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Aliases for ZNF541 Gene

Aliases for ZNF541 Gene

  • Zinc Finger Protein 541 2 3 5

External Ids for ZNF541 Gene

Previous GeneCards Identifiers for ZNF541 Gene

  • GC00U914378
  • GC19M052716
  • GC19M052717
  • GC19M048023
  • GC19M044451

Summaries for ZNF541 Gene

GeneCards Summary for ZNF541 Gene

ZNF541 (Zinc Finger Protein 541) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include chromatin binding. An important paralog of this gene is TRERF1.

UniProtKB/Swiss-Prot for ZNF541 Gene

  • Component of some chromatin remodeling multiprotein complex that plays a role during spermatogenesis.

Additional gene information for ZNF541 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 ZNF541 Gene

Genomics for ZNF541 Gene

GeneHancer (GH) Regulatory Elements for ZNF541 Gene

Promoters and enhancers for ZNF541 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
GH19I047573 Enhancer 0.9 FANTOM5 Ensembl ENCODE 552.7 -0.2 -176 0.8 E2F1 L3MBTL2 NRF1 MGA ZNF541 SLC8A2 GC19P047588
GH19I047607 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 16.2 -37.8 -37831 6.9 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B ZNF207 ZNF143 BICRA ZNF541 ZC3H4 MEIS3 PRKD2 CCDC9 LIG1 KPTN ENSG00000268746 ENSG00000277383
GH19I047598 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 15.9 -27.0 -26982 4.2 HDGF PKNOX1 SMAD1 FOXA2 ARNT ARID4B SIN3A ZNF2 YY1 SLC30A9 ZNF541 NAPA NOP53 SNORD23 BBC3 BICRA INAFM1 GC19P047605 GC19P047592
GH19I047657 Enhancer 1.4 Ensembl ENCODE dbSUPER 11.4 -90.0 -90025 10.6 PKNOX1 ATF1 FOXA2 MLX ARNT SIN3A BRCA1 YY1 ZNF121 ELK1 ENSG00000278999 BICRA NOP53 ZC3H4 ZNF541 SNORD23 SULT2A1 GRWD1 BICRA-AS1 ENSG00000268746
GH19I047496 Enhancer 1.1 ENCODE dbSUPER 11.6 +75.6 75592 1.9 HDAC1 PKNOX1 ATF1 ARNT TCF12 ZNF766 GATA2 CREM ZBTB2 NCOA1 MEIS3 ZNF541 BICRA TMEM143 ENSG00000279861 NAPA-AS1 NAPA GC19M047497
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZNF541 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZNF541 gene promoter:

Genomic Locations for ZNF541 Gene

Genomic Locations for ZNF541 Gene
52,554 bases
Minus strand

Genomic View for ZNF541 Gene

Genes around ZNF541 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNF541 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNF541 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZNF541 Gene

Proteins for ZNF541 Gene

  • Protein details for ZNF541 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger protein 541
    Protein Accession:
    Secondary Accessions:
    • Q8NDK8

    Protein attributes for ZNF541 Gene

    1346 amino acids
    Molecular mass:
    145587 Da
    Quaternary structure:
    • Interacts with DNTTIP1 (PubMed:21573134). Identified in a complex with KCDT19, HDAC1 and HSPA2 (By similarity). Component of a histone deacetylase complex containing DNTTIP1, ZNF541, HDAC1 and HDAC2 (PubMed:21573134).
    • Sequence=AAI01051.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI01052.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI01053.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI01054.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAB66780.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAD38720.2; Type=Frameshift; Positions=473; Evidence={ECO:0000305};

    Alternative splice isoforms for ZNF541 Gene


neXtProt entry for ZNF541 Gene

Post-translational modifications for ZNF541 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ZNF541 Gene

Domains & Families for ZNF541 Gene

Gene Families for ZNF541 Gene

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

Suggested Antigen Peptide Sequences for ZNF541 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZNF541: view

No data available for UniProtKB/Swiss-Prot for ZNF541 Gene

Function for ZNF541 Gene

Molecular function for ZNF541 Gene

UniProtKB/Swiss-Prot Function:
Component of some chromatin remodeling multiprotein complex that plays a role during spermatogenesis.

Phenotypes From GWAS Catalog for ZNF541 Gene

Gene Ontology (GO) - Molecular Function for ZNF541 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IBA --
GO:0008134 transcription factor binding IBA --
GO:0044212 transcription regulatory region DNA binding IBA --
genes like me logo Genes that share ontologies with ZNF541: view
genes like me logo Genes that share phenotypes with ZNF541: view

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for ZNF541 Gene

Localization for ZNF541 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNF541 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 ZNF541 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZNF541 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000118 histone deacetylase complex ISS --
GO:0005634 nucleus IEA,ISS --
GO:0005667 transcription factor complex IBA --
genes like me logo Genes that share ontologies with ZNF541: view

Pathways & Interactions for ZNF541 Gene

SuperPathways for ZNF541 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZNF541 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA --
GO:0007275 multicellular organism development IEA --
GO:0007283 spermatogenesis IEA --
genes like me logo Genes that share ontologies with ZNF541: view

No data available for Pathways by source and SIGNOR curated interactions for ZNF541 Gene

Drugs & Compounds for ZNF541 Gene

No Compound Related Data Available

Transcripts for ZNF541 Gene

Unigene Clusters for ZNF541 Gene

Zinc finger protein 541:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZNF541 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: - -
SP2: -

Relevant External Links for ZNF541 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZNF541 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZNF541 Gene

mRNA differential expression in normal tissues according to GTEx for ZNF541 Gene

This gene is overexpressed in Testis (x30.1).

Protein differential expression in normal tissues from HIPED for ZNF541 Gene

This gene is overexpressed in Pancreatic juice (40.0) and Heart (27.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ZNF541 Gene

Protein tissue co-expression partners for ZNF541 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZNF541 Gene:


SOURCE GeneReport for Unigene cluster for ZNF541 Gene:

genes like me logo Genes that share expression patterns with ZNF541: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZNF541 Gene

Orthologs for ZNF541 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZNF541 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZNF541 33 34
  • 99.23 (n)
(Canis familiaris)
Mammalia ZNF541 33 34
  • 84.17 (n)
(Bos Taurus)
Mammalia ZNF541 33 34
  • 81.68 (n)
(Rattus norvegicus)
Mammalia Zfp541 33
  • 79.77 (n)
(Mus musculus)
Mammalia Zfp541 33 16 34
  • 77.94 (n)
(Monodelphis domestica)
Mammalia ZNF541 34
  • 71 (a)
(Gallus gallus)
Aves ZNF541 34
  • 33 (a)
(Anolis carolinensis)
Reptilia ZNF541 34
  • 41 (a)
(Danio rerio)
Actinopterygii ZNF541 34
  • 22 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG16779 34
  • 6 (a)
(Caenorhabditis elegans)
Secernentea saeg-1 34
  • 11 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 24 (a)
Species where no ortholog for ZNF541 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)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for ZNF541 Gene

Gene Tree for ZNF541 (if available)
Gene Tree for ZNF541 (if available)

Paralogs for ZNF541 Gene

Paralogs for ZNF541 Gene

(14) SIMAP similar genes for ZNF541 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with ZNF541: view

Variants for ZNF541 Gene

Sequence variations from dbSNP and Humsavar for ZNF541 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
VAR_035717 A breast cancer sample p.Ser712Leu
rs386834267 uncertain-significance, not provided 47,544,921(-) C/T coding_sequence_variant, intron_variant, non_coding_transcript_variant, synonymous_variant
rs1000016070 -- 47,542,841(-) A/G intron_variant
rs1000097108 -- 47,547,629(-) G/C intron_variant
rs1000200464 -- 47,558,358(-) G/T genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for ZNF541 Gene

Variant ID Type Subtype PubMed ID
esv2758765 CNV loss 17122850
nsv1056887 CNV gain 25217958
nsv1131434 CNV deletion 24896259
nsv428366 CNV loss 18775914
nsv579888 CNV gain 21841781

Variation tolerance for ZNF541 Gene

Gene Damage Index Score: 8.75; 86.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZNF541 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZNF541 Gene

Disorders for ZNF541 Gene

Additional Disease Information for ZNF541

No disorders were found for ZNF541 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZNF541 Gene

Publications for ZNF541 Gene

  1. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4 58
  2. 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
  3. 19q13.32 microdeletion syndrome: three new cases. (PMID: 25230004) Castillo A … Graham JM (European journal of medical genetics 2014) 3 58
  4. Nuclear cGMP-dependent kinase regulates gene expression via activity-dependent recruitment of a conserved histone deacetylase complex. (PMID: 21573134) Hao Y … Mak HY (PLoS genetics 2011) 4 58
  5. The consensus coding sequences of human breast and colorectal cancers. (PMID: 16959974) Sjöblom T … Velculescu VE (Science (New York, N.Y.) 2006) 4 58

Products for ZNF541 Gene

Sources for ZNF541 Gene

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