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ZXDB Gene

protein-coding   GIFtS: 43
GCID: GC0XP057634

Zinc Finger, X-Linked, Duplicated B

  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, X-Linked, Duplicated B1 2
ZNF9052
dJ83L6.12
Zinc Finger X-Linked Protein ZXDB2

External Ids:    HGNC: 131991   Entrez Gene: 1585862   Ensembl: ENSG000001984557   OMIM: 3002365   UniProtKB: P981693   

Export aliases for ZXDB gene to outside databases

Previous GC identifers: GC0XU990242 GC0XP055586 GC0XP056223 GC0XM056901 GC0XP056585 GC0XP057484 GC0XP054679


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for ZXDB Gene:
The ZXDB gene is one of a pair of duplicated zinc finger genes on chromosome Xp11.21 (Greig et al., 1993 (PubMed
8268913)); see also ZXDA (MIM 300235).(supplied by OMIM, Jul 2010)

GeneCards Summary for ZXDB Gene:
ZXDB (zinc finger, X-linked, duplicated B) is a protein-coding gene. Diseases associated with ZXDB include turner syndrome. GO annotations related to this gene include nucleic acid binding. An important paralog of this gene is ZXDA.

UniProtKB/Swiss-Prot: ZXDB_HUMAN, P98169
Function: Cooperates with CIITA to promote transcription of MHC class I and MHC class II genes (By similarity)




(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_000023.11  NC_018934.2  NT_011630.15  
Regulatory elements:
   Regulatory transcription factor binding sites in the ZXDB gene promoter:
         AREB6   PPAR-gamma1   Pax-5   AML1a   Nkx2-2   Lmo2   ARP-1   PPAR-gamma2   E47   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZXDB promoter sequence
   Search Chromatin IP Primers for ZXDB

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


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

Entrez Gene cytogenetic band: Xp11.21   Ensembl cytogenetic band:  Xp11.21   HGNC cytogenetic band: Xp11.1

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

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP057634:  view genomic region     (about GC identifiers)

Start:
57,618,269 bp from pter      End:
57,623,910 bp from pter
Size:
5,642 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: ZXDB_HUMAN, P98169 (See protein sequence)
Recommended Name: Zinc finger X-linked protein ZXDB  
Size: 803 amino acids; 84792 Da
Subunit: Self-associates. Interacts with ZXDC and CIITA (By similarity)
Secondary accessions: A8K151 Q9UBB3

Explore the universe of human proteins at neXtProt for ZXDB: NX_P98169

Explore proteomics data for ZXDB at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins: NP_009088.1  
    ENSEMBL proteins: 
     ENSP00000364023  

    ZXDB Human Recombinant Protein Products:

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    Cloud-Clone Corp. CLIAs for ZXDB


    (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

    3 InterPro protein domains:
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry P98169

    ProtoNet protein and cluster: P98169

    UniProtKB/Swiss-Prot: ZXDB_HUMAN, P98169
    Similarity: Belongs to the ZXD family
    Similarity: Contains 10 C2H2-type zinc fingers


    ZXDB 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: ZXDB_HUMAN, P98169
    Function: Cooperates with CIITA to promote transcription of MHC class I and MHC class II genes (By similarity)

         Genatlas biochemistry entry for ZXDB:
    zinc finger protein (C2H2 type),X linked,duplicated B

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0003676nucleic acid binding IEA--
    GO:0046872metal ion binding IEA--
         
    ZXDB for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ZXDB
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    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate ZXDB (see all 18):
    hsa-miR-124* hsa-miR-1178 hsa-miR-3673 hsa-miR-361-5p hsa-miR-578 hsa-miR-138-2* hsa-miR-223 hsa-miR-3658
    SwitchGear 3'UTR luciferase reporter plasmidZXDB 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat ZXDB

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    Browse Sino Biological Human cDNA Clones
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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
    ZXDB_HUMAN, P98169: Nucleus (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    ZXDB 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 ZXDB
    Interactions:

        Search GeneGlobe Interaction Network for ZXDB

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for ZXDB (ENSP000003640234) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0008150biological_process ND--

    ZXDB 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 ZXDB



    (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,
    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 ZXDB gene: 
    NM_007157.3  

    Unigene Cluster for ZXDB:

    Zinc finger, X-linked, duplicated B
    Hs.156257  [show with all ESTs]
    Unigene Representative Sequence: NM_007157
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000374888(uc004dvd.3)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate ZXDB (see all 18):
    hsa-miR-124* hsa-miR-1178 hsa-miR-3673 hsa-miR-361-5p hsa-miR-578 hsa-miR-138-2* hsa-miR-223 hsa-miR-3658
    SwitchGear 3'UTR luciferase reporter plasmidZXDB 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for ZXDB
    Predesigned siRNA for gene silencing in human, mouse, rat ZXDB
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    GenScript: all cDNA clones in your preferred vector: ZXDB (NM_007157)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat ZXDB
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat ZXDB
      QuantiTect SYBR Green Assays in human, mouse, rat ZXDB
      QuantiFast Probe-based Assays in human, mouse, rat ZXDB

    Additional mRNA sequence: 

    AK124513.1 AK289766.1 L14788.1 

    3 DOTS entries:

    DT.95120992  DT.109565  DT.101981193 

    Selected AceView cDNA sequences (see all 48):

    AI868484 BM701206 AI335812 AW150690 BU076306 BG563527 Z41985 AA400709 
    L14788 AA400675 NM_007157 BE044323 AI360269 CA433211 BE677308 BM674105 
    BF132264 BU076572 BG403766 BF114955 AK124513 BM069864 BF981502 BU173052 

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

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

    ZXDB Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.156257

    UniProtKB/Swiss-Prot: ZXDB_HUMAN, P98169
    Tissue specificity: May be expressed in brain, heart, kidney, liver, lung, muscle and placenta

        Custom PCR Arrays for ZXDB
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZXDB

    (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 animals and fungi.

    Orthologs for ZXDB gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Zxdb1 , 5 zinc finger, X-linked, duplicated B1, 5 82.29(n)1
    82.12(a)1
      X (41.68 cM)5
    6681661  NM_001081473.11  NP_001074942.11 
     947245695 
    chicken
    (Gallus gallus)
    Aves --
    --
    50(a)
    1 → many
    12(10656611-10666374)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    45(a)
    1 → many
    2(169122892-169230882)
    zebrafish
    (Danio rerio)
    Actinopterygii ZXDC6
    ZXD family zinc finger C
    26(a)
    1 → many
    6(23710138-23727533) ENSDARG00000052351
    fruit fly
    (Drosophila melanogaster)
    Insecta CG96096
    --
    22(a)
    1 → many
    X(16679398-16681011)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SWI56
    ACE26
    Transcription factor that activates transcription ...
    Transcription factor required for septum destructi...
    7(a)
    7(a)
    many ↔ many
    many ↔ many
    IV(748613-750742) YDR146C
    XII(404510-406822) YLR131C


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZXDB gene
    ZXDA2  GTF3A2  ZXDC2  
    4 SIMAP similar genes for ZXDB using alignment to 1 protein entry:     ZXDB_HUMAN:
    ZXDA    ZXDC    ZNF32    ZNF323

    ZXDB 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 ZXDB (see all 113)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1416847441,2
    Cuntested157616848(+) GGATGA/C/TGTACA 1 -- us2k10--------
    rs1922009711,2
    --57616301(+) AAACAC/TGAAAA 1 -- us2k10--------
    rs1844914601,2
    --57616344(+) CCCACA/CAGTAG 1 -- us2k10--------
    rs30152761,2
    C,F,A,H--57616441(-) ttgggC/Gaagct 1 -- us2k15Minor allele frequency- G:0.11NS EA WA 420
    rs1379821271,2
    C--57616465(+) CAATTG/TGGCAT 1 -- us2k10--------
    rs29822521,2
    C,F,A,H--57617016(-) CACCTG/ATGTAA 1 -- us2k113Minor allele frequency- A:0.20NS EA NA WA CSA 1367
    rs1873322361,2
    --57617039(+) AAATAA/GTCTAA 1 -- us2k10--------
    rs1928647281,2
    --57617212(+) CATTAA/CAAGAG 1 -- us2k10--------
    rs1844772861,2
    --57617567(+) GTGCTC/GGAGAA 1 -- us2k10--------
    rs1895177641,2
    C--57618070(+) AACATA/GTCTAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ZXDB (57618269 - 57623910 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for ZXDB:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv6919CNV Insertion18451855
    dgv514n21CNV Gain19592680

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

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 300236    OMIM disorders: --

    1 disease for ZXDB:    
    About MalaCards
    turner syndrome

    1 disease from the University of Copenhagen DISEASES database for ZXDB:
    Turner syndrome

    ZXDB for disorders           About GeneDecksing


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

    1. Duplicated zinc finger protein genes on the proximal short arm of the human X chromosome: isolation, characterization and X-inactivation studies. (PubMed id 8268913)1, 2, 3 Greig G.M.... Willard H.F. (Hum. Mol. Genet. 1993)
    2. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    3. Genome-wide association study identifies loci affecting blood copper, selenium and zinc. (PubMed id 23720494)1 Evans D.M....Whitfield J.B. (Hum. Mol. Genet. 2013)
    4. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (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: 158586 HGNC: 13199 AceView: ZXDB Ensembl:ENSG00000198455 euGenes: HUgn158586
    ECgene: ZXDB H-InvDB: ZXDB

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for ZXDB 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 ZXDB gene:
    Search GeneIP for patents involving ZXDB

    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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