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SPATA16 Gene

protein-coding   GIFtS: 48
GCID: GC03M172607

Spermatogenesis Associated 16

  See SPATA16-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
Spermatogenesis Associated 161 2
Testis Development Protein NYD-SP122 3
SPGF62 5
NYD-SP122
Spermatogenesis-Associated Protein 162
Testis-Specific Golgi Protein2

External Ids:    HGNC: 299351   Entrez Gene: 838932   Ensembl: ENSG000001449627   OMIM: 6098565   UniProtKB: Q9BXB73   

Export aliases for SPATA16 gene to outside databases

Previous GC identifers: GC03M174090 GC03M169978


(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 SPATA16 Gene:
This gene encodes a testis-specific protein that belongs to the tetratricopeptide repeat-like superfamily. The
encoded protein localizes to the Golgi apparatus and may play a role in spermatogenesis. (provided by RefSeq, May
2010)

GeneCards Summary for SPATA16 Gene:
SPATA16 (spermatogenesis associated 16) is a protein-coding gene. Diseases associated with SPATA16 include globozoospermia, and spermatogenic failure 6.

UniProtKB/Swiss-Prot: SPT16_HUMAN, Q9BXB7
Function: Involved in the formation of sperm acrosome, which implicated its potential role in spermatogenesis and
sperm-egg fusion




(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_000003.11  NT_005612.17  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SPATA16 gene promoter:
         Pax-6   Bach2   NF-AT   C/EBPalpha   NF-AT4   NF-AT2   IRF-7A   NF-AT3   Pax-4a   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSPATA16 promoter sequence
   Search Chromatin IP Primers for SPATA16

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SPATA16


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

Entrez Gene cytogenetic band: 3q26.31   Ensembl cytogenetic band:  3q26.31   HGNC cytogenetic band: 3q26.31

SPATA16 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPATA16 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M172607:  view genomic region     (about GC identifiers)

Start:
172,607,147 bp from pter      End:
172,859,058 bp from pter
Size:
251,912 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, 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: SPT16_HUMAN, Q9BXB7 (See protein sequence)
Recommended Name: Spermatogenesis-associated protein 16  
Size: 569 amino acids; 65263 Da
Miscellaneous: Association analysis reveals significant frequency of a synonymous (Ser-225) sequence polymorphism
among clinical groups with different sperm traits: the donor group, which has the highest sperm count and
motility level, has a significant higher polymorphism frequency compared to normal and asthenozoopermia groups
Secondary accessions: Q0R0N4 Q0R0S0 Q0R0W2 Q0R129 Q0R131 Q0R140 Q0R1B8 Q0R1G5 Q0R1I2 Q0R1J6
Q0R1S4 Q0R202 Q0R280 Q0R2F8 Q0R2N6 Q0R2N7 Q0R2R0 Q0R2R1 Q0R2S3 Q0R2S4 Q0R2S5 Q0R2T4 Q0R2T7
Q0R2U2 Q0R2U8 Q0R2U9 Q0R2V5 Q0R2V7 Q8NE67

Explore the universe of human proteins at neXtProt for SPATA16: NX_Q9BXB7

Explore proteomics data for SPATA16 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SPATA16 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_114161.3  
    ENSEMBL proteins: 
     ENSP00000341765  

    SPATA16 Human Recombinant Protein Products:

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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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    1 InterPro protein domain:
     IPR011990 TPR-like_helical

    Graphical View of Domain Structure for InterPro Entry Q9BXB7

    ProtoNet protein and cluster: Q9BXB7

    UniProtKB/Swiss-Prot: SPT16_HUMAN, Q9BXB7
    Similarity: Belongs to the SPATA16 family


    Find genes that share domains with SPATA16           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: SPT16_HUMAN, Q9BXB7
    Function: Involved in the formation of sperm acrosome, which implicated its potential role in spermatogenesis and
    sperm-egg fusion

    Animal Models:

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    1 qRT-PCR Assays for microRNA that regulate SPATA16:
    hsa-miR-137
    SwitchGear 3'UTR luciferase reporter plasmidSPATA16 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 UniProtKB/Swiss-Prot
    SPT16_HUMAN, Q9BXB7: Golgi apparatus. Note=Localized to the perinuclear region
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    golgi apparatus5
    nucleus3
    cytosol2

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005794Golgi apparatus IEA--

    Find genes that share ontologies with SPATA16           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 SPATA16
    Interactions:

        Search GeneGlobe Interaction Network for SPATA16

    1 Interacting protein for SPATA16 (Q9BXB72) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    --P310162MINT-8107267
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--
    GO:0007283spermatogenesis IEA--
    GO:0030154cell differentiation IEA--

    Find genes that share ontologies with SPATA16           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 SPATA16 (SPT16)



    (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 SPATA16 gene: 
    NM_031955.5  

    Unigene Cluster for SPATA16:

    Spermatogenesis associated 16
    Hs.444236  [show with all ESTs]
    Unigene Representative Sequence: NM_031955
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000351008(uc003fin.4)
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate SPATA16:
    hsa-miR-137
    SwitchGear 3'UTR luciferase reporter plasmidSPATA16 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat SPATA16

    Additional mRNA sequence: 

    AF345909.2 AF404758.1 AK093041.1 BC034496.2 

    4 DOTS entries:

    DT.100017336  DT.100744575  DT.100699380  DT.91924658 

    Selected AceView cDNA sequences (see all 26):

    BC034496 AX747878 BX281066 AK093041 AA383485 BP370007 BI829426 BI830435 
    BG722348 BM563232 NM_031955 BG773156 BG189141 AF345909 BM563796 AA902823 
    AF404758 BF061951 BE502467 BP370042 AI476510 BQ429605 BG219271 AI655299 

    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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    SPATA16 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATTGAGGAAG
    SPATA16 Expression
    About this image

    SPATA16 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SPATA16 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.444236

    UniProtKB/Swiss-Prot: SPT16_HUMAN, Q9BXB7
    Tissue specificity: Expressed in testis

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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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    This gene was present in the common ancestor of chordates.

    Orthologs for SPATA16 gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Spata161 , 5 spermatogenesis associated 161, 5 81.87(n)1
    79.23(a)1
      3 (10.74 cM)5
    708621  NM_029150.41  NP_083426.11 
     266376205 
    chicken
    (Gallus gallus)
    Aves SPATA161 spermatogenesis associated 16 69.24(n)
    60.53(a)
      429157  XM_426712.4  XP_426712.4 
    lizard
    (Anolis carolinensis)
    Reptilia SPATA166
    spermatogenesis associated 16
    75(a)
    1 ↔ 1
    3(6018494-6073751)


    ENSEMBL Gene Tree for SPATA16 (if available)
    TreeFam Gene Tree for SPATA16 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SPATA16 gene

    Find genes that share paralogs with SPATA16           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for SPATA16
    PGOHUM00000246932


    (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 SPATA16 (see all 4850)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0383344
    Spermatogenic failure 6 (SPGF6)4--see VAR_0383342 R Q mis40--------
    rs1378531181,2
    Cpathogenic1172600052(-) TGCCCG/AGTATG 2 /Q /R mis11Minor allele frequency- A:0.00NA 4550
    rs669695511,2
    C--169983242(+) AAAAA-/AA/AAA
            
    GCCAA
    1 -- int11NA 2
    rs2019458501,2
    --169983243(+) AAAAA-/AGCCAAA 1 -- int10--------
    rs1129946791,2
    C--170010301(+) TAAGGA/-AAAAA 1 -- int11Minor allele frequency- -:0.00CSA 2
    rs1512150641,2
    C--170047820(+) AGGTA-/CT/TC 
            
    TAATC
    1 -- int10--------
    rs2016285691,2
    --170049796(+) TTTCT-/CTCTTT 1 -- int10--------
    rs105247391,2
    C--170057892(+) GTGAC-/ACTT  
            
    AAGCA
    1 -- int10--------
    rs105375131,2
    C--170057893(+) TGACA-/CTTA  
            
    AGCAG
    1 -- int10--------
    rs1996131361,2
    C--170057895(-) TGCTTA/GAGTGT 1 -- int10--------

    HapMap Linkage Disequilibrium report for SPATA16 (172607147 - 172857147 bp, first 250kb of SPATA16)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for SPATA16:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2556969CNV Deletion19546169
    nsv519482CNV Loss19592680
    nsv877992CNV Loss21882294
    nsv4119CNV Loss18451855
    nsv829795CNV Gain17160897
    nsv7356OTHER Inversion18451855

    Human Gene Mutation Database (HGMD): SPATA16
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SPATA16
    DNA2.0 Custom Variant and Variant Library Synthesis for SPATA16

    (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: 609856   
    OMIM disorders: 102530  
    UniProtKB/Swiss-Prot: SPT16_HUMAN, Q9BXB7
  • Spermatogenic failure 6 (SPGF6) [MIM:102530]: An infertility disorder caused by spermatogenesis defects.
    The most prominent feature is the malformation of the acrosome, which can be totally absent in most severe cases.
    Additional features are an abnormal nuclear shape and abnormal arrangement of the mitochondria of the
    spermatozoon. Note=The disease is caused by mutations affecting the gene represented in this entry. An autosomal
    recessive variation of SPATA16 has been shown to be responsible for the disease in a consanguineous family with
    members homozygous for the variation

  • 3 diseases for SPATA16:    
    About MalaCards
    globozoospermia    spermatogenic failure 6    spermatogenic failure

    1 disease from the University of Copenhagen DISEASES database for SPATA16:
    Male infertility

    Find genes that share disorders with SPATA16           About GenesLikeMe

    Genetic Association Database (GAD): SPATA16
    Human Genome Epidemiology (HuGE) Navigator: SPATA16 (1 document)

    Export disorders for SPATA16 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 SPATA16 gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with SPATA16)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of a novel human testis-specific Golgi protein, NYD-SP12. (PubMed id 12529416)1, 2, 3, 9 Xu M.... Sha J. (Mol. Hum. Reprod. 2003)
    2. Homozygous mutation in SPATA16 is associated with male infertility in human globozoospermia. (PubMed id 17847006)1, 2, 3 Dam A.H.... Viville S. (Am. J. Hum. Genet. 2007)
    3. A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. (PubMed id 22219177)1, 4 Tao S....Sun J. (Carcinogenesis 2012)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    5. Rapid evolution, genetic variations, and functional association of the human spermatogenesis-related gene NYD-SP12. (PubMed id 17665087)1, 2 Zhang Q.... Su B. (J. Mol. Evol. 2007)
    6. The SH3 domain of postsynaptic density 95 mediates inflammatory pain through phosphatidylinositol-3-kinase recruitment. (PubMed id 20467438)1 Arbuckle M.I....Grant S.G. (EMBO Rep. 2010)
    7. Genome-wide association with bone mass and geometry in the Framingham Heart Study. (PubMed id 17903296)4 Kiel D.P....Karasik D. (BMC Med. Genet. 2007)
    8. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (Nature 2006)
    9. Gene functional research using polyethylenimine-mediated in vivo gene transfection into mouse spermatogenic cells. (PubMed id 16372119)1 Lu L....Sha J.H. (Asian J. Androl. 2006)
    10. 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)

    (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: 83893 HGNC: 29935 AceView: NYD-SP12 Ensembl:ENSG00000144962 euGenes: HUgn83893
    ECgene: SPATA16 H-InvDB: SPATA16

    (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 SPATA16 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    (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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