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ZNF396 Gene

protein-coding   GIFtS: 46
GCID: GC18M032946

Zinc Finger Protein 396

Microbiology & Infectious Diseases Congress
  See related disease
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 3961 2
Zinc Finger And SCAN Domain-Containing Protein 142 3
ZSCAN142 3

External Ids:    HGNC: 188241   Entrez Gene: 2528842   Ensembl: ENSG000001864967   OMIM: 6096005   UniProtKB: Q96N953   

Export aliases for ZNF396 gene to outside databases

Previous GC identifers: GC18M032978 GC18M032766 GC18M032721 GC18M031198 GC18M031200 GC18M029806


(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 ZNF396 Gene:
ZNF396 (zinc finger protein 396) is a protein-coding gene. Diseases associated with ZNF396 include prostatitis. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity. An important paralog of this gene is ZNF446.

UniProtKB/Swiss-Prot: ZN396_HUMAN, Q96N95
Function: Isoform 1 and isoform 2 act as DNA-dependent transcriptional repressors




(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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RefSeq DNA sequence:
NC_000018.10  NT_010966.15  NC_018929.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZNF396 gene promoter:
         Max1   GATA-3   MyoD   GATA-2   E47   PPAR-alpha   AREB6   Nkx6-1   Cart-1   Msx-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZNF396 promoter sequence
   Search Chromatin IP Primers for ZNF396

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ZNF396


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

Entrez Gene cytogenetic band: 18q12   Ensembl cytogenetic band:  18q12.2   HGNC cytogenetic band: 18p12

ZNF396 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZNF396 gene location

GeneLoc information about chromosome 18         GeneLoc Exon Structure

GeneLoc location for GC18M032946:  view genomic region     (about GC identifiers)

Start:
32,946,661 bp from pter      End:
32,957,301 bp from pter
Size:
10,641 bases      Orientation:
minus 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: ZN396_HUMAN, Q96N95 (See protein sequence)
Recommended Name: Zinc finger protein 396  
Size: 335 amino acids; 38612 Da
Subunit: Isoforms 1 and 2 can both homo- and hetero-associate
Secondary accessions: A1L3V0 Q8NF98 Q8TD80
Alternative splicing: 3 isoforms:  Q96N95-1   Q96N95-2   Q96N95-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ZNF396: NX_Q96N95

Explore proteomics data for ZNF396 at MOPED


See ZNF396 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_665699.1  
ENSEMBL proteins: 
 ENSP00000302310   ENSP00000466500   ENSP00000467275   ENSP00000468381   ENSP00000465440  

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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

5 InterPro protein domains:
 IPR008916 Retrov_capsid_C
 IPR003309 Tscrpt_reg_SCAN
 IPR015880 Znf_C2H2-like
 IPR013087 Znf_C2H2/integrase_DNA-bd
 IPR007087 Znf_C2H2

Graphical View of Domain Structure for InterPro Entry Q96N95

ProtoNet protein and cluster: Q96N95

1 Blocks protein domain: IPB003309 Transcriptional regulator SCAN

UniProtKB/Swiss-Prot: ZN396_HUMAN, Q96N95
Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
Similarity: Contains 3 C2H2-type zinc fingers
Similarity: Contains 1 SCAN box domain


ZNF396 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: ZN396_HUMAN, Q96N95
Function: Isoform 1 and isoform 2 act as DNA-dependent transcriptional repressors

     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding IEA--
GO:0003700sequence-specific DNA binding transcription factor activity IEA--
GO:0046872metal ion binding IEA--
     
ZNF396 for ontologies           About GeneDecksing


Animal Models:
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SwitchGear 3'UTR luciferase reporter plasmidZNF396 3' UTR sequence
Inhib. RNA
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Predesigned siRNA for gene silencing in human, mouse, rat ZNF396

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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
ZN396_HUMAN, Q96N95: Isoform 1: Nucleus
ZN396_HUMAN, Q96N95: Isoform 2: Nucleus. Cytoplasm
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--
GO:0005737cytoplasm IEA--

ZNF396 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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ZNF396
Interactions:

    Search GeneGlobe Interaction Network for ZNF396

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for ZNF396 (Q96N953 ENSP000003023104) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
ZNF397Q8NF993, ENSP000003315774I2D: score=1 STRING: ENSP00000331577
ZSCAN1Q8NBB43, ENSP000002823264I2D: score=1 STRING: ENSP00000282326
About this table

Gene Ontology (GO): 2 biological process terms:    About this table

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

ZNF396 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 ZNF396 (ZN396)



(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 ZNF396 gene: 
NM_145756.2  

Unigene Cluster for ZNF396:

Zinc finger protein 396
Hs.351005  [show with all ESTs]
Unigene Representative Sequence: AK055775
6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000306346(uc010xcf.1) ENST00000589332 ENST00000586585 ENST00000586687
ENST00000585522 ENST00000587422
Congresses - knowledge worth sharing:
European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

miRNA
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Selected qRT-PCR Assays for microRNAs that regulate ZNF396 (see all 14):
hsa-miR-1290 hsa-miR-187* hsa-miR-1283 hsa-miR-516b hsa-miR-4251 hsa-miR-29a hsa-miR-29c hsa-miR-3647-3p
SwitchGear 3'UTR luciferase reporter plasmidZNF396 3' UTR sequence
Inhib. RNA
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  QuantiFast Probe-based Assays in human, mouse, rat ZNF396

Additional mRNA sequence: 

AF492004.3 AF533251.2 AK055775.1 BC130288.1 BC136314.1 

4 DOTS entries:

DT.75173220  DT.95362071  DT.97835087  DT.97798153 

20 AceView cDNA sequences:

BC031580 AF533251 BM713411 BC036765 F04323 BM546448 H38834 NM_145756 
AI950122 AF492004 AK055775 AA852801 AV753241 AA019834 AA909548 H38591 
F08086 N20629 BI517675 N29000 

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™, 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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ZNF396 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GCAACGTGTA
ZNF396 Expression
About this image

ZNF396 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

ZNF396 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.351005

UniProtKB/Swiss-Prot: ZN396_HUMAN, Q96N95
Tissue specificity: Expressed strongly in liver, moderately in skeletal muscle and weakly in kidney, pancreas,
spleen and prostate

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In Situ
Assay Products:
 

 
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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 ZNF396 gene from Selected species (see all 3)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
dog
(Canis familiaris)
Mammalia ZNF3961 zinc finger protein 396 81.22(n)
70.78(a)
  100684525  XM_005622881.1  XP_005622938.1 


ENSEMBL Gene Tree for ZNF396 (if available)
TreeFam Gene Tree for ZNF396 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for ZNF396 gene
ZNF4462  ZSCAN92  ZKSCAN12  ZNF3972  ZNF5002  ZNF2132  ZNF2322  ZSCAN302  
ZNF1742  ZNF32  ZKSCAN42  ZSCAN122  ZNF3942  ZSCAN212  ZSCAN232  ZNF1652  
ZSCAN162  ZKSCAN82  ZSCAN222  ZSCAN312  ZNF242  ZKSCAN32  ZNF182  
Selected SIMAP similar genes for ZNF396 using alignment to 3 protein entries:     ZN396_HUMAN (see all proteins) (see all similar genes):
ZNF483    LOC100128510    ZSCAN29    ZNF213    SCAND1    ZSCAN18
ZNF323    ZSCAN30    ZNF197    ZSCAN23    ZSCAN10    ZSCAN31
ZKSCAN8    ZNF202    ZNF394    ZNF444    ZNF137P    ZNF24

ZNF396 for paralogs           About GeneDecksing


1 Pseudogenes.org Pseudogene for ZNF396
PGOHUM00000234666


(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 ZNF396 (see all 294)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 18 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs734285841,2
C--32946174(+) TTCCCT/CCTAGA 1 -- ds50013Minor allele frequency- C:0.09WA NA EA 242
rs29093381,2
C,F,A,H--32946200(+) CCCTAA/CCAGAC 1 -- ds500121Minor allele frequency- C:0.24NA NS EA WA CSA 1117
rs1129989241,2
C,F--32946206(+) CAGACG/ACAGTT 1 -- ds50011Minor allele frequency- A:0.50WA 2
rs1911235071,2
--32946328(+) CAGCTC/TTCTCG 1 -- ds50010--------
rs1835896231,2
--32946374(+) CAGTCA/GTCATT 1 -- ds50010--------
rs80950541,2
C,F--32946451(+) AACCAT/CCAAAG 1 -- ds50014Minor allele frequency- C:0.45NA WA 124
rs176464681,2
C,F--32946758(+) TTATAT/AAAACT 1 -- ut31 ese311Minor allele frequency- A:0.22NA WA EA 498
rs1404784021,2
--32946766(+) ACTAGC/TACCAT 1 -- ut310--------
rs99647781,2
C--32946854(+) TTAGAC/TGATAT 1 -- ut314Minor allele frequency- T:0.02NA WA 258
rs99647901,2
C,F,H--32946885(+) GGAAAC/TACTCA 1 -- ut3115Minor allele frequency- T:0.09NS EA NA WA 1428

HapMap Linkage Disequilibrium report for ZNF396 (32946661 - 32957301 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for ZNF396:    About this table    
Variant IDTypeSubtypePubMed ID
esv2660816CNV Deletion23128226

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing ZNF396
DNA2.0 Custom Variant and Variant Library Synthesis for ZNF396

(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: 609600    OMIM disorders: --

1 disease for ZNF396:    About MalaCards
prostatitis


ZNF396 for disorders           About GeneDecksing


Export disorders for ZNF396 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 ZNF396 gene integrated from 10 sources:
(articles sorted by number of sources associating them with ZNF396)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  2. Identification and characterization of two novel human SCAN domain- containing zinc finger genes ZNF396 and ZNF397. (PubMed id 12801647)1, 2 Wu Y.... Zhao S. (Gene 2003)
  3. An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)1 Ravasi T....Hayashizaki Y. (Cell 2010)
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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)
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Entrez Gene: 252884 HGNC: 18824 AceView: ZNF396 Ensembl:ENSG00000186496 euGenes: HUgn252884
ECgene: ZNF396 H-InvDB: ZNF396

(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 ZNF396 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 ZNF396 gene:
Search GeneIP for patents involving ZNF396

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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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