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

ZSWIM3 Gene

protein-coding   GIFtS: 47
GCID: GC20P044486

zinc finger, SWIM-type containing 3

(Previous name: chromosome 20 open reading frame 164 )
(Previous symbol: C20orf164)
  Search for ZSWIM3
in
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 Human Malady Compendium 
Biological research products
for ZSWIM3    

Aliases
for ZSWIM3 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
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, SWIM-Type Containing 31 2
C20orf1641 2 3
Chromosome 20 Open Reading Frame 1641
DJ337O18.71
Zinc Finger SWIM Domain-Containing Protein 32
Zinc Finger, SWIM Domain Containing 32

External Ids:    HGNC: 161571   Entrez Gene: 1408312   Ensembl: ENSG000001328017   UniProtKB: Q96MP53   
ORGUL members:         
NONCODE:n410486    

Export aliases for ZSWIM3 gene to outside databases

Previous GC identifers: GC20P045171 GC20P043919 GC20P041227


Summaries
for ZSWIM3 gene

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

Genomic Views
for ZSWIM3 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NC_018931.1  NT_011362.10  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ZSWIM3 gene promoter:
         Egr-3   AML1a   Egr-1   Lmo2   MIF-1   Tal-1beta   E47   Egr-2   PPAR-alpha   Msx-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: ZSWIM3 promoter sequence
   Search SABiosciences Chromatin IP Primers for ZSWIM3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZSWIM3


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

Entrez Gene cytogenetic band: 20q13.12   Ensembl cytogenetic band:  20q13.12   HGNC chromosome: 20

ZSWIM3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZSWIM3 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P044486:  view genomic region     (about GC identifiers)

Start:
 44,486,256 bp from pter      End:
 44,507,770 bp from pter
Size:
 21,515 bases      Orientation:
 plus strand

Proteins
for ZSWIM3 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: ZSWM3_HUMAN, Q96MP5 (See protein sequence)
Recommended Name: Zinc finger SWIM domain-containing protein 3  
Size: 696 amino acids; 79454 Da
Secondary accessions: Q9BR13

Explore the universe of human proteins at neXtProt for ZSWIM3: NX_Q96MP5

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96MP5

    • ZSWIM3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_542790.2  
    ENSEMBL proteins: 
     ENSP00000255152   ENSP00000406313  

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    Protein Domains /
    Families
    for ZSWIM3 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    ZSWIM3 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR006564 Znf_PMZ
     IPR018289 MULE_transposase_dom
     IPR007527 Znf_SWIM

    Graphical View of Domain Structure for InterPro Entry Q96MP5

    ProtoNet protein and cluster: Q96MP5

    1 Blocks protein family: IPB007527 SWIM Zn-finger

    UniProtKB/Swiss-Prot: ZSWM3_HUMAN, Q96MP5
    Similarity: Contains 1 SWIM-type zinc finger


    Function
    for ZSWIM3 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    miRNA
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    Inhib. RNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008270zinc ion binding IEA--


    ZSWIM3 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for ZSWIM3:
     Increased circadian period len 


    Pathways & Interactions
    for ZSWIM3 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for ZSWIM3

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

    1 Interacting protein for ZSWIM3 (ENSP000002551524) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPP1CAENSP000003260314STRING: ENSP00000326031
    About this table

    Drugs & Compounds
    for ZSWIM3 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 ZSWIM3
    Search CenterWatch for drugs/clinical trials and news about ZSWIM3 / ZSWM3 

    Transcripts
    for ZSWIM3 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
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    About This Section
    REFSEQ mRNAs for ZSWIM3 gene: 
    NM_080752.3  

    Unigene Cluster for ZSWIM3:

    Zinc finger, SWIM-type containing 3
    Hs.292135  [show with all ESTs]
    Unigene Representative Sequence: NR_037628
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000255152(uc010zxg.2 uc002xqd.3) ENST00000454862

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    hsa-miR-4311 hsa-miR-15a hsa-miR-2278 hsa-miR-497 hsa-miR-583 hsa-miR-570 hsa-miR-1276 hsa-miR-424
    SwitchGear 3'UTR luciferase reporter plasmid: ZSWIM3 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AK056641.1 AK302767.1 AK316214.1 BC027611.2 NR_037628.1 

    6 DOTS entries:

    DT.110578  DT.120817277  DT.100733069  DT.102842140  DT.100698535  DT.120817331 

    24/53 AceView cDNA sequences (see all 53):

    BM719735 AI887681 AW452119 BX385024 BX460726 CR597199 BM930315 AI672559 
    BC027611 AW450049 AA810666 AI675974 AW139278 BG723647 AI357875 AK056641 
    AI094229 BX400749 BX375212 BU680532 AI801911 BU196900 AA194468 BX383841 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for ZSWIM3    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b
    SP1:                              
    SP2:              -               


    ECgene alternative splicing isoforms for ZSWIM3

    Expression
    for ZSWIM3 gene

    (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

    ZSWIM3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CAGACCGAGG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    ZSWIM3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    OvaryAntral FollicleSecondary OocyteFemale Gametocytes, Germ Cells
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See ZSWIM3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ZSWIM3

    SOURCE GeneReport for Unigene cluster: Hs.292135
        SABiosciences Custom PCR Arrays for ZSWIM3
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    In Situ
    Assay Products:     
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    Orthologs
    for ZSWIM3 gene

    (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 ZSWIM3 gene from 3/9 species (see all 9)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves ZSWIM31 zinc finger, SWIM-type containing 3 57.36(n)
    45.24(a)    		   428161  XM_425719.2  XP_425719.2 
    lizard
    (Anolis carolinensis)    		 Reptilia ZSWIM36
    		 --
    		 46(a)
    		 1 ↔ 1
    		 GL344721.1(14551-17596)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.151742 Xenopus laevis transcribed sequence with weak similarity more 77.54(n)    BJ615033.1 


    ENSEMBL Gene Tree for ZSWIM3 (if available)
    TreeFam Gene Tree for ZSWIM3 (if available) 

    Paralogs
    for ZSWIM3 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for ZSWIM3 gene
    ZSWIM12  
    1 SIMAP similar gene for ZSWIM3 using alignment to 2 protein entries:     ZSWM3_HUMAN (see all proteins):
    ZSWIM1

    ZSWIM3 for paralogs           About GeneDecksing



    Genomic Variants
    for ZSWIM3 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/456 NCBI SNPs in ZSWIM3 are shown (see all 456)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 20 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs2009177581,2
    		C--44488061(+) AATGTA/GGAAAA 2 -- int10--------
    rs2016128611,2
    		--44488074(+) AAAAA-/GAAAAA 2 -- int10--------
    rs287181131,2
    		C,F,--44488077(+) AAAAAA/GAAGAA 2 -- int1 trp35Minor allele frequency- G:0.44WA NA CSA 9
    rs1419476871,2
    		C--44488077(+) AAAAA-/GAAGAA 2 -- int10--------
    rs19676561,2
    		C,F,O,A,H,--44488199(-) AATTAA/GCCACA 2 -- int133Minor allele frequency- N:0.00NS EA NA WA 3408
    rs1867810171,2
    		--44488407(+) TAGGAC/GCTTGC 2 -- int10--------
    rs2001081161,2
    		C--44488431(+) GAATAA/CAAAAA 2 -- int10--------
    rs775040181,2
    		C,--44488455(+) AAAAAC/ACCACA 2 -- int12Minor allele frequency- A:0.25NA 4
    rs1468309091,2
    		C,--44488455(+) AAAAA-/ACCCACA 2 -- int10--------
    rs711818691,2
    		C--44488456(+) AAACCC/-ACAGT 2 -- int11Minor allele frequency- -:0.00NA 2

    HapMap Linkage Disequilibrium report for ZSWIM3 (44486256 - 44507770 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for ZSWIM3
         1 CNV: 50668
         1 Indel: 12191

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    Disorders / Diseases
    for ZSWIM3 gene

    (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.)
    About This Section
    		   --

    Publications
    for ZSWIM3 gene

    (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 ZSWIM3 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with ZSWIM3)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (2001)
    4. 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)
    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)
    6. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (2001)

    External Searches for ZSWIM3 gene

    (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)

    Genome Databases showing ZSWIM3 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 140831 HGNC: 16157 AceView: ZSWIM3 Ensembl:ENSG00000132801 euGenes: HUgn140831
    ECgene: ZSWIM3 H-InvDB: ZSWIM3

    Other Databases showing ZSWIM3 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing ZSWIM3 gene

    (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 ZSWIM3 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for ZSWIM3 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for ZSWIM3 gene:
    Search GeneIP for patents involving ZSWIM3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for ZSWIM3 gene

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    About This Section

     
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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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    VWF
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    von Willebrand factor
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