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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

SPATA9 Gene

protein-coding GIFtS: 39
GCID: GC05M095013

spermatogenesis associated 9

Explore 4 diseases affiliated with
SPATA9 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Spermatogenesis Associated 9¹ ²
NYD-SP16¹ ²
Testis Development Protein NYD-SP16² ³
FLJ35906¹
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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000005.9 NC_018916.1 NT_034772.6

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the SPATA9 gene promoter:
AREB6 HOXA3
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: SPATA9 promoter sequence

Search SABiosciences Chromatin IP Primers for SPATA9

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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, 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: SPAT9_HUMAN, Q9BWV2 (See protein sequence)

Recommended Name: Spermatogenesis-associated protein 9

Size: 254 amino acids; 28740 Da

Subcellular location: Membrane; Single-pass membrane protein (Potential)

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

SPATA9 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_114158.2

ENSEMBL proteins:

ENSP00000427257 ENSP00000325491 ENSP00000274432 ENSP00000420883 ENSP00000379236

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	Uscn Proteins for SPATA9

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0016021	integral to membrane	IEA	--

SPATA9 for ontologies About GeneDecksing

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

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,
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: SPAT9_HUMAN, Q9BWV2

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

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(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 Central^TM Interacting Genes and Proteins Networks for SPATA9

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007275	multicellular organismal development	IEA	--
GO:0007283	spermatogenesis	IEA	--
GO:0030154	cell differentiation	IEA	--

SPATA9 for ontologies About GeneDecksing

(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

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(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 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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Additional cDNA sequence:

AK292338.1 AK310260.1 BC047333.1

6 DOTS entries:

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

24/36 AceView cDNA sequences (see all 36):

BX282523 BC047333 NM_031952 NM_173360 BC032832 AA954970 BG723029 AK093225

BF223136 AA758202 BI829173 AA776716 AI970130 BI831509 AI824998 AI699532

AI962769 AI187784 AI695909 AI341284 BE501110 BF592939 AI015246 AY027526

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™, 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

SPATA9 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ATAGAGTAAA

About this image
See SPATA9 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SPATA9

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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In Situ
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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)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for SPATA9 gene from 2/7 species (see all 7) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Spata9^{1 , 5}	spermatogenesis associated 9^{1, 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	--	43(a)	1 ↔ 1	2(25934606-25941507)

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)
About This Section

(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

SNP ID	Valid	Clinical significance	Chr 5 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs146032096^1,2		--	94993568(+)	`CTTCAA/GTGCCC`	1	--	int¹		0	--	--	--	--
rs150549^1,2	C,F,O,A,H,	--	94993572(-)	`GACTGG/CGCATT`	1	--	int¹		16		MN NA NS EA WA	1100
rs80322625^1,2	C	--	94993645(+)	`AAAAC-/TGTAGCC`	1	--	int¹		0	--	--	--	--
rs77091976^1,2		--	94993717(+)	`GTGTGC/TACTTG`	1	--	int¹		0	--	--	--	--
rs115446935^1,2	F,	--	94993788(+)	`TTCATA/GTACAG`	1	--	int¹		1		WA	118
rs116814388^1,2	F,	--	94993878(+)	`TTGCAA/GGTGAT`	1	--	int¹		1		WA	118
rs148479810^1,2	C,	--	94993905(+)	`GGCAG-/ACTCAA ACTCT`	1	--	int¹		0	--	--	--	--
rs143425059^1,2		--	94994030(+)	`AAAAAA/CATTAA`	1	--	ut3¹		0	--	--	--	--
rs151268051^1,2		--	94994110(+)	`GTTCAC/TTAAAA`	1	--	ut3¹		0	--	--	--	--
rs189092952^1,2		--	94994127(+)	`AGTCAC/GTACAT`	1	--	ut3¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for SPATA9 (94987885 - 95034415 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for SPATA9
1 CNV: 99211

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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.)
About This Section

SPATA9 for disorders           About GeneDecksing

OMIM gene information: 608039    OMIM disorders: --

4 diseases for SPATA9:    About MalaCards

sertoli cell-only syndrome male infertility infertility prostatitis

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)
About This Section

PubMed articles for SPATA9 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SPATA9)

Utopia: connect your pdf to the dynamic
world of online information

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

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

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

(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

Name	Description
PharmGKB entry for SPATA9	Pharmacogenomics, SNPs, Pathways

Intellectual Property for SPATA9 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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),
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About This Section


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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SPATA9

GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
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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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Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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spermatogenesis associated 9

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SPATA9 Gene

spermatogenesis associated 9

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