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ZNF540 Gene

protein-coding   GIFtS: 47
GCID: GC19P038086

Zinc Finger Protein 540

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Zinc Finger Protein 5401 2
Nbla105122
Putative Protein Product Of Nbla105122

External Ids:    HGNC: 253311   Entrez Gene: 1632552   Ensembl: ENSG000001718177   OMIM: 6139035   UniProtKB: Q8NDQ63   

Export aliases for ZNF540 gene to outside databases

Previous GC identifers: GC00U914377 GC19P042735 GC19P042736 GC19P038039 GC19P034535


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ZNF540 Gene:
ZNF540 (zinc finger protein 540) is a protein-coding gene. Diseases associated with ZNF540 include breast and colorectal cancer, and tonsillitis. GO annotations related to this gene include translation repressor activity, nucleic acid binding. An important paralog of this gene is ZNF334.

UniProtKB/Swiss-Prot: ZN540_HUMAN, Q8NDQ6
Function: May act as a transcriptional repressor




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the ZNF540 gene promoter:
         FOXJ2 (long isoform)   FOXJ2   POU6F1 (c2)   LCR-F1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): ZNF540 promoter sequence
   Search Chromatin IP Primers for ZNF540

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZNF540


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.12   Ensembl cytogenetic band:  19q13.12   HGNC cytogenetic band: 19q13.13

ZNF540 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZNF540 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P038086:  view genomic region     (about GC identifiers)

Start:
38,042,308 bp from pter      End:
38,105,000 bp from pter
Size:
62,693 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: ZN540_HUMAN, Q8NDQ6 (See protein sequence)
Recommended Name: Zinc finger protein 540  
Size: 660 amino acids; 77094 Da
Subunit: May interact with MVP
Sequence caution: Sequence=AAH17940.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential
poly-A sequence; Sequence=CAD97942.1; Type=Frameshift; Positions=580;
Secondary accessions: A0AVS5 A8K371 Q05D58 Q3LIC5 Q6ZN36 Q7Z3C8 Q86T31
Alternative splicing: 3 isoforms:  Q8NDQ6-1   Q8NDQ6-2   Q8NDQ6-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ZNF540: NX_Q8NDQ6

Explore proteomics data for ZNF540 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ZNF540 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001165696.1  NP_001165697.1  NP_689819.1  

    ENSEMBL proteins: 
     ENSP00000466274   ENSP00000467118   ENSP00000324598   ENSP00000467667   ENSP00000465503  
     ENSP00000468113   ENSP00000343768  
    Reactome Protein details: Q8NDQ6

    ZNF540 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ZNF: Zinc fingers, C2H2-type

    4 InterPro protein domains:
     IPR001909 Krueppel-associated_box
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q8NDQ6

    ProtoNet protein and cluster: Q8NDQ6

    1 Blocks protein domain: IPB001909 KRAB box

    UniProtKB/Swiss-Prot: ZN540_HUMAN, Q8NDQ6
    Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
    Similarity: Contains 17 C2H2-type zinc fingers
    Similarity: Contains 1 KRAB domain


    ZNF540 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ZN540_HUMAN, Q8NDQ6
    Function: May act as a transcriptional repressor

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000900translation repressor activity, nucleic acid binding IMP16815308
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity IBA--
    GO:0005515protein binding IPI16815308
         
    ZNF540 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for ZNF540:
     Downregulation of NF-kappaB pa 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ZNF540
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    hsa-mir-375 (MIRT019918)

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    SwitchGear 3'UTR luciferase reporter plasmidZNF540 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    ZN540_HUMAN, Q8NDQ6: Nucleus. Cytoplasm
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--
    GO:0043231intracellular membrane-bounded organelle IDA--

    ZNF540 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for ZNF540 About    
    See pathways by source

    SuperPathContained pathways About
    1Gene Expression
    Generic Transcription Pathway0.40
    Gene Expression0.40

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for ZNF540
        Generic Transcription Pathway



    ZNF540 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ZNF540
    Interactions:

        GeneGlobe Interaction Network for ZNF540

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0017148negative regulation of translation IMP16815308
    GO:0045892negative regulation of transcription, DNA-templated IDA16815308

    ZNF540 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for ZNF540 (ZN540)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for ZNF540 gene (3 alternative transcripts): 
    NM_001172225.2  NM_001172226.2  NM_152606.4  

    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000592533 ENST00000589117 ENST00000587220 ENST00000589857 ENST00000316433(uc002ogq.3 uc002ogu.3)
    ENST00000590588 ENST00000586134 ENST00000586792 ENST00000343599(uc010efq.3)
    ENST00000589285
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat ZNF540
      QuantiFast Probe-based Assays in human, mouse, rat ZNF540

    Selected AceView cDNA sequences (see all 133):

    CK430096 N89873 BX118256 AI023879 CR616392 AL518023 AI803971 BX117928 
    AL832687 NM_152606 AL832315 BC063448 CK821801 AK131388 BX647800 AA321768 
    AI032287 BX115985 BE219465 AA781724 AK122597 BX097888 AA905311 AL524892 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for ZNF540 (see all 6)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c · 5d · 5e
    SP1:                                -                                 
    SP2:                                -                                 
    SP3:                          -     -                                 
    SP4:                                                                  
    SP5:                    -           -                                 


    ECgene alternative splicing isoforms for ZNF540

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    ZNF540 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGGCACCTT
    ZNF540 Expression
    About this image


    ZNF540 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Pancreas (Endocrine System)
             Islets of Langerhans
    ZNF540 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ZNF540 Protein Expression

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

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of mammals.

    Orthologs for ZNF540 gene from Selected species (see all 3)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    oppossum
    (Monodelphis domestica)
    Mammalia --
    Uncharacterized protein
    46(a)
    1 → many
    Un(55789330-55802580)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZNF540 gene
    ZNF3342  ZNF4202  ZNF780A2  ZNF6652  ZNF72  ZNF232  ZNF33A2  RBAK2  
    ZNF7172  ZNF302  ZNF5732  ZNF33B2  ZNF2512  ZNF6052  ZNF842  ZNF1892  
    ZNF5712  ZNF6302  ZNF3372  ZNF2832  ZNF4042  ZNF1352  ZNF4842  ZNF122  
    ZNF3452  ZNF1842  ZNF6992  ZNF412  ZNF6152  ZNF4702  ZNF5692  
    Selected SIMAP similar genes for ZNF540 using alignment to 4 protein entries:     ZN540_HUMAN (see all proteins) (see all similar genes):
    POM121C    ZNF83    ZNF283    ZNF616    ZNF738    ZNF420
    ZNF232    ZFP90    ZNF614    ZNF818P    ZNF81    ZNF761
    MGC12518    ZNF350    ZNF529    ZNF826P    ZSCAN16    ZNF230

    ZNF540 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for ZNF540 (see all 357)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0355864
    A colorectal cancer sample4--see VAR_0355862 K I mis40--------
    rs796469981,2
    F--38087680(+) GGCATC/TTATTT 3 -- int11Minor allele frequency- T:0.03EA 120
    rs37950701,2
    C,F,H--38087769(-) GATAAT/CATACG 3 -- int15Minor allele frequency- C:0.02NS EA 526
    rs1865063851,2
    --38087782(+) AATAAA/GTAGCA 3 -- int10--------
    rs1914010611,2
    --38087932(+) CAGAAC/GTCAGA 3 -- int10--------
    rs1442824351,2
    C--38087939(+) CAGAT-/GTCTTG 3 -- int10--------
    rs15315491,2
    C,F,O,A,H--38088009(+) CATTGT/CAGAAC 3 -- int112Minor allele frequency- C:0.41NA WA CSA EA 512
    rs1442856721,2
    --38088032(+) TAAATA/CGCTAT 3 -- int10--------
    rs1452898681,2
    C--38088067(+) GTTGA-/TTTTTT 3 -- int10--------
    rs1139833131,2
    C--38088156(+) CTGCAG/AGGACC 3 -- int12Minor allele frequency- A:0.03NA 122

    HapMap Linkage Disequilibrium report for ZNF540 (38042308 - 38105000 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for ZNF540:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2718520CNV Deletion23290073
    esv2718521CNV Deletion23290073
    esv270543CNV Insertion20981092
    nsv2478CNV Loss18451855
    nsv833819CNV Gain17160897
    dgv1081e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 613903    OMIM disorders: --

    9 diseases for ZNF540:    
    About MalaCards
    breast and colorectal cancer    tonsillitis    neuroblastoma    intellectual disability
    cerebritis    colorectal cancer    thyroiditis    endotheliitis
    prostatitis


    ZNF540 for disorders           About GeneDecksing


    Export disorders for ZNF540 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for ZNF540 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with ZNF540)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel human zinc finger protein ZNF540 interacts with MVP and inhibits transcriptional activities of the ERK signal pathway. (PubMed id 16815308)1, 2 Xiang Z.... Li Y. (Biochem. Biophys. Res. Commun. 2006)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    5. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    6. Diagnostic exome sequencing in persons with severe intellectual disability. (PubMed id 23033978)2 de Ligt J.... Vissers L.E. (N. Engl. J. Med. 2012)
    7. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    8. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    9. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (Science 2006)
    10. Neuroblastoma oligo-capping cDNA project: toward the understanding of the genesis and biology of neuroblastoma. (PubMed id 12880961)2 Ohira M.... Nakagawara A. (Cancer Lett. 2003)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 163255 HGNC: 25331 AceView: ZNF540 Ensembl:ENSG00000171817 euGenes: HUgn163255
    ECgene: ZNF540 H-InvDB: ZNF540

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for ZNF540 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ZNF540 gene:
    Search GeneIP for patents involving ZNF540

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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