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SCAND2P Gene

pseudogene   GIFtS: 38
GCID: GC15P085179

SCAN Domain Containing 2 Pseudogene

(Previous names: SCAN domain-containing 2, SCAN domain containing 2)
(Previous symbol: SCAND2)
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(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
SCAN Domain Containing 2 Pseudogene1 2
SCAND21 2 3 5
SCAN Domain Containing 21
SCAN Domain-Containing 21
SCAN Domain-Containing Protein 2 Pseudogene3

External Ids:    HGNC: 105671   Entrez Gene: 545812   Ensembl: ENSG000001767007   OMIM: 6104175   UniProtKB: Q9GZW53   
ORGUL members:         

Export aliases for SCAND2P gene to outside databases

Previous GC identifer: GC15P085178


(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 SCAND2P Gene:
SCAND2P (SCAN domain containing 2 pseudogene) is a pseudogene, and is affiliated with the antisense RNA class. GO annotations related to this gene include sequence-specific DNA binding transcription factor 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000015.9  NC_018926.2  NT_010194.18  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SCAND2P
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCAND2P promoter sequence
   Search Chromatin IP Primers for SCAND2P

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SCAND2P


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

Entrez Gene cytogenetic band: 15q25.2   Ensembl cytogenetic band:  15q25.2   HGNC cytogenetic band: 15q25.2

SCAND2P Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCAND2P gene location

GeneLoc information about chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15P085179:  view genomic region     (about GC identifiers)

Start:
85,174,682 bp from pter      End:
85,185,695 bp from pter
Size:
11,014 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SCAND2P

(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: SCND2_HUMAN, Q9GZW5 (See protein sequence)
Recommended Name: Putative SCAN domain-containing protein SCAND2P  
Size: 306 amino acids; 34217 Da
Caution: Could be the product of a pseudogene
Secondary accessions: A8K374 Q9H9G1
Alternative splicing: 2 isoforms:  Q9GZW5-1   Q9GZW5-2   (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 SCAND2P: NX_Q9GZW5

Explore proteomics data for SCAND2P at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SCAND2P Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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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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    2 InterPro protein domains:
     IPR008916 Retrov_capsid_C
     IPR003309 Tscrpt_reg_SCAN

    Graphical View of Domain Structure for InterPro Entry Q9GZW5

    ProtoNet protein and cluster: Q9GZW5

    1 Blocks protein domain: IPB003309 Transcriptional regulator SCAN

    UniProtKB/Swiss-Prot: SCND2_HUMAN, Q9GZW5
    Similarity: Contains 1 SCAN box domain


    Find genes that share domains with SCAND2P           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): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
         
    Find genes that share ontologies with SCAND2P           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SCAND2P:
     Increased gamma-H2AX phosphory 

    Animal Models:
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    hsa-mir-26b-5p (MIRT029695), hsa-mir-335-5p (MIRT018118)

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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
    SCND2_HUMAN, Q9GZW5: Nucleus (Potential)

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005634nucleus IEA--

    Find genes that share ontologies with SCAND2P           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 SCAND2P
    Interactions:

        Search GeneGlobe Interaction Network for SCAND2P

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    Find genes that share ontologies with SCAND2P           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
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    Browse Tocris compounds for SCAND2P (SCND2)



    (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 SCAND2P gene (6 alternative transcripts): 
    NM_022050.3  NM_033633.2  NM_033634.2  NM_033635.2  NM_033636.2  NM_033640.2  

    Unigene Cluster for SCAND2P:

    SCAN domain containing 2 pseudogene
    Hs.658114  [show with all ESTs]
    Unigene Representative Sequence: NR_004859
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000348993(uc002bks.3 uc002bku.2 uc002bkt.2) ENST00000427525
    ENST00000558612 ENST00000530891 ENST00000560416 ENST00000541103 ENST00000560678
    ENST00000560543 ENST00000558508 ENST00000541482
    miRNA
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    Additional mRNA sequence: 

    AK290489.1 AL109690.1 BC093922.1 BC093924.1 BC143241.1 BC143243.1 NR_003654.2 NR_004859.1 

    11 DOTS entries:

    DT.95155565  DT.100647236  DT.121025572  DT.91770657  DT.95281432  DT.121025609  DT.91770656  DT.99993448 
    DT.100650259  DT.40128523  DT.95096836 

    Selected AceView cDNA sequences (see all 85):

    AI081918 NM_033633 BE856722 BC011547 CA447553 AI247235 BF001494 NM_033635 
    AW341587 AA378684 AA731454 NM_033634 AI218957 CR594703 AW085215 BX370292 
    BC012929 BV184770 AI344580 BX344432 AW268399 AL109690 AI092124 AI669216 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SCAND2P    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b
    SP1:                    -     -           -                           
    SP2:                                      -                           
    SP3:                    -     -                                       
    SP4:                                                                  


    ECgene alternative splicing isoforms for SCAND2P

    (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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    SCAND2P expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SCAND2P Expression
    About this image

    SCAND2P Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SCAND2P Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.658114
        Custom PCR Arrays for SCAND2P
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    In Situ
    Assay Products:
     

     
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    (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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      --

    ENSEMBL Gene Tree for SCAND2P (if available)
    TreeFam Gene Tree for SCAND2P (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SCAND2P gene
    10 SIMAP similar genes for SCAND2P using alignment to 1 protein entry:     SCND2_HUMAN:
    ZSCAN31    ZNF202    ZNF263    ZKSCAN2    ZSCAN20    ZKSCAN5
    ZNF213    ZNF397    ZSCAN32    ZNF500

    Find genes that share paralogs with SCAND2P           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 SCAND2P (see all 290)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 15 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1838092011,2
    --85172843(+) TTCCAC/TGGCCC 2 -- us2k10--------
    rs1137286741,2
    F--85172855(+) GCTTCG/ACAACT 2 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs1166359921,2
    C,F--85173004(+) ACAATG/ACAGGG 2 -- us2k11Minor allele frequency- A:0.03WA 118
    rs6097391,2
    H--85173024(-) TCTGAG/AAAGGA 2 -- us2k1 trp35Minor allele frequency- A:0.00MN NS EA 590
    rs1869050471,2
    --85173078(+) CTGCAC/TGATTC 2 -- us2k10--------
    rs4816531,2
    H--85173083(-) GCCCAG/AAATCG 2 -- us2k15Minor allele frequency- A:0.00MN NS EA 556
    rs114426111,2
    C--85173107(+) CTTGGT/-TTTTT 2 -- us2k1 trp31Minor allele frequency- -:0.50NA 2
    rs1380727911,2
    --85173212(+) CAAGCA/GATTCT 2 -- us2k10--------
    rs169744601,2
    C,F,H--85173479(+) TAATAG/ACACTG 2 -- us2k19Minor allele frequency- A:0.02NA NS EA WA 798
    rs29794531,2
    H--85173530(+) TTTTAG/AAAAAT 2 -- us2k14Minor allele frequency- A:0.00NS EA 420

    HapMap Linkage Disequilibrium report for SCAND2P (85174682 - 85185695 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SCAND2P: --
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing SCAND2P
    DNA2.0 Custom Variant and Variant Library Synthesis for SCAND2P

    (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: 610417    OMIM disorders: --


    Find genes that share disorders with SCAND2P           About GenesLikeMe


    Export disorders for SCAND2P 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 SCAND2P gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SCAND2P)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mapping, characterization, and expression analysis of the SM-20 human homologue, C1orf12, and identification of a novel related gene, SCAND2. (PubMed id 11056053)1, 2, 3 Dupuy D.... Arveiler B. (Genomics 2000)
    2. 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)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. SCAN domain-containing 2 gene (SCAND2) is a novel nuclear protein derived from the zinc finger family by exon shuffling. (PubMed id 12036577)1, 3 Dupuy D....Arveiler B. (Gene 2002)
    5. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
    6. CAMOS, a nonprogressive, autosomal recessive, congenital cerebellar ataxia, is caused by a mutant zinc-finger protein, ZNF592. (PubMed id 20531441)1 Nicolas E....Delague V. (Eur. J. Hum. Genet. 2010)
    7. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1 Olsen J.V....Mann M. (Cell 2006)
    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 zinc finger-associated SCAN box is a conserved oligomerization domain. (PubMed id 10567577)1 Williams A.J....Collins T. (Mol. Cell. Biol. 1999)

    (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: 54581 HGNC: 10567 AceView: SCAND2 Ensembl:ENSG00000176700 euGenes: HUgn54581
    ECgene: SCAND2P H-InvDB: SCAND2P

    (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)
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    NameDescription
    PharmGKB entry for SCAND2P 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 SCAND2P gene:
    Search GeneIP for patents involving SCAND2P

    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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