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SPATA9 Gene

protein-coding   GIFtS: 42
GCID: GC05M095013

Spermatogenesis Associated 9

  Search for SPATA9
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 91 2
Testis Development Protein NYD-SP162 3
NYD-SP162
Spermatogenesis-Associated Protein 92

External Ids:    HGNC: 229881   Entrez Gene: 838902   Ensembl: ENSG000001457577   OMIM: 6080395   UniProtKB: Q9BWV23   

Export aliases for SPATA9 gene to outside databases

Previous GC identifers: GC05M095016 GC05M095061 GC05M090184


(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 SPATA9 Gene:
SPATA9 (spermatogenesis associated 9) is a protein-coding gene.

UniProtKB/Swiss-Prot: SPAT9_HUMAN, Q9BWV2
Function: May play a role in testicular development/spermatogenesis and may be an important factor in male
infertility




(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_000005.9  NT_034772.7  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SPATA9 gene promoter:
         AREB6   HOXA3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSPATA9 promoter sequence
   Search Chromatin IP Primers for SPATA9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SPATA9


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

Entrez Gene cytogenetic band: 5q15   Ensembl cytogenetic band:  5q15   HGNC cytogenetic band: 5q15

SPATA9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPATA9 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M095013:  view genomic region     (about GC identifiers)

Start:
94,987,885 bp from pter      End:
95,034,415 bp from pter
Size:
46,531 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,
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UniProtKB/Swiss-Prot: SPAT9_HUMAN, Q9BWV2 (See protein sequence)
Recommended Name: Spermatogenesis-associated protein 9  
Size: 254 amino acids; 28740 Da
Secondary accessions: A8K8H3 Q4G122 Q86X33 Q8NA28
Alternative splicing: 3 isoforms:  Q9BWV2-1   Q9BWV2-2   Q9BWV2-3   (No experimental confirmation available. 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 SPATA9: NX_Q9BWV2

Explore proteomics data for SPATA9 at MOPED


See SPATA9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_114158.2  
ENSEMBL proteins: 
 ENSP00000427257   ENSP00000325491   ENSP00000274432   ENSP00000420883   ENSP00000379236  

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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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ProtoNet protein and cluster: Q9BWV2


(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: SPAT9_HUMAN, Q9BWV2
Function: May play a role in testicular development/spermatogenesis and may be an important factor in male
infertility

Animal Models:

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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
SPAT9_HUMAN, Q9BWV2: Membrane; Single-pass membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol3
mitochondrion2
endoplasmic reticulum1
peroxisome1

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

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane IEA--

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(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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Interactions:

    Search GeneGlobe Interaction Network for SPATA9

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 SPATA9           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 Tocris compounds for SPATA9 (SPAT9)



(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 SPATA9 gene (2 alternative transcripts): 
NM_173361.1  NM_031952.3  

Unigene Cluster for SPATA9:

Spermatogenesis associated 9
Hs.50499  [show with all ESTs]
Unigene Representative Sequence: AK310260
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000477715(uc010jbh.1 uc003klh.1 uc003kli.1) ENST00000477047
ENST00000316087 ENST00000274432(uc003klj.1) ENST00000379990 ENST00000489917
ENST00000395899
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hsa-miR-578 hsa-miR-497*
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Additional mRNA sequence: 

AK292338.1 AK310260.1 BC047333.1 

6 DOTS entries:

DT.206352  DT.95299614  DT.120797446  DT.100016391  DT.91956362  DT.95140409 

Selected AceView cDNA sequences (see all 36):

BC032832 NM_031952 NM_173360 BC047333 BX282523 BI831509 BI829173 BF592939 
AA776716 BF223136 BE501110 AI699532 AA758202 AX747999 AI962769 AI824998 
AA954970 AA971333 AI015246 BQ013593 AI341284 AI970130 BM991650 AI695909 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for SPATA9    About this scheme

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


ECgene alternative splicing isoforms for SPATA9

(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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SPATA9 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ATAGAGTAAA
SPATA9 Expression
About this image

SPATA9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SPATA9 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.50499

UniProtKB/Swiss-Prot: SPAT9_HUMAN, Q9BWV2
Tissue specificity: Highly expressed in testes and pancreas. Low levels found in the heart, lungs, and brain. Very
low expression detected in the placenta. No expression seen in skeletal muscle, liver, kidney, thymus, small
intestine, colons, spleen, leukocytes, prostate gland, and ovary. In the adult testes, expression was about
6.44-fold higher than in the embryo testes. No expression in testes of patients with Sertoli-cell-only syndrome.
In patients with arrest at spermatogonium and primary spermatocyte stages, no expression was detected. In
patients with arrest at the spermatid stage, expression level was weak or absent. Variable expression was seen in
patients with spermatogenic arrest

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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 SPATA9 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Spata91 , 5 spermatogenesis associated 91, 5 82.6(n)1
79.28(a)1
  13 (40.95 cM)5
755711  NM_029343.31  NP_083619.11 
 759677395 
lizard
(Anolis carolinensis)
Reptilia SPATA96
spermatogenesis associated 9
39(a)
1 ↔ 1
2(25934465-25941786)


ENSEMBL Gene Tree for SPATA9 (if available)
TreeFam Gene Tree for SPATA9 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(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 SPATA9 (see all 502)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 5 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1460320961,2
--94993568(+) CTTCAA/GTGCCC 1 -- int10--------
rs1505491,2
C,F,O,A,H--94993572(-) GACTGG/CGCATT 1 -- int116Minor allele frequency- C:0.34MN NA NS EA WA 1100
rs803226251,2
C--94993645(+) AAAAC-/GT/TG 
        
TAGCC
1 -- int10--------
rs770919761,2
F--94993717(+) GTGTGC/TACTTG 1 -- int10--------
rs1154469351,2
C,F--94993788(+) TTCATA/GTACAG 1 -- int11Minor allele frequency- G:0.09WA 118
rs1168143881,2
C,F--94993878(+) TTGCAA/GGTGAT 1 -- int11Minor allele frequency- G:0.07WA 118
rs1484798101,2
C--94993905(+) GGCAG-/ACTCAA
        
ACTCT
1 -- int10--------
rs1434250591,2
--94994030(+) AAAAAA/CATTAA 1 -- ut310--------
rs1512680511,2
--94994110(+) GTTCAC/TTAAAA 1 -- ut310--------
rs1890929521,2
--94994127(+) AGTCAC/GTACAT 1 -- ut310--------

HapMap Linkage Disequilibrium report for SPATA9 (94987885 - 95034415 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for SPATA9:    About this table    
Variant IDTypeSubtypePubMed ID
esv273462CNV Insertion20981092
esv1052640CNV Insertion17803354
esv267864CNV Insertion20981092
nsv507274CNV Insertion20534489
esv2513210CNV Insertion19546169
nsv830409CNV Gain17160897

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(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: 608039    OMIM disorders: --


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Genetic Association Database (GAD): SPATA9

Export disorders for SPATA9 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 SPATA9 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SPATA9)
    Utopia: connect your pdf to the dynamic
world of online information

  1. NYD-SP16, a novel gene associated with spermatogenesis of human testis. (PubMed id 12493713)1, 2, 3 Cheng L.J....Sha J.H. (Biol. Reprod. 2003)
  2. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. (PubMed id 21946350)1, 4 Soler Artigas M....Tobin M.D. (Nat. Genet. 2011)
  3. 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)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  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. (Genome Res. 2006)
  6. Human testicular protein NYD-SP16 is involved in sperm capacitation and the acrosome reaction. (PubMed id 16963046)1 Lu Y....Sha J. (Fertil. Steril. 2006)
  7. 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)

(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: 83890 HGNC: 22988 AceView: SPATA9 Ensembl:ENSG00000145757 euGenes: HUgn83890
ECgene: SPATA9 H-InvDB: SPATA9

(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 SPATA9 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 SPATA9 gene:
Search GeneIP for patents involving SPATA9

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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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SPATA9
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SPATA9
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 Search Addgene for plasmids for SPATA9
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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 , 21 Aug 2014 , 8 Sep 2014

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