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

ZNF253 Gene

protein-coding   GIFtS: 44
GCID: GC19P019978

Zinc Finger Protein 253

(Previous name: zinc finger protein 411)
(Previous symbol: ZNF411)
  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)
About This Section

Aliases
Zinc Finger Protein 2531 2     BMZF-12 3
Zinc Finger Protein 4111 2 3     BMZF12 3
ZNF4111 2 3     DNA-Binding Protein2
Bone Marrow Zinc Finger 12 3     

External Ids:    HGNC: 134971   Entrez Gene: 562422   Ensembl: ENSG000002567717   OMIM: 6069545   UniProtKB: O753463   

Export aliases for ZNF253 gene to outside databases

Previous GC identifers: GC19U990224 GC19P020380 GC19P019821 GC19P019850


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

GeneCards Summary for ZNF253 Gene: 
ZNF253 (zinc finger protein 253) is a protein-coding gene. Diseases associated with ZNF253 include sertoli cell-only syndrome, and among its related super-pathways are Gene Expression. GO annotations related to this gene include DNA binding and zinc ion binding. An important paralog of this gene is ZNF85.

UniProtKB/Swiss-Prot: ZN253_HUMAN, O75346
Function: May function as a transcription factor. Seem to have a transcriptional repression activity




(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
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZNF253 gene promoter:
         AREB6   MEF-2A   AP-1   MEF-2   ATF-2   aMEF-2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZNF253 promoter sequence
   Search SABiosciences Chromatin IP Primers for ZNF253

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZNF253


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

Entrez Gene cytogenetic band: 19p13.11   Ensembl cytogenetic band:  19p13.11   HGNC cytogenetic band: 19p13.1

ZNF253 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZNF253 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P019978:  view genomic region     (about GC identifiers)

Start:
19,976,695 bp from pter      End:
20,005,483 bp from pter
Size:
28,789 bases      Orientation:
plus strand

(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: ZN253_HUMAN, O75346 (See protein sequence)
Recommended Name: Zinc finger protein 253  
Size: 499 amino acids; 57602 Da
Subcellular location: Nucleus (Probable)
Sequence caution: Sequence=AAH14148.2; Type=Erroneous initiation; Sequence=BAC11257.1; Type=Erroneous initiation;
Secondary accessions: A4FVA7 Q0P6G3 Q6P0L2 Q8NCA3 Q8NCF9
Alternative splicing: 2 isoforms:  O75346-1   O75346-2   

Explore the universe of human proteins at neXtProt for ZNF253: NX_O75346

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_O75346

  • ZNF253 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --
    REFSEQ proteins: NP_066385.2  
    ENSEMBL proteins: 
     ENSP00000467235   ENSP00000468720   ENSP00000347868  
    Reactome Protein details: O75346
    Human Recombinant Protein Products for ZNF253: 
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    Cloud-Clone Corp. Proteins for ZNF253 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus NAS--

    ZNF253 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 O75346

    ProtoNet protein and cluster: O75346

    2 Blocks protein domains:
    IPB001909 KRAB box
    IPB007086 C2H2-type zinc finger signature


    UniProtKB/Swiss-Prot: ZN253_HUMAN, O75346
    Similarity: Belongs to the krueppel C2H2-type zinc-finger protein family
    Similarity: Contains 11 C2H2-type zinc fingers
    Similarity: Contains 1 KRAB domain


    ZNF253 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: ZN253_HUMAN, O75346
    Function: May function as a transcription factor. Seem to have a transcriptional repression activity

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0008270zinc ion binding NAS10585455
    GO:0046872metal ion binding ----
         
    ZNF253 for ontologies           About GeneDecksing


    Animal Models:
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZNF253


    (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

    SuperPaths for ZNF253 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Generic Transcription Pathway
    Generic Transcription Pathway0.47
    Gene Expression0.47

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2        Reactome Pathways for ZNF253
        Generic Transcription Pathway
    Gene Expression



    ZNF253 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ZNF253

    2 Interacting proteins for ZNF253 (O753462, 3) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    LDOC1O957512, 3MINT-51631 MINT-51632 I2D: score=1 
    AKR1B1P151213I2D: score=1 
    About this table

    Gene Ontology (GO): 3 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 NAS10585455
    GO:0045892negative regulation of transcription, DNA-dependent NAS10585455

    ZNF253 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
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for ZNF253 (ZN253)

    Search CenterWatch for drugs/clinical trials and news about ZNF253 / ZN253

    (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 ZNF253 gene: 
    NM_021047.2  

    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000592725 ENST00000589717 ENST00000355650(uc002noj.3 uc002nok.3 uc002nol.3)
    ENST00000589668
    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmidZNF253 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for ZNF253
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat ZNF253
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat ZNF253
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat ZNF253

    24/57 AceView cDNA sequences (see all 57):

    BC065572 BF438321 AI867517 BC014148 BG504312 AK074872 AI694256 BU173345 
    AA359112 AA642366 BG142261 BU940607 BQ881665 BC022891 CB217123 BX419616 
    N41945 BU186714 BX090541 AA628456 BE881871 BG676762 AL596638 BX472765 

    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

    ZNF253 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGAAGAGGA
    ZNF253 Expression
    About this image


    Genevestigator expression for ZNF253

    UniProtKB/Swiss-Prot: ZN253_HUMAN, O75346
    Tissue specificity: Expressed in bone marrow and in monocytic and immature erythroid cell lines

        SABiosciences Custom PCR Arrays for ZNF253
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZNF253

    (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

    This gene was present in the common ancestor of chordates.

    Orthologs for ZNF253 gene from 1/4 species (see all 4)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    23(a)
    1 → many
    GL343733.1(125230-159240)
            Species with no ortholog for ZNF253

    ENSEMBL Gene Tree for ZNF253 (if available)
    TreeFam Gene Tree for ZNF253 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZNF253 gene
    ZNF852  ZNF4862  ZNF1952  ZNF7272  ZNF922  ZNF1002  ZNF7322  ZNF6752  
    ZNF1382  ZNF5062  ZNF662  ZNF2732  ZNF6952  ZNF6262  ZNF6802  ZNF4792  
    ZNF6822  ZNF4922  ZNF6762  ZNF6812  ZNF1412  ZNF7362  ZNF6792  ZNF2572  
    ZNF2672  ZNF2542  ZNF7372  ZNF982  ZNF7162  ZNF7142  ZNF5192  ZNF4302  
    ZNF7302  ZNF7082  ZNF1172  ZNF4312  ZNF902  ZNF7262  ZNF7282  
    18/541 SIMAP similar genes for ZNF253 using alignment to 2 protein entries:     ZN253_HUMAN (see all proteins) (see all similar genes):
    MGC12518    ZNF56    ZNF78L1    ZNF818P    ZNF66    ZNF738
    kr-znf3    ZNF737    ZNF273    ZNF492    DKFZp686M04222    ZNF232
    ZNF98    ZNF626    ZFS-5    ZFS-6    ZNF429    ZNF506

    ZNF253 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

    10/640 SNPs in ZNF253 are shown (see all 640)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs121042821,2
    C,H--19974727(+) cagctC/Ttgaat 1 -- us2k16Minor allele frequency- T:0.00NS EA NA 410
    rs121042841,2
    C,H--19974866(+) tctgtC/Ttaggc 1 -- us2k14Minor allele frequency- T:0.00NS EA 420
    rs1930568841,2
    --19975040(+) TCGCCC/TAGGCT 1 -- us2k10--------
    rs3762674691,2
    C--19975141(+) CTACA-/GCGCC 
     CGCCACC
    CGCCC
    1 -- us2k10--------
    rs1463622111,2
    C--19975490(+) AAGGT-/TTTA  
            
    TTTAT
    1 -- us2k10--------
    rs570877921,2
    C--19975491(+) TTTAT-/TTA   
      T
    /TTTA
    GTATT
    1 -- us2k10--------
    rs1506248471,2
    C--19975568(+) ATCTTC/GGCTCA 1 -- us2k10--------
    rs1391967211,2
    --19975659(+) ACGCCC/TGGGTA 1 -- us2k10--------
    rs126103901,2
    C,A,H--19975662(+) cccggC/Gtaatt 1 -- us2k10--------
    rs1476103751,2
    --19975749(+) CTCCTC/TAGCCT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ZNF253 (19976695 - 20005483 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for ZNF253:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2718296CNV Deletion23290073
    esv2718299CNV Deletion23290073
    esv2259143CNV Deletion18987734
    dgv550e201CNV Deletion23290073
    esv2718298CNV Deletion23290073
    dgv3791n71CNV Loss21882294
    nsv138332CNV Loss16902084
    dgv3792n71CNV Gain21882294
    nsv519535CNV Gain19592680

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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
    OMIM gene information: 606954    OMIM disorders: --

    2 diseases for ZNF253:    About MalaCards
    sertoli cell-only syndrome    

    1 disease from the University of Copenhagen DISEASES database for ZNF253:
    Sertoli cell-only syndrome

    ZNF253 for disorders           About GeneDecksing


    Export disorders for ZNF253 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)
    About This Section

    PubMed articles for ZNF253 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with ZNF253)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning of six novel Kruppel-like zinc finger genes from hematopoietic cells and identification of a novel transregulatory domain KRNB. (PubMed id 10585455)1, 2, 3 Han Z.-G.... Chen Z. (1999)
    2. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    3. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (2004)
    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. (2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    6. 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: 56242 HGNC: 13497 AceView: ZNF253 Ensembl:ENSG00000256771 euGenes: HUgn56242
    ECgene: ZNF253 H-InvDB: ZNF253

    (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 ZNF253 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 ZNF253 gene:
    Search GeneIP for patents involving ZNF253

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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
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