Free for academic non-profit institutions. Other users need a Commercial license

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. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and translation repressor activity, nucleic acid binding. An important paralog of this gene is ZNF780B.

UniProtKB/Swiss-Prot for ZNF540 Gene

  • May act as a transcriptional repressor.

Additional gene information for ZNF540 Gene

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

Genomics for ZNF540 Gene

GeneHancer (GH) Regulatory Elements for ZNF540 Gene

Promoters and enhancers for ZNF540 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I037593 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 634.9 +43.3 43330 2.2 PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 SLC30A9 ZNF213 ZNF571 ZNF540 ZNF567 ZNF527 ZFP30 ZNF383 HKR1 ZNF345 ZNF585A ZNF607
GH19I037550 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 567.4 +0.3 274 1.7 MEIS2 CTCF PKNOX1 ATF1 PHF20 POLR2A CREM CHD2 ZNF639 RFX1 ZNF540 PIR61079 LINC01535 ZNF607 ZFP30 ZNF781 ZNF527 ZNF571 ZNF529 ZNF585B
GH19I037576 Promoter 0.5 EPDnew 550.3 +24.9 24935 0.1 ZNF540 ZFP30 ZNF527 GC19P037580 GC19P037570 ZNF571 ZNF571-AS1
GH19I037778 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 73.3 +228.1 228092 2.3 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 YY1 POLR2B ZNF766 ZNF573 LOC728533 ZNF345 ZNF383 ZFP30 ZNF527 ZNF585B ZNF790 ZNF781 ZNF571
GH19I037370 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 72.4 -180.3 -180331 1.9 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF213 ZNF527 ZNF567 ZNF383 ZNF345 ZFP30 ZNF571 HKR1 ZNF850 ZNF793 ZNF790
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZNF540 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZNF540 gene promoter:

Genomic Locations for ZNF540 Gene

Genomic Locations for ZNF540 Gene
chr19:37,551,371-37,614,179
(GRCh38/hg38)
Size:
62,809 bases
Orientation:
Plus strand
chr19:38,042,308-38,105,000
(GRCh37/hg19)

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:
    Q8NDQ6-ZN540_HUMAN
    Recommended name:
    Zinc finger protein 540
    Protein Accession:
    Q8NDQ6
    Secondary Accessions:
    • A0AVS5
    • A8K371
    • Q05D58
    • Q3LIC5
    • Q6ZN36
    • Q7Z3C8
    • Q86T31

    Protein attributes for ZNF540 Gene

    Size:
    660 amino acids
    Molecular mass:
    77094 Da
    Quaternary structure:
    • May interact with MVP.
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

neXtProt entry for ZNF540 Gene

Post-translational modifications for ZNF540 Gene

No Post-translational modifications

No data available for DME Specific Peptides for ZNF540 Gene

Domains & Families for ZNF540 Gene

Gene Families for ZNF540 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

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

Q8NDQ6

UniProtKB/Swiss-Prot:

ZN540_HUMAN :
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
Family:
  • Belongs to the krueppel C2H2-type zinc-finger protein family.
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.

Phenotypes From GWAS Catalog for ZNF540 Gene

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 DNA binding transcription factor activity 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

miRNA for ZNF540 Gene

miRTarBase miRNAs that target ZNF540

Clone 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

COMPARTMENTS
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 ZNF540 gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZNF540 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005634 nucleus IDA,IEA 16815308
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA,IDA 16815308
GO:0005829 cytosol 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

Drugs & Compounds for ZNF540 Gene

No Compound Related Data Available

Transcripts for ZNF540 Gene

Unigene Clusters for ZNF540 Gene

Zinc finger protein 540:
Representative Sequences:

Clone 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: - -
SP4:
SP5: - -
SP6: - - -

Relevant External Links for ZNF540 Gene

GeneLoc Exon Structure for
ZNF540
ECgene alternative splicing isoforms for
ZNF540

Expression for ZNF540 Gene

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

NURSA nuclear receptor signaling pathways regulating expression of ZNF540 Gene:

ZNF540

SOURCE GeneReport for Unigene cluster for ZNF540 Gene:

Hs.728927

mRNA Expression by UniProt/SwissProt for ZNF540 Gene:

Q8NDQ6-ZN540_HUMAN
Tissue specificity: Expressed in several fetal tissues, including gut, heart, brain, muscle, lung, testis and liver.

Evidence on tissue expression from TISSUES for ZNF540 Gene

  • Nervous system(4.8)
  • Heart(4.2)
genes like me logo Genes that share expression patterns with ZNF540: view

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 , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia ZNF540 33 34
  • 99.55 (n)
cow
(Bos Taurus)
Mammalia ZNF383 34
  • 50 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 46 (a)
OneToMany
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

ENSEMBL:
Gene Tree for ZNF540 (if available)
TreeFam:
Gene Tree for ZNF540 (if available)

Paralogs for ZNF540 Gene

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 Variation AA Info Type
VAR_035586 A colorectal cancer sample p.Lys275Ile
rs1000033413 -- 37,549,428(+) T/G upstream_transcript_variant
rs1000104470 -- 37,556,768(+) G/A/T genic_upstream_transcript_variant, intron_variant
rs1000105307 -- 37,567,646(+) G/T genic_upstream_transcript_variant, intron_variant
rs1000112342 -- 37,612,782(+) G/A/C coding_sequence_variant, missense_variant

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

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

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)

Additional Variant Information for ZNF540 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZNF540

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

Disorders for ZNF540 Gene

Additional Disease Information for ZNF540

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 (Biochemical and biophysical research communications 2006) 3 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. 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
  4. Diagnostic exome sequencing in persons with severe intellectual disability. (PMID: 23033978) de Ligt J … Vissers LE (The New England journal of medicine 2012) 4 58
  5. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L … Andersson-Svahn H (Molecular & cellular proteomics : MCP 2008) 3 58

Products for ZNF540 Gene

Sources for ZNF540 Gene

Content
Loading form....