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SPIN4 Gene

protein-coding   GIFtS: 45
GCID: GC0XM062569

Spindlin Family, Member 4

  See 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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Aliases
Spindlin Family, Member 41 2
spindlin-42

External Ids:    HGNC: 270401   Entrez Gene: 1398862   Ensembl: ENSG000001867677   UniProtKB: Q56A733   

Export aliases for SPIN4 gene to outside databases

Previous GC identifers: GC0XM062484 GC0XM062568 GC0XM056393


(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 SPIN4 Gene:
SPIN4 (spindlin family, member 4) is a protein-coding gene. Diseases associated with SPIN4 include cysticercosis, and meningoencephalitis. An important paralog of this gene is SPIN2B.


(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_011651.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the SPIN4 gene promoter:
         MAZR   ATF-2   MIF-1   Evi-1   E47   HNF-1A   NRF-2   HNF-1   ZID   NF-kappaB1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SPIN4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SPIN4


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

Entrez Gene cytogenetic band: Xq11.1   Ensembl cytogenetic band:  Xq11.1   HGNC cytogenetic band: Xq11.1

SPIN4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPIN4 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM062569:  view genomic region     (about GC identifiers)

Start:
62,567,107 bp from pter      End:
62,571,223 bp from pter
Size:
4,117 bases      Orientation:
minus 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: SPIN4_HUMAN, Q56A73 (See protein sequence)
Recommended Name: Spindlin-4  
Size: 249 amino acids; 28660 Da
Sequence caution: Sequence=CAI41371.1; Type=Erroneous initiation;
Secondary accessions: Q5JUL2

Explore the universe of human proteins at neXtProt for SPIN4: NX_Q56A73

Explore proteomics data for SPIN4 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys50
  • Modification sites at PhosphoSitePlus

  • See SPIN4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001012986.2  
    ENSEMBL proteins: 
     ENSP00000364018   ENSP00000334163  

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    Cloud-Clone Corp. CLIAs for SPIN4


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR003671 Spin_Ssty

    Graphical View of Domain Structure for InterPro Entry Q56A73

    ProtoNet protein and cluster: Q56A73

    1 Blocks protein domain: IPB003671 Spindlin/spermiogenesis-specific protein

    UniProtKB/Swiss-Prot: SPIN4_HUMAN, Q56A73
    Similarity: Belongs to the SPIN/STSY family


    SPIN4 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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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SPIN4
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    hsa-mir-24-3p (MIRT030544), hsa-mir-29c-3p (MIRT020392), hsa-mir-192-5p (MIRT026613), hsa-mir-340-5p (MIRT019605), hsa-mir-96-5p (MIRT027915)

    Block miRNA regulation of human, mouse, rat SPIN4 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SPIN4 (see all 10):
    hsa-miR-3163 hsa-miR-576-5p hsa-miR-3673 hsa-miR-513a-3p hsa-miR-548k hsa-miR-3065-5p hsa-miR-33a hsa-miR-9*
    SwitchGear 3'UTR luciferase reporter plasmidSPIN4 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPIN4


    (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
    mitochondrion2
    nucleus2
    cytosol1

    (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 SPIN4
    Interactions:

        Search GeneGlobe Interaction Network for SPIN4

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for SPIN4 (ENSP000003341634) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCENSP000003448184STRING: ENSP00000344818
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007276gamete generation IEA--

    SPIN4 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 SPIN4



    (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 SPIN4 gene: 
    NM_001012968.2  

    Unigene Cluster for SPIN4:

    Spindlin family, member 4
    Hs.612782  [show with all ESTs]
    Unigene Representative Sequence: AL833314
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000374884 ENST00000335144(uc004dvf.3)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SPIN4 (see all 10):
    hsa-miR-3163 hsa-miR-576-5p hsa-miR-3673 hsa-miR-513a-3p hsa-miR-548k hsa-miR-3065-5p hsa-miR-33a hsa-miR-9*
    SwitchGear 3'UTR luciferase reporter plasmidSPIN4 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for SPIN4
    Predesigned siRNA for gene silencing in human, mouse, rat SPIN4
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    GenScript: all cDNA clones in your preferred vector: SPIN4 (NM_001012968)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SPIN4
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SPIN4
      QuantiTect SYBR Green Assays in human, mouse, rat SPIN4
      QuantiFast Probe-based Assays in human, mouse, rat SPIN4

    Additional mRNA sequence: 

    AK021705.1 AK126931.1 AL833314.1 BC035088.1 BC043412.1 BC112360.1 

    2 DOTS entries:

    DT.108130  DT.100746759 

    Selected AceView cDNA sequences (see all 40):

    AK126931 AL135659 BX282201 BG059887 BC043412 BU069192 AL833314 BM144682 
    BQ424587 BM667539 AA598803 BC035088 BE042460 BG023952 AK021705 CB114607 
    AI471422 BI491676 AA776212 BI549232 AU118795 BU688875 BU158675 BE042498 

    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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    SPIN4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGTGGATTTT
    SPIN4 Expression
    About this image

    SPIN4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SPIN4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.612782
        Custom PCR Arrays for SPIN4
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for SPIN4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPIN4

    (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 SPIN4 gene from Selected species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Spin41 , 5 spindlin family, member 41, 5 88.62(n)1
    95.98(a)1
      X (41.83 cM)5
    2706241  NM_178753.41  NP_848868.11 
     950225105 
    zebrafish
    (Danio rerio)
    Actinopterygii SPIN4 (3 of 3)6
    CABZ01112877.16
    (see all 3)
    Uncharacterized protein
    (see all 3)
    68(a)
    54(a)
    (see all 3)
    1 ↔ many
    1 ↔ many
    (see all 3)
    10(2595456-2607514) ENSDARG00000058949
    2(55803426-55814829) ENSDARG00000001817


    ENSEMBL Gene Tree for SPIN4 (if available)
    TreeFam Gene Tree for SPIN4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SPIN4 gene
    SPIN2B2  SPIN2A2  SPIN12  SPIN32  
    4 SIMAP similar genes for SPIN4 using alignment to 1 protein entry:     SPIN4_HUMAN:
    SPIN2A    SPIN3    SPIN1    SPIN2B

    SPIN4 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 SPIN4 (see all 84)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1426585171,2
    --62566626(+) GGAGTA/GGTAAA 1 -- ds50010--------
    rs1896485921,2
    --62566766(+) CATCAC/TTCATG 1 -- ds50010--------
    rs1812494991,2
    --62567360(+) GTCATC/TAGGAT 1 -- ut310--------
    rs1863485871,2
    --62567368(+) GATTAG/TATTGT 1 -- ut310--------
    rs1509903471,2
    C--62567389(+) GTCCTA/GGCTAA 1 -- ut310--------
    rs1895943051,2
    --62567552(+) TACTTG/TGGAAT 1 -- ut310--------
    rs1395464961,2
    C--62567735(+) ACAATC/TTTATC 1 -- ut310--------
    rs1433096801,2
    C--62567877(+) AATAGA/GGAATA 1 -- ut310--------
    rs735225381,2
    C,F--62567892(+) TCCCTG/ATTAAT 1 -- ut311Minor allele frequency- A:0.50WA 2
    rs1817069421,2
    --62567941(+) CAGTCA/CCGTCT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for SPIN4 (62567107 - 62571223 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for SPIN4:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1584074OTHER Inversion17803354

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SPIN4
    DNA2.0 Custom Variant and Variant Library Synthesis for SPIN4

    (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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    3 diseases for SPIN4:    
    About MalaCards
    cysticercosis    meningoencephalitis    eclampsia

    2 diseases from the University of Copenhagen DISEASES database for SPIN4:
    Cysticercosis     Eclampsia

    SPIN4 for disorders           About GeneDecksing


    Export disorders for SPIN4 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 SPIN4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SPIN4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    2. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    3. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    4. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    5. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
    6. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (Nature 2005)
    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)

    (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: 139886 HGNC: 27040 AceView: LOC139886 Ensembl:ENSG00000186767 euGenes: HUgn139886
    ECgene: SPIN4 H-InvDB: SPIN4

    (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 SPIN4 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 SPIN4 gene:
    Search GeneIP for patents involving SPIN4

    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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