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ZACN Gene

protein-coding   GIFtS: 46
GCID: GC17P074075

Zinc Activated Ligand-Gated Ion Channel

(Previous names: ligand-gated ion channel, zinc activated 1)
(Previous symbol: LGICZ1)
  See ZACN-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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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Zinc Activated Ligand-Gated Ion Channel1 2     Ligand-Gated Ion-Channel Receptor L22 3
LGICZ11 2 3 5     LGICZ2 3
L22 3 5     ZAC12
ZAC2 3 5     Ligand-Gated Ion Channel Subunit2
Ligand-Gated Ion Channel, Zinc Activated 11 2     Zinc Activated Ligand-Gated Ion Channel 12
Ligand-Gated Ion Channel Zinc-Activated 12 3     Zinc-Activated Ligand-Gated Ion Channel2

External Ids:    HGNC: 295041   Entrez Gene: 3531742   Ensembl: ENSG000001869197   OMIM: 6109355   UniProtKB: Q401N23   
ORGUL members:         

Export aliases for ZACN gene to outside databases

Previous GC identifers: GC17P071588 GC17P069504


(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 ZACN Gene:
LGICZ1 is a zinc-activated ligand-gated ion channel that defines a new subgroup of the cysteine-loop superfamily
of ligand-gated ion channels (Davies et al., 2003 (PubMed 12381728)).(supplied by OMIM, Mar 2008)

GeneCards Summary for ZACN Gene:
ZACN (zinc activated ligand-gated ion channel) is a protein-coding gene. Diseases associated with ZACN include transient neonatal diabetes mellitus, and idiopathic generalized epilepsy. GO annotations related to this gene include extracellular ligand-gated ion channel activity. An important paralog of this gene is HTR3E.

UniProtKB/Swiss-Prot: ZACN_HUMAN, Q401N2
Function: Zinc-activated ligand-gated ion channel

Gene Wiki entry for ZACN (Zinc-activated ion channel) Gene


(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 ZACN gene promoter:
         USF1   FAC1   USF-1   RREB-1   MyoD   YY1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidZACN promoter sequence
   Search Chromatin IP Primers for ZACN

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


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

Entrez Gene cytogenetic band: 17q25.3   Ensembl cytogenetic band:  17q25.1   HGNC cytogenetic band: 17q25.3

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

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P074075:  view genomic region     (about GC identifiers)

Start:
74,068,042 bp from pter      End:
74,079,747 bp from pter
Size:
11,706 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: ZACN_HUMAN, Q401N2 (See protein sequence)
Recommended Name: Zinc-activated ligand-gated ion channel precursor  
Size: 412 amino acids; 45816 Da
Miscellaneous: The mouse and rat orthologous proteins do not exist
Caution: It is uncertain whether Met-1 or Met-2 is the initiator
Sequence caution: Sequence=AAI10598.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=AAO20969.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=EAW89365.1;
Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: Q2TB29 Q6ZWK3 Q86YW4
Alternative splicing: 3 isoforms:  Q401N2-1   Q401N2-2   Q401N2-3   (No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for ZACN: NX_Q401N2

Explore proteomics data for ZACN at MOPED

Post-translational modifications: 

  • Glycosylated1
  • Glycosylation2 at Asn41, Asn55, Asn99, Asn170

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

    REFSEQ proteins: NP_851321.2  
    ENSEMBL proteins: 
     ENSP00000334854   ENSP00000397489   ENSP00000391936   ENSP00000376291  

    ZACN Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for ZACN

     
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    Search eBioscience for ELISAs for ZACN 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ZACN: Ligand-gated ion channels / Zinc activated channels

    IUPHAR Guide to PHARMACOLOGY protein family classification: ZAC
    ZAC

    5 InterPro protein domains:
     IPR027361 Acetylcholine_rcpt_TM
     IPR018000 Neurotransmitter_ion_chnl_CS
     IPR006201 Neur_channel
     IPR006202 Neur_chan_lig-bd
     IPR006029 Neurotrans-gated_channel_TM

    Graphical View of Domain Structure for InterPro Entry Q401N2

    ProtoNet protein and cluster: Q401N2

    1 Blocks protein domain: IPB006201 Neurotransmitter-gated ion-channel

    UniProtKB/Swiss-Prot: ZACN_HUMAN, Q401N2
    Similarity: Belongs to the ligand-gated ion channel (TC 1.A.9) family


    Find genes that share domains with ZACN           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ZACN_HUMAN, Q401N2
    Function: Zinc-activated ligand-gated ion channel

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005230extracellular ligand-gated ion channel activity IEA--
    GO:0008270zinc ion binding IC12381728
         
    Find genes that share ontologies with ZACN           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for ZACN
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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
    ZACN_HUMAN, Q401N2: Cell membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    endoplasmic reticulum1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IDA16083862
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with ZACN           About GenesLikeMe


    (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 ZACN
    Interactions:

        Search GeneGlobe Interaction Network for ZACN

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport ----
    GO:0006811ion transport ----
    GO:0010043response to zinc ion IDA12381728

    Find genes that share ontologies with ZACN           About GenesLikeMe



    (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 ZACN

    2 IUPHAR Ligands for ZACN (ZAC )    About this table
    LigandTypeActionAffinityPubmed IDs
    (+)-tubocurarine
    AntagonistAntagonist5.212381728
    Zn2+
    AgonistAgonist3.312381728

    3 Novoseek inferred chemical compound relationships for ZACN gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    potassium 33.9 1 14657415 (1)
    calcium 31.7 2 14657414 (1), 18702192 (1)
    sodium 21 1 14657413 (1)



    Find genes that share compounds with ZACN           About GenesLikeMe



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for ZACN gene: 
    NM_180990.3  

    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000591500 ENST00000524242 ENST00000334586 ENST00000425015(uc002jqn.2 uc002jqo.2 uc010dgu.2)
    ENST00000421794 ENST00000590045 ENST00000392503
    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat ZACN
      QuantiFast Probe-based Assays in human, mouse, rat ZACN

    6 AceView cDNA sequences:

    AK122638 NM_180990 AF512521 AW263938 W05282 N75473 

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

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

    ZACN Protein Expression

    UniProtKB/Swiss-Prot: ZACN_HUMAN, Q401N2
    Tissue specificity: Detected in pancreas, brain, liver, placenta, trachea, kidney, spinal cord, stomach and fetal
    brain. In the adult brain region expression is detected in the hippocampus, striatum, amygdala and thalamus

        Custom PCR Arrays for ZACN
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ZACN

    (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 chordates.

    Orthologs for ZACN gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    dog
    (Canis familiaris)
    Mammalia ZACN1 zinc activated ligand-gated ion channel 82.69(n)
    78.15(a)
      483326  NM_001010955.1  NP_001010955.1 
    chicken
    (Gallus gallus)
    Aves ZACN6
    zinc activated ligand-gated ion channel
    15(a)
    1 ↔ 1
    18(10892021-10897084)
    lizard
    (Anolis carolinensis)
    Reptilia ZACN6
    zinc activated ligand-gated ion channel
    40(a)
    1 ↔ 1
    2(113110404-113116948)
    zebrafish
    (Danio rerio)
    Actinopterygii ZACN (5 of 5)6
    ZACN (1 of 5)6
    (see all 5)
    zinc activated ligand-gated ion channel
    (see all 5)
    21(a)
    20(a)
    (see all 5)
    1 ↔ many
    1 ↔ many
    (see all 5)
    3(58907062-58914120) ENSDARG00000097566
    12(33460536-33466279) ENSDARG00000074824


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ZACN gene
    HTR3E2  HTR3A2  CHRNA102  CHRNA92  HTR3B2  CHRNA72  CHRFAM7A2  HTR3C2  
    HTR3D2  

    Find genes that share paralogs with ZACN           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for ZACN
    PGOHUM00000246020


    (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 ZACN (see all 123)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1143662091,2
    F--74074119(+) CTGGCG/ACAAGC 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs24576951,2
    C--74074196(-) GAGTTC/TTACCT 1 -- us2k112Minor allele frequency- T:0.01NA WA CSA EA 374
    rs24576941,2
    C,F--74074210(-) AACCTC/TTGGGA 1 -- us2k11Minor allele frequency- T:0.17EA 120
    rs1180439541,2
    F--74074404(+) CAGGCG/ATCGAC 1 -- us2k11Minor allele frequency- A:0.01NA 120
    rs1155194281,2
    F--74074547(+) TTTTGT/CTGTTG 1 -- us2k11Minor allele frequency- C:0.03WA 118
    rs1861577281,2
    --74074587(+) AATCTC/TGCTCT 1 -- us2k10--------
    rs1402734011,2
    --74074625(+) AATCTC/TGGCTC 1 -- us2k10--------
    rs1897458601,2
    --74074636(+) ACTGCA/CACCTC 1 -- us2k10--------
    rs1453651461,2
    --74074710(+) CACCAC/TGCCCA 1 -- us2k10--------
    rs1812935791,2
    --74074793(+) AGTCTG/TCCCTC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ZACN (74068042 - 74079747 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for ZACN:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv2142CNV Insertion18451855
    nsv509674CNV Insertion20534489
    nsv833546CNV Loss17160897
    nsv908824CNV Loss21882294
    dgv3270n71CNV Loss21882294

    Human Gene Mutation Database (HGMD): ZACN
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ZACN
    DNA2.0 Custom Variant and Variant Library Synthesis for ZACN

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 610935    OMIM disorders: --

    2 diseases for ZACN:    
    About MalaCards
    transient neonatal diabetes mellitus    idiopathic generalized epilepsy


    Find genes that share disorders with ZACN           About GenesLikeMe

    1 Novoseek inferred disease relationship for ZACN gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    epilepsy 0 2 12752457 (1), 14501839 (1)


    Export disorders for ZACN 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 ZACN gene, integrated from 10 sources (see all 58):
    (articles sorted by number of sources associating them with ZACN)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and expression of ligand-gated ion-channel receptor L2 in central nervous system. (PubMed id 16083862)1, 2, 3, 9 Houtani T.... Sugimoto T. (Biochem. Biophys. Res. Commun. 2005)
    2. A novel class of ligand-gated ion channel is activated by Zn2+. (PubMed id 12381728)1, 2, 3, 9 Davies P.A.... Kirkness E.F. (J. Biol. Chem. 2003)
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    4. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)2 Zody M.C.... Nusbaum C. (Nature 2006)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. Impaired glucose homeostasis in transgenic mice expressing the human transient neonatal diabetes mellitus locus, TNDM. (PubMed id 15286800)1 Ma D....Kelsey G. (J. Clin. Invest. 2004)
    7. 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)
    8. 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)
    9. The Seventh Annual Ion Channel Retreat Vancouver, Canada, June 29-July 1, 2009. (PubMed id 20158438)9 Brugger S....King N. (Assay Drug Dev Technol 2010)
    10. The sixth annual Ion Channel Retreat Vancouver, Canada, June 23-25, 2008. (PubMed id 19231940)9 Choy N....Liang S. (Assay Drug Dev Technol 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Aliases
    Disorders
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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: 353174 HGNC: 29504 AceView: LGICZ Ensembl:ENSG00000186919 euGenes: HUgn353174
    ECgene: ZACN H-InvDB: ZACN

    (According to HUGE)
    About This Section

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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 ZACN 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 ZACN gene:
    Search GeneIP for patents involving ZACN

    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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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