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

SPATA6 Gene

protein-coding   GIFtS: 44
GCID: GC01M048763

Spermatogenesis Associated 6

  Search for SPATA6
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Spermatogenesis Associated 61 2
Spermatogenesis-Related Factor-11 2
HASH2
SRF-12
SRF12
Spermatogenesis-Associated Protein 62

External Ids:    HGNC: 183091   Entrez Gene: 545582   Ensembl: ENSG000001321227   OMIM: 6139475   UniProtKB: Q9NWH73   

Export aliases for SPATA6 gene to outside databases

Previous GC identifers: GC01M048388 GC01M047653 GC01M048085 GC01M048134 GC01M048476 GC01M048536 GC01M046877


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

GeneCards Summary for SPATA6 Gene: 
SPATA6 (spermatogenesis associated 6) is a protein-coding gene. An important paralog of this gene is SPATA6L.

UniProtKB/Swiss-Prot: SPAT6_HUMAN, Q9NWH7
Function: May play a role in spermatid maturation or sperm function (By similarity)




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NT_032977.9  NC_018912.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SPATA6 gene promoter:
         RFX1   ATF-2   AP-4   FOXL1   C/EBPalpha   Evi-1   SRY   Cart-1   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSPATA6 promoter sequence
   Search SABiosciences Chromatin IP Primers for SPATA6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SPATA6


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

Entrez Gene cytogenetic band: 1p33   Ensembl cytogenetic band:  1p33   HGNC cytogenetic band: 1p32.3

SPATA6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPATA6 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M048763:  view genomic region     (about GC identifiers)

Start:
48,761,044 bp from pter      End:
48,937,876 bp from pter
Size:
176,833 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SPAT6_HUMAN, Q9NWH7 (See protein sequence)
Recommended Name: Spermatogenesis-associated protein 6 precursor  
Size: 488 amino acids; 55989 Da
Subcellular location: Secreted (Potential)
Secondary accessions: Q5T3N7 Q8WUE6
Alternative splicing: 2 isoforms:  Q9NWH7-1   Q9NWH7-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SPATA6: NX_Q9NWH7

Explore proteomics data for SPATA6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9NWH7

  • SPATA6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SPATA6 Protein Expression
    REFSEQ proteins: NP_061946.1  
    ENSEMBL proteins: 
     ENSP00000360913   ENSP00000360909   ENSP00000474844   ENSP00000360907   ENSP00000474642  
     ENSP00000379502  

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    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    SPATA6 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR027207 Spata6

    Graphical View of Domain Structure for InterPro Entry Q9NWH7

    ProtoNet protein and cluster: Q9NWH7

    UniProtKB/Swiss-Prot: SPAT6_HUMAN, Q9NWH7
    Similarity: Belongs to the SPATA6 family


    SPATA6 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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SPAT6_HUMAN, Q9NWH7
    Function: May play a role in spermatid maturation or sperm function (By similarity)

    Phenotypes:
         1 GenomeRNAi human phenotype for SPATA6:

     Decreased number of cells in m 

    Animal Models:
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section




    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SPATA6

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

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

    SPATA6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SPATA6 (SPAT6)

    Search CenterWatch for drugs/clinical trials and news about SPATA6 / SPAT6

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SPATA6 gene: 
    NM_019073.2  

    Unigene Cluster for SPATA6:

    Spermatogenesis associated 6
    Hs.538103  [show with all ESTs]
    Unigene Representative Sequence: NM_019073
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000371847(uc001crr.2 uc001crs.2 uc010omv.2) ENST00000371843
    ENST00000603831 ENST00000371841 ENST00000490850 ENST00000487629 ENST00000463938
    ENST00000487543 ENST00000465990 ENST00000471975 ENST00000396199
    miRNA
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    hsa-miR-610 hsa-miR-198 hsa-miR-410 hsa-miR-1257 hsa-miR-382 hsa-miR-338-5p hsa-miR-514 hsa-miR-1193
    SwitchGear 3'UTR luciferase reporter plasmidSPATA6 3' UTR sequence
    Inhib. RNA
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SPATA6

    Additional mRNA sequence: 

    AK000869.1 AK301770.1 BC020660.1 BC040655.1 

    8 DOTS entries:

    DT.402310  DT.422664  DT.75162246  DT.100694113  DT.75155833  DT.91741203  DT.92014802  DT.99931765 

    24/39 AceView cDNA sequences (see all 39):

    AU116876 CR592303 AA769927 AK000869 BX099038 NM_019073 BU684281 BC020660 
    BF109318 CB989040 BG503847 BG771751 BI520668 AA476607 BX371524 BI827849 
    BI562550 BF980014 AW183572 AA758994 AW303869 AI375752 BE550330 BG718353 

    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™, 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

    SPATA6 expression in normal human tissues (normalized intensities)      SPATA6 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATAAACCTCA
    SPATA6 Expression
    About this image


    SPATA6 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/4 selected tissues (see all 4) fully expand
     
     Testis (Reproductive System)    fully expand to see all 3 entries
             Leydig Cells Testis Interstitium
             Testis Interstitium
     
     Epithelium (Respiratory System)    fully expand to see all 2 entries
             bronchial epithelial cells   
     
     Gut Tube (Gastrointestinal Tract)
             Definitive endoderm-like cells ( A scalable, suspension protocol for derivation of...
     
     Brain (Nervous System)
             Oligodendrocyte Precursor Cells Forebrain White Matter

    See SPATA6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SPATA6

    SOURCE GeneReport for Unigene cluster: Hs.538103
        SABiosciences Custom PCR Arrays for SPATA6
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPATA6

    (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 SPATA6 gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Spata61 , 5 spermatogenesis associated 61, 5 90.64(n)1
    90.57(a)1
      4 (51.53 cM)5
    679461  NM_026470.31  NP_080746.31 
     1117199845 
    chicken
    (Gallus gallus)
    Aves SPATA61 spermatogenesis associated 6 64.69(n)
    55.84(a)
      424626  XM_003641689.1  XP_003641737.1 
    lizard
    (Anolis carolinensis)
    Reptilia SPATA66
    Uncharacterized protein
    47(a)
    1 ↔ 1
    GL343249.1(286509-305232)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.335022 Xenopus laevis transcribed sequence with weak similarity more 74.15(n)    BQ733475.1 
    zebrafish
    (Danio rerio)
    Actinopterygii spata61 spermatogenesis associated 6 51.74(n)
    41.48(a)
      550512  NM_001017814.1  NP_001017814.1 


    ENSEMBL Gene Tree for SPATA6 (if available)
    TreeFam Gene Tree for SPATA6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SPATA6 gene
    SPATA6L2  
    1 SIMAP similar gene for SPATA6 using alignment to 3 protein entries:     SPAT6_HUMAN (see all proteins):
    SPATA6L

    SPATA6 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) 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

    10/3332 SNPs in SPATA6 are shown (see all 3332)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1149493341,2
    C,F--48760698(+) ATACAT/CTTTTA 1 -- int11Minor allele frequency- C:0.02NA 120
    rs1814978071,2
    --48760709(+) TATACC/TCTCTA 1 -- int10--------
    rs728879931,2
    C,F--48760866(+) CAAAAT/CGTTGA 1 -- int12Minor allele frequency- C:0.14WA 120
    rs1864723181,2
    --48760868(+) AAATGC/TTGAAC 1 -- int10--------
    rs1912080121,2
    --48760956(+) ACTTGC/TATACA 1 -- int10--------
    rs1434943541,2
    --48761021(+) TATCAA/CTTGAA 1 -- int10--------
    rs1509966811,2
    --48761099(+) TCATAC/TGTGTT 1 -- ut310--------
    rs1820481011,2
    --48761100(+) CATACA/GTGTTA 1 -- ut310--------
    rs49267231,2
    C,F,A,H--48761154(+) ccacaT/Aacaat 1 -- ut3114Minor allele frequency- A:0.36NS EA NA WA CSA 790
    rs1408061741,2
    --48761295(+) CTTTTA/GGGAGT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for SPATA6 (48761044 - 48937876 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for SPATA6:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2566377CNV Deletion19546169
    nsv508182CNV Loss20534489
    nsv870765CNV Loss21882294
    nsv461461CNV Gain19166990
    nsv871053CNV Gain21882294

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SPATA6 for disorders           About MalaCards
    OMIM gene information: 613947    OMIM disorders: --


    SPATA6 for disorders           About GeneDecksing


    Export disorders for SPATA6 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)
    About This Section

    PubMed articles for SPATA6 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SPATA6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    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. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Phosphoproteome analysis of capacitated human sperm. Evidence of tyrosine phosphorylation of a kinase-anchoring protein 3 and valosin-containing protein/p97 during capacitation. (PubMed id 12509440)1, 2 Ficarro S....Visconti P.E. (2003)
    5. 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)
    6. 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)
    7. A novel spermatogenesis-related factor-1 gene expressed in maturing rat testis. (PubMed id 11735130)1 Yamano Y....Morishima I. (2001)

    (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)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 54558 HGNC: 18309 AceView: SPATA6 Ensembl:ENSG00000132122 euGenes: HUgn54558
    ECgene: SPATA6 H-InvDB: SPATA6

    (According to HUGE)
    About This Section
      --

    (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 SPATA6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SPATA6 gene:
    Search GeneIP for patents involving SPATA6

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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