
  • Putative Protein Product Of Nbla10512 3
  • CTD-3064H18.6 3
  • Nbla10512 3

External Ids for ZNF540 Gene

Previous GeneCards Identifiers for ZNF540 Gene

  • GC00U914377
  • GC19P042735
  • GC19P042736
  • GC19P038039
  • GC19P034535
  • GC19P038086

Summaries for ZNF540 Gene

GeneCards Summary for ZNF540 Gene

ZNF540 (Zinc Finger Protein 540) is a Protein Coding gene. Among its related pathways are Gene Expression. GO annotations related to this gene include nucleic acid binding and translation repressor activity, nucleic acid binding. An important paralog of this gene is ZNF546.

UniProtKB/Swiss-Prot for ZNF540 Gene

  • May act as a transcriptional repressor.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZNF540 Gene

Genomics for ZNF540 Gene

Regulatory Elements for ZNF540 Gene

Enhancers for ZNF540 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
GH19F037451 0.6 FANTOM5 11.8 -100.1 -100112 0.3 SOX5 SOX13 ESRRA CHD1 SIN3A DPF2 NR3C1 OSR2 CTBP1 GATA3 ZNF540 ZNF571 ENSG00000180458 ZNF383 LINC01535 ZNF573 ZNF793 ZNF527 ZNF607 ZNF570
GH19F037513 0.2 ENCODE 11 -37.8 -37778 0.2 SIN3A IRF3 BCL11B ZNF335 POLR2A EED PRDM10 FOS SP3 SMAD5 ENSG00000180458 ZNF540 ZNF571 ZNF781 ZNF793-AS1 GC19M037947
GH19F037718 0.7 ENCODE 10.8 +168.1 168064 2.0 ATF1 CREB3L1 ZNF493 ZNF133 ARID4B SIN3A DMAP1 ZNF48 ZNF2 ZNF121 ZNF383 ZNF345 ZNF850 ZNF607 ZNF781 ZNF585B LINC01535 ZNF420 WDR87 ZNF793
GH19F037698 0.2 ENCODE 10.1 +148.0 147977 0.7 GLIS2 GLIS1 TEAD4 ZNF76 ZNF18 ZNF573 ZNF571 ZNF540 LOC100129085 GC19P037712
GH19F037333 0.2 ENCODE 9.9 -216.5 -216548 1.7 PKNOX1 ATF1 WRNIP1 SIN3A BRCA1 ZNF2 ETS1 GLIS2 ELK1 ZNF143 ZNF383 ZNF850 ZNF345 ZNF793 ZNF573 ZNF527 ZNF567 ZNF540 ZNF571 ENSG00000267682
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around ZNF540 on UCSC Golden Path with GeneCards custom track

Promoters for ZNF540 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for ZNF540 Gene

37,551,371 bp from pter
37,614,179 bp from pter
62,809 bases
Plus strand

Genomic View for ZNF540 Gene

Genes around ZNF540 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNF540 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNF540 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZNF540 Gene

Proteins for ZNF540 Gene

  • Protein details for ZNF540 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger protein 540
    Protein Accession:
    Secondary Accessions:
    • A0AVS5
    • A8K371
    • Q05D58
    • Q3LIC5
    • Q6ZN36
    • Q7Z3C8
    • Q86T31

    Protein attributes for ZNF540 Gene

    660 amino acids
    Molecular mass:
    77094 Da
    Quaternary structure:
    • May interact with MVP.
    • Sequence=AAH17940.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=CAD97942.1; Type=Frameshift; Positions=580; Evidence={ECO:0000305};

    Alternative splice isoforms for ZNF540 Gene


neXtProt entry for ZNF540 Gene

Post-translational modifications for ZNF540 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ZNF540 Gene

Domains & Families for ZNF540 Gene

Gene Families for ZNF540 Gene

Protein Domains for ZNF540 Gene

Suggested Antigen Peptide Sequences for ZNF540 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 KRAB domain.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Contains 17 C2H2-type zinc fingers.
  • Contains 1 KRAB domain.
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
  • Contains 17 C2H2-type zinc fingers.
genes like me logo Genes that share domains with ZNF540: view

Function for ZNF540 Gene

Molecular function for ZNF540 Gene

UniProtKB/Swiss-Prot Function:
May act as a transcriptional repressor.

Gene Ontology (GO) - Molecular Function for ZNF540 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000900 translation repressor activity, nucleic acid binding IMP 16815308
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IBA --
GO:0005515 protein binding IPI 16815308
genes like me logo Genes that share ontologies with ZNF540: view

Phenotypes for ZNF540 Gene

GenomeRNAi human phenotypes for ZNF540:
genes like me logo Genes that share phenotypes with ZNF540: view

Animal Model Products

miRNA for ZNF540 Gene

miRTarBase miRNAs that target ZNF540

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZNF540 Gene

Localization for ZNF540 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNF540 Gene

Nucleus. Cytoplasm.

Subcellular locations from

Jensen Localization Image for ZNF540 Gene COMPARTMENTS Subcellular localization image for ZNF540 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for ZNF540 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IEA,IDA 16815308
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA,IDA 16815308
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with ZNF540: view

Pathways & Interactions for ZNF540 Gene

SuperPathways for ZNF540 Gene

SuperPathway Contained pathways
1 Gene Expression
genes like me logo Genes that share pathways with ZNF540: view

Pathways by source for ZNF540 Gene

2 Reactome pathways for ZNF540 Gene

Gene Ontology (GO) - Biological Process for ZNF540 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0017148 negative regulation of translation IMP 16815308
GO:0045892 negative regulation of transcription, DNA-templated IDA 16815308
genes like me logo Genes that share ontologies with ZNF540: view

No data available for SIGNOR curated interactions for ZNF540 Gene

Transcripts for ZNF540 Gene

Unigene Clusters for ZNF540 Gene

Zinc finger protein 540:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZNF540 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c · 5d · 5e
SP1: -
SP2: -
SP3: - -
SP5: - -
SP6: - - -

Relevant External Links for ZNF540 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZNF540 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ZNF540 Gene

NURSA nuclear receptor signaling pathways regulating expression of ZNF540 Gene:


SOURCE GeneReport for Unigene cluster for ZNF540 Gene:


mRNA Expression by UniProt/SwissProt for ZNF540 Gene:

Tissue specificity: Expressed in several fetal tissues, including gut, heart, brain, muscle, lung, testis and liver.
genes like me logo Genes that share expression patterns with ZNF540: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for ZNF540 Gene

Orthologs for ZNF540 Gene

This gene was present in the common ancestor of mammals.

Orthologs for ZNF540 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZNF540 34 35
  • 99.55 (n)
(Bos Taurus)
Mammalia ZNF383 35
  • 50 (a)
(Monodelphis domestica)
Mammalia -- 35
  • 46 (a)
Species where no ortholog for ZNF540 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)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • 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)
  • mouse (Mus musculus)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for ZNF540 Gene

Gene Tree for ZNF540 (if available)
Gene Tree for ZNF540 (if available)

Paralogs for ZNF540 Gene

(531) SIMAP similar genes for ZNF540 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with ZNF540: view

Variants for ZNF540 Gene

Sequence variations from dbSNP and Humsavar for ZNF540 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
VAR_035586 A colorectal cancer sample
rs10153500 -- 37,582,366(+) GTCAG(C/T)TGGCT intron-variant
rs10403173 -- 37,587,779(+) tcccc(A/G)ctaac intron-variant
rs10406832 -- 37,554,717(+) AGATC(A/T)CCAAG intron-variant
rs10407657 -- 37,579,190(+) GTCCC(A/G)CCTCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ZNF540 Gene

Variant ID Type Subtype PubMed ID
esv2718520 CNV deletion 23290073
esv2718521 CNV deletion 23290073
esv2758759 CNV loss 17122850
esv3355793 CNV insertion 20981092
nsv1134790 CNV deletion 24896259
nsv2478 CNV deletion 18451855
nsv474205 CNV novel sequence insertion 20440878
nsv579468 CNV gain 21841781
nsv833819 CNV gain 17160897
nsv953295 CNV deletion 24416366

Variation tolerance for ZNF540 Gene

Residual Variation Intolerance Score: 18.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.56; 88.93% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZNF540 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZNF540 Gene

Disorders for ZNF540 Gene

Relevant External Links for ZNF540

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for ZNF540 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZNF540 Gene

Publications for ZNF540 Gene

  1. A novel human zinc finger protein ZNF540 interacts with MVP and inhibits transcriptional activities of the ERK signal pathway. (PMID: 16815308) Xiang Z. … Li Y. (Biochem. Biophys. Res. Commun. 2006) 3 4 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. 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
  4. Diagnostic exome sequencing in persons with severe intellectual disability. (PMID: 23033978) de Ligt J. … Vissers L.E. (N. Engl. J. Med. 2012) 4 64
  5. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L. … Andersson-Svahn H. (Mol. Cell Proteomics 2008) 3 64

Products for ZNF540 Gene

Sources for ZNF540 Gene

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