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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

ZNF542 Gene

pseudogene   GIFtS: 32
GCID: GC19P056880

Zinc Finger Protein 542

  Search for ZNF542
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Zinc Finger Protein 5421 2

External Ids:    HGNC: 253931   Entrez Gene: 1479472   Ensembl: ENSG000002402257   UniProtKB: Q5EBM43   
ORGUL members:         
NONCODE14:n406554 n346082 n405884      

Export aliases for ZNF542 gene to outside databases

Previous GC identifers: GC00U914380 GC19P061571 GC19U901000 GC19P053188


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for ZNF542 Gene: 
ZNF542 (zinc finger protein 542) is a pseudogene, and is affiliated with the lncRNA class. GO annotations related to this gene include DNA binding and zinc ion binding.

UniProtKB/Swiss-Prot: ZN542_HUMAN, Q5EBM4
Function: May be involved in transcriptional regulation




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.2  NT_011109.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZNF542 gene promoter:
         AREB6   PPAR-alpha   Ik-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for ZNF542

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZNF542


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

Entrez Gene cytogenetic band: 19q13.43   Ensembl cytogenetic band:  19q13.43   HGNC cytogenetic band: 19q13.43

ZNF542 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZNF542 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P056880:  view genomic region     (about GC identifiers)

Start:
56,879,468 bp from pter      End:
56,891,197 bp from pter
Size:
11,730 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for ZNF542

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: ZN542_HUMAN, Q5EBM4 (See protein sequence)
Recommended Name: Putative zinc finger protein 542  
Size: 170 amino acids; 19729 Da
Subcellular location: Nucleus (Probable)
Caution: Could be the product of a pseudogene
Sequence caution: Sequence=CAE45809.1; Type=Erroneous translation; Note=Wrong choice of CDS;
Secondary accessions: B3KUG2 B4DLV1 Q6N061

Explore the universe of human proteins at neXtProt for ZNF542: NX_Q5EBM4

ZNF542 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--

ZNF542 for ontologies           About GeneDecksing



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

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

Graphical View of Domain Structure for InterPro Entry Q5EBM4

ProtoNet protein and cluster: Q5EBM4

1 Blocks protein domain: IPB007086 C2H2-type zinc finger signature

UniProtKB/Swiss-Prot: ZN542_HUMAN, Q5EBM4
Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
Similarity: Contains 3 C2H2-type zinc fingers
Similarity: Contains 1 KRAB domain


ZNF542 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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:

     UniProtKB/Swiss-Prot Summary: ZN542_HUMAN, Q5EBM4
Function: May be involved in transcriptional regulation

     Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding IEA--
GO:0046872metal ion binding IEA--
     
ZNF542 for ontologies           About GeneDecksing


Phenotypes:
     1 GenomeRNAi human phenotype for ZNF542:
 Synthetic lethal with Ras 

Animal Models:
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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ZNF542

Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006351transcription, DNA-dependent IEA--
GO:0006355regulation of transcription, DNA-dependent IEA--

ZNF542 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
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Browse Tocris compounds for ZNF542 (ZN542)

Search CenterWatch for drugs/clinical trials and news about ZNF542

(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,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for ZNF542 gene: 
NM_194319.1  

Unigene Cluster for ZNF542:

Zinc finger protein 542
Hs.467326  [show with all ESTs]
Unigene Representative Sequence: NR_033418
12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000467807 ENST00000462524 ENST00000589844 ENST00000490123(uc010etj.3)
ENST00000468396 ENST00000488113 ENST00000495307(uc002qmu.4 uc010ygj.2 uc002qmv.4 uc010etk.3 uc010ygk.2)
ENST00000596094 ENST00000587341 ENST00000595222 ENST00000587208 ENST00000482727

miRNA
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                     Customized lentivirus expression plasmids for stable overexpression of ZNF542 
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Additional mRNA sequence: 

AK097128.1 AK130322.1 AK297170.1 AL833621.1 BC064603.1 BC089419.1 BX640680.1 BX647919.1 
NR_003127.2 NR_024055.2 NR_024056.2 NR_024057.2 NR_033418.1 

10 DOTS entries:

DT.210582  DT.97795561  DT.95295155  DT.101954865  DT.101975338  DT.310057  DT.100650742  DT.121490985 
DT.95153852  DT.121490977 

24/76 AceView cDNA sequences (see all 76):

CA389398 AI018813 BX378986 CD678891 AA868077 BI769075 AI143141 AI348456 
AI090827 AA286842 BU733698 CR622292 BP429366 BC064603 AL539099 BG682393 
AK130322 BX510277 BV179700 BX115685 AW576383 AA476530 AW503572 BX348289 

GeneLoc Exon Structure


(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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

ZNF542 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GTGGCACCCA
ZNF542 Expression
About this image


Genevestigator expression for ZNF542

SOURCE GeneReport for Unigene cluster: Hs.467326
    SABiosciences Custom PCR Arrays for ZNF542
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZNF542

(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)
About This Section
  --

ENSEMBL Gene Tree for ZNF542 (if available)
TreeFam Gene Tree for ZNF542 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for ZNF542 gene
18/134 SIMAP similar genes for ZNF542 using alignment to 1 protein entry:     ZN542_HUMAN(see all similar genes):
ZNF570    ZNF211    ZKSCAN1    ZIK1    ZNF112    ZNF782
ZNF83    ZKSCAN7    ZNF286B    ZNF33A    ZNF418    ZNF420
ZNF544    ZNF548    ZNF665    ZNF678    ZNF701    ZNF888

ZNF542 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/293 SNPs in ZNF542 are shown (see all 293)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1391053171,2
--56877593(+) GGATCA/CCGAGG 5 -- us2k10--------
rs711843541,2
C--56877792(-) GTTTCT/-TTTTT 5 -- us2k11Minor allele frequency- -:0.00NA 2
rs1831142851,2
--56878096(+) GCTGCA/CTGTGA 5 -- us2k10--------
rs1430155521,2
--56878121(+) ATTCAC/TGAACT 5 -- us2k10--------
rs347545891,2
C,F--56878140(+) CTTAAA/GCTCTT 5 -- us2k15Minor allele frequency- G:0.12NA WA 244
rs104133411,2
C,F,H--56878167(+) ctaagT/Cttata 5 -- us2k117Minor allele frequency- C:0.20NS EA NA CSA WA 1209
rs1170912871,2
C,F--56878175(+) ATATAT/CTATTT 5 -- us2k11Minor allele frequency- C:0.02EA 120
rs1879511521,2
--56878207(+) CCCTCC/TCACAA 5 -- us2k10--------
rs1905876591,2
--56878346(+) TTAACA/TCATTA 5 -- us2k10--------
rs1832964091,2
--56878428(+) TTTATA/TGATCA 5 -- us2k10--------

HapMap Linkage Disequilibrium report for ZNF542 (56879468 - 56891197 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for ZNF542:    About this table     
Variant IDTypeSubtypePubMed ID
nsv912516CNV Gain21882294

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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.)
About This Section
  --

(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)
About This Section

PubMed articles for ZNF542 gene integrated from 9 sources:
(articles sorted by number of sources associating them with ZNF542)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
  2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1 Gerhard D.S....Malek J. (2004)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 147947 HGNC: 25393 AceView: ZNF542 Ensembl:ENSG00000240225 euGenes: HUgn147947
ECgene: ZNF542 H-InvDB: ZNF542

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for ZNF542 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for ZNF542 gene:
Search GeneIP for patents involving ZNF542

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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 Gene Synthesis
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 Protein Production and Purification
 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZNF542
 Browse SwitchGear 3'UTR luciferase reporter plasmids for ZNF542
 Browse SwitchGear Promoter luciferase reporter plasmids for ZNF542
 Search ThermoFisher Antibodies for ZNF542
 Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat ZNF542
 inGenious Targeting Laboratory - Custom generated mouse model solutions for ZNF542
 inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for ZNF542
Customized:
 lentivirus for stable overexpression of ZNF542
 lentivirus expression plasmids for stable overexpression of ZNF542
 adenovirus for overexpression of ZNF542
 Search LSBio for Antibodies for ZNF542
Customized transgenic rodents for:
 Humanization
 Biomarker expression
 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
 Time-controlled gene expresssion
       
GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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transforming growth factor, beta 1
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