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

SPATA6 Gene

protein-coding   GIFtS: 43
GCID: GC01M048763

spermatogenesis associated 6
  Search for SPATA6
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SPATA6    

Aliases
for SPATA6 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Spermatogenesis Associated 61 2     HASH2
SRF-11 2     Spermatogenesis-Associated Protein 62
SRF11 2     Spermatogenesis-Related Factor-12
FLJ100071     

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


Summaries
for SPATA6 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: SPAT6_HUMAN, Q9NWH7
Function: May play a role in spermatid maturation or sperm function (By similarity)




Genomic Views
for SPATA6 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.1  NT_032977.9  
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 plasmid: SPATA6 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

Proteins
for SPATA6 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NWH7

    • SPATA6 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_061946.1  
    ENSEMBL proteins: 
     ENSP00000360913   ENSP00000360909   ENSP00000360907   ENSP00000379502  

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    Uscn Proteins for SPATA6

    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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    Protein Domains /
    Families
    for SPATA6 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    SPATA6 for domains           About GeneDecksing

    1 InterPro domain/family:
     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


    Function
    for SPATA6 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

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

    miRNA
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    1 GenomeRNAi human phenotype for SPATA6:
     Decreased number of cells in m 


    Pathways & Interactions
    for SPATA6 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 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



    Drugs & Compounds
    for SPATA6 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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
    Search CenterWatch for drugs/clinical trials and news about SPATA6 / SPAT6 

    Transcripts
    for SPATA6 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
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    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
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000371847(uc001crr.2 uc001crs.2 uc010omv.2) ENST00000371843
    ENST00000371841 ENST00000490850 ENST00000487629 ENST00000463938 ENST00000487543
    ENST00000465990 ENST00000471975 ENST00000396199

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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 plasmid: SPATA6 3' UTR sequence
    Inhib. RNA
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    Clone
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    Primer
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    Additional cDNA 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):

    BU684281 CR592303 BC020660 AK000869 BF109318 AA769927 AU116876 BX099038 
    NM_019073 CB989040 AW183572 BI827849 AW303869 AW592920 BI562550 BG503847 
    BI520668 BG771751 BX348773 BG718353 AW340418 AI375752 AA758994 BX371524 

    GeneLoc Exon Structure


    Expression
    for SPATA6 gene

    (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)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATAAACCTCA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    SPATA6 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Definitive endoderm-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    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
    Primer
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    In Situ
    Assay Products:     
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    Orthologs
    for SPATA6 gene

    (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 4/14 species (see all 14)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    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
    		 --
    		 49(a)
    		 1 ↔ 1
    		 GL343249.1(286737-305232)
    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
    for SPATA6 gene

    (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



    Genomic Variants
    for SPATA6 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/2705 NCBI SNPs in SPATA6 are shown (see all 2705)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 1 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1149493341,2
    		F,--48760698(+) ATACAT/CTTTTA 1 -- int11Minor allele frequency- C:0.02NA 120
    rs1814978071,2
    		--48760709(+) TATACC/TCTCTA 1 -- int10--------
    rs728879931,2
    		C,--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 (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for SPATA6
         1 Indel: 39600

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    Disorders / Diseases
    for SPATA6 gene

    (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.)
    About This Section
    SPATA6 for disorders           About MalaCards

    SPATA6 for disorders           About GeneDecksing

    OMIM gene information: 613947    OMIM disorders: --


    Export disorders for SPATA6 gene to outside databases

    Publications
    for SPATA6 gene

    (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. 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)
    5. 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 Ficarro S....Visconti P.E. (2003)
    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)

    External Searches for SPATA6 gene

    (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)

    Genome Databases showing SPATA6 gene

    (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

    Other Databases showing SPATA6 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing SPATA6 gene

    (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

    Intellectual Property
    for SPATA6 gene

    (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



    Products
    for SPATA6 gene

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    About This Section

     
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