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SCAND3 Gene

protein-coding   GIFtS: 46
GCID: GC06M028539

SCAN Domain Containing 3

(Previous names: zinc finger protein 305 pseudogene 2, zinc finger protein...)
(Previous symbols: ZNF305P2, ZNF452)
  Search for SCAND3
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
SCAN Domain Containing 31 2     Buster42 3
ZNF305P21 2 3     KIAA19253 5
ZNF4521 2 3     ZFP38-L2
ZBED92 3 5     dJ1186N24.32
Zinc Finger Protein 305 Pseudogene 21 2     DJ1186N24.3 (Novel Zinc Finger Protein)2
Zinc Finger Protein 4521 2     SCAN Domain-Containing Protein 32
Transposon-Derived Buster4 Transposase-Like Protein2 3     Protein ZNF4523
Zinc Finger BED Domain-Containing Protein 92 3     BUSTER45

External Ids:    HGNC: 138511   Entrez Gene: 1148212   Ensembl: ENSG000002320407   OMIM: 6152545   UniProtKB: Q6R2W33   

Export aliases for SCAND3 gene to outside databases

Previous GC identifers: GC06M028648 GC06M028347


(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 SCAND3 Gene:
SCAND3 (SCAN domain containing 3) is a protein-coding gene. GO annotations related to this gene include protein dimerization activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is ZBED5.

Gene Wiki entry for SCAND3 (ZNF452) 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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RefSeq DNA sequence:
NT_113891.3  NC_000006.12  NC_018917.2  NT_007592.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the SCAND3 gene promoter:
         RFX1   NRSF form 1   Olf-1   NRSF form 2   TGIF   MRF-2   Roaz   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCAND3 promoter sequence
   Search Chromatin IP Primers for SCAND3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SCAND3


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

Entrez Gene cytogenetic band: 6p22.1   Ensembl cytogenetic band:  6p22.1   HGNC cytogenetic band: 6p21.33

SCAND3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCAND3 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M028539:  view genomic region     (about GC identifiers)

Start:
28,539,407 bp from pter      End:
28,583,989 bp from pter
Size:
44,583 bases      Orientation:
minus strand

1 alternative location:
Chr6-,NT_113891.2 61,611-77,316     

(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: SCND3_HUMAN, Q6R2W3 (See protein sequence)
Recommended Name: SCAN domain-containing protein 3  
Size: 1325 amino acids; 151666 Da
Secondary accessions: Q2NKL9 Q5SRJ3 Q8TCN2 Q96MV9 Q96PW3

Explore the universe of human proteins at neXtProt for SCAND3: NX_Q6R2W3

Explore proteomics data for SCAND3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SCAND3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_443155.1  
    ENSEMBL proteins: 
     ENSP00000395259  

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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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    Selected InterPro protein domains (see all 6):
     IPR025398 DUF4371
     IPR008916 Retrov_capsid_C
     IPR001584 Integrase_cat-core
     IPR003309 Tscrpt_reg_SCAN
     IPR008906 HATC_dom_C

    Graphical View of Domain Structure for InterPro Entry Q6R2W3

    ProtoNet protein and cluster: Q6R2W3

    2 Blocks protein domains:
    IPB003309 Transcriptional regulator SCAN
    IPB008906 HAT dimerisation


    UniProtKB/Swiss-Prot: SCND3_HUMAN, Q6R2W3
    Similarity: Contains 1 integrase catalytic domain
    Similarity: Contains 1 SCAN box domain


    Find genes that share domains with SCAND3           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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         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0046983protein dimerization activity IEA--
         
    Find genes that share ontologies with SCAND3           About GenesLikeMe


    Animal Models:
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    2 qRT-PCR Assays for microRNAs that regulate SCAND3:
    hsa-miR-548am hsa-miR-548x
    SwitchGear 3'UTR luciferase reporter plasmidSCAND3 3' UTR sequence
    Inhib. RNA
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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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    golgi apparatus1

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

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

    Find genes that share ontologies with SCAND3           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 SCAND3
    Interactions:

        Search GeneGlobe Interaction Network for SCAND3

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006355regulation of transcription, DNA-templated ----
    GO:0015074DNA integration IEA--

    Find genes that share ontologies with SCAND3           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 SCAND3 (SCND3)



    (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 SCAND3 gene: 
    NM_052923.1  

    Unigene Cluster for SCAND3:

    SCAN domain containing 3
    Hs.176980  [show with all ESTs]
    Unigene Representative Sequence: AY517631
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000452236(uc003nlo.3) ENST00000530247 ENST00000526291 ENST00000524745

    miRNA
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    2 qRT-PCR Assays for microRNAs that regulate SCAND3:
    hsa-miR-548am hsa-miR-548x
    SwitchGear 3'UTR luciferase reporter plasmidSCAND3 3' UTR sequence
    Inhib. RNA
    Products:
         
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    Predesigned siRNA for gene silencing in human, mouse, rat SCAND3
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    GenScript: all cDNA clones in your preferred vector: SCAND3 (NM_052923)
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      QuantiTect SYBR Green Assays in human, mouse, rat SCAND3
      QuantiFast Probe-based Assays in human, mouse, rat SCAND3

    Additional mRNA sequence: 

    AB067512.1 AK056369.1 AL832486.1 AY517631.1 BC110834.1 BC111741.1 BC111742.1 BX647791.1 

    2 DOTS entries:

    DT.101963668  DT.121384762 

    22 AceView cDNA sequences:

    AY517631 CA396529 AA480069 AI820939 AB067512 NM_052923 AL708822 BX647791 
    AL712109 AA481935 BU567407 AA642183 AL703533 AK056369 BX642445 BU506797 
    AL832486 AL713690 CD656189 AI338991 AI827682 AW341389 

    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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    SCAND3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTCATAATT
    SCAND3 Expression
    About this image

    SCAND3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SCAND3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.176980
        Custom PCR Arrays for SCAND3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCAND3

    (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 SCAND3 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    32(a)
    many ↔ many
    1(129248563-129250292)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1017336571 SCAN domain-containing protein 3-like 51.36(n)
    42.71(a)
      101733657  XM_004917387.1  XP_004917444.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BX664605.16
    Uncharacterized protein
    34(a)
    many ↔ many
    4(39828194-39829633) ENSDARG00000006874
            Species with no ortholog for SCAND3

    ENSEMBL Gene Tree for SCAND3 (if available)
    TreeFam Gene Tree for SCAND3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SCAND3 gene
    ZBED52  KRBA22  C5orf542  GTF2IRD22  FAM200A2  FAM200B2  EPM2AIP12  GTF2IRD2B2  
    16 SIMAP similar genes for SCAND3 using alignment to 1 protein entry:     SCND3_HUMAN:
    LOC100128510    SCAND1    ZSCAN16    ZSCAN23    ZSCAN31    ZNF24
    ZNF396    ZSCAN9    ZNF174    DKFZp434K202    ZNF483    FAM200A
    ZBED5    ZSCAN18    ZNF397    ZBED8

    Find genes that share paralogs with SCAND3           About GenesLikeMe



    (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 SCAND3 (see all 336)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1899385681,2
    --28538929(+) CTACTA/GTAAAT 1 -- int10--------
    rs1423166501,2
    --28539067(+) GCCTGC/GGCAAC 1 -- int10--------
    rs1832770861,2
    --28539084(+) AGACCC/TTGCCT 1 -- int10--------
    rs1858316101,2
    --28539221(+) CTAACC/TACTCT 1 -- int10--------
    rs4490741,2
    C,F,A,H--28539308(+) CTTCCT/CTTCAC 1 -- int118Minor allele frequency- C:0.07EA NS NA WA CSA 2401
    rs1163857141,2
    C,F--28539373(+) TTAACA/GTGCTA 1 -- int11Minor allele frequency- G:0.04WA 118
    rs1910891691,2
    --28539376(+) ACATGA/CTAATG 1 -- int10--------
    rs2007105211,2
    C--28539850(+) GTTGAC/GGGGAA 2 P syn10--------
    rs1838066701,2
    C--28539859(+) AAAAGA/CAGCAG 2 L syn10--------
    rs1891634801,2
    C--28539878(+) AAGCAA/GTCTCA 2 T I mis10--------

    HapMap Linkage Disequilibrium report for SCAND3 (28539407 - 28583989 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for SCAND3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv830621CNV Gain17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SCAND3
    DNA2.0 Custom Variant and Variant Library Synthesis for SCAND3

    (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: 615254    OMIM disorders: --


    Find genes that share disorders with SCAND3           About GenesLikeMe

    Genetic Association Database (GAD): SCAND3

    Export disorders for SCAND3 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 SCAND3 gene, integrated from 10 sources (see all 14):
    (articles sorted by number of sources associating them with SCAND3)
        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. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    4. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. (PubMed id 11572484)1, 2 Nagase T.... Ohara O. (DNA Res. 2001)
    5. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PubMed id 23533661)2 Hayward A.... Jern P. (PLoS ONE 2013)
    6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    7. Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study. (PubMed id 17903294)4 Yang Q....O'Donnell C.J. (BMC Med. Genet. 2007)
    8. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    9. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (Nucleic Acids Res. 2006)
    10. From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)1 Wiemann S....Poustka A. (Genome Res. 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: 114821 HGNC: 13851 AceView: ZNF452 Ensembl:ENSG00000232040 euGenes: HUgn114821
    ECgene: SCAND3 H-InvDB: SCAND3

    (According to HUGE)
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    HUGE: KIAA1925

    (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 SCAND3 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 SCAND3 gene:
    Search GeneIP for patents involving SCAND3

    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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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