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SPATA1 Gene

protein-coding   GIFtS: 37
GCID: GC01P084971

Spermatogenesis Associated 1

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(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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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Spermatogenesis Associated 11 2     Spermatogenesis Associated Protein 12
Sperm-Specific Protein SP-22 3     Spermatogenesis-Associated Protein 12
SP-22     ASEF25
SPAP12     SPATA135

External Ids:    HGNC: 146821   Entrez Gene: 1005057412   Ensembl: ENSG000001224327   OMIM: 6133245   UniProtKB: Q5VX523   
ORGUL members:         

Export aliases for SPATA1 gene to outside databases

Previous GC identifers: GC01M085538 GC01P084109 GC01P084260 GC01P084394 GC01P084684 GC01P084744


(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 SPATA1 Gene:
SPATA1 (spermatogenesis associated 1) is a protein-coding 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000001.10  NT_032977.10  NC_018912.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SPATA1 gene promoter:
         Nkx3-1   Nkx3-1 v4   Nkx3-1 v1   C/EBPalpha   Nkx3-1 v2   AREB6   CHOP-10   NF-AT4   NF-AT3   Nkx3-1 v3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 3): SPATA1 promoter sequence
   Search Chromatin IP Primers for SPATA1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SPATA1


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

Entrez Gene cytogenetic band: 1p22.3   Ensembl cytogenetic band:  1p22.3   HGNC cytogenetic band: 1p22.3

SPATA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPATA1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P084971:  view genomic region     (about GC identifiers)

Start:
84,971,974 bp from pter      End:
85,031,877 bp from pter
Size:
59,904 bases      Orientation:
plus 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: SPAT1_HUMAN, Q5VX52 (See protein sequence)
Recommended Name: Spermatogenesis-associated protein 1  
Size: 437 amino acids; 50307 Da
Sequence caution: Sequence=AAG22047.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=AAI19642.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAI19643.1;
Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=AAI27635.1; Type=Erroneous
initiation; Note=Translation N-terminally shortened; Sequence=CAH70205.2; Type=Erroneous initiation;
Note=Translation N-terminally shortened; Sequence=CAM13069.1; Type=Erroneous gene model prediction;
Secondary accessions: A0PJU9 Q0VDJ9 Q0VDK0 Q6P386 Q9HAR4
Alternative splicing: 3 isoforms:  Q5VX52-1   Q5VX52-2   Q5VX52-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SPATA1: NX_Q5VX52

Explore proteomics data for SPATA1 at MOPED


See SPATA1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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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: Q5VX52


(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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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 COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
golgi apparatus1
mitochondrion1

(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 SPATA1
Interactions:

    Search GeneGlobe Interaction Network for SPATA1

(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 SPATA1 (SPAT1)



(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 SPATA1 gene (2 alternative transcripts): 
NM_001081472.1  NM_022354.1  

Unigene Cluster for SPATA1:

Spermatogenesis associated 1
Hs.584956  [show with all ESTs]
Unigene Representative Sequence: BC119642
10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000370638(uc001djx.3) ENST00000484939 ENST00000490879(uc001djy.2)
ENST00000468437 ENST00000431031 ENST00000554297 ENST00000485121 ENST00000473108
ENST00000460286 ENST00000263717(uc021opb.1)
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Additional mRNA sequence: 

BC119641.1 BC119642.1 

7 DOTS entries:

DT.91751364  DT.91974728  DT.75160642  DT.95148407  DT.95231208  DT.97809837  DT.121427686 

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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SPATA1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GAACTATAAG
SPATA1 Expression
About this image


SPATA1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Eye (Sensory Organs)    fully expand to see all 2 entries
         Mature Rod Cells Outer Nuclear Layer
         Retina
 
 Neurons
         Mature Rod Cells Outer Nuclear Layer
 
 Testis (Reproductive System)
SPATA1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SPATA1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.584956
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPATA1

(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 SPATA1 gene from Selected species (see all 8)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Spata11 , 5 spermatogenesis associated 11, 5 85.93(n)1
78.66(a)1
  3 (71.30 cM)5
709511  NM_027617.31  NP_081893.11 
 1464572035 
chicken
(Gallus gallus)
Aves SPATA11 spermatogenesis associated 1 66.28(n)
56.07(a)
  424537  XM_004936651.1  XP_004936708.1 
tropical clawed frog
(Xenopus tropicalis)
Amphibia spata11 spermatogenesis associated 1 57.78(n)
48.58(a)
  100498562  XM_002931696.2  XP_002931742.2 
zebrafish
(Danio rerio)
Actinopterygii LOC1018858341 spermatogenesis-associated protein 1-like 48.47(n)
35.51(a)
  101885834  XM_005155817.1  XP_005155874.1 


ENSEMBL Gene Tree for SPATA1 (if available)
TreeFam Gene Tree for SPATA1 (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 SPATA1 (see all 896)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs790631241,2
C,F--83086419(+) AGAATG/TTGGGG 1 -- int12Minor allele frequency- T:0.40NA 10
rs57757891,2
C,F--83096423(+) ATTGAT/-TTTTT 1 -- int1 trp32Minor allele frequency- -:0.50NA 4
rs120218851,2
H--84976324(+) atgtcC/Tcagga 1 -- int14Minor allele frequency- T:0.00NS EA 420
rs346488301,2
C--84980475(+) GAAAA-/ACCTGT 1 -- int10--------
rs2012064761,2
C--84981938(+) AAAAA-/ACTATT 1 -- ut510--------
rs1468019791,2
--84988506(+) AGCTCA/GTTAAA 1 -- us2k10--------
rs1476289161,2
C--84988585(+) ATGTC-/TTGGTG 1 -- us2k10--------
rs75472081,2
C,F--84988604(+) GATCCC/TGACCA 1 -- us2k13Minor allele frequency- T:0.05WA NA EA 358
rs75241951,2
C,F--84988640(+) GGTAGG/AATCAG 1 -- us2k11Minor allele frequency- A:0.03WA 118
rs38136071,2
C,F,A,H--84988654(-) CTAATT/CCCCCA 1 -- us2k18Minor allele frequency- C:0.15EA WA NA 1658

HapMap Linkage Disequilibrium report for SPATA1 (84971974 - 85031877 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SPATA1: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SPATA1
DNA2.0 Custom Variant and Variant Library Synthesis for SPATA1

(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: 613324    OMIM disorders: --


Find genes that share disorders with SPATA1           About GenesLikeMe

Genetic Association Database (GAD): SPATA1
Human Genome Epidemiology (HuGE) Navigator: SPATA1 (1 document)

Export disorders for SPATA1 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 SPATA1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SPATA1)
    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. (Nature 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. (Genome Res. 2004)
  3. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  4. Single-nucleotide polymorphisms, acute rejection, and severity of tubulitis in kidney transplantation, accounting for center-to-center variation. (PubMed id 21085059)4 Israni A....Oetting W.S. (Transplantation 2010)
  5. 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)
  6. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)
  7. Creation of genome-wide protein expression libraries using random activation of gene expression. (PubMed id 11329013)1 Harrington J.J.... Ducar M. (Nat. Biotechnol. 2001)
  8. (PubMed id )2 

(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: 100505741 HGNC: 14682 Ensembl:ENSG00000122432 euGenes: HUgn100505741 ECgene: SPATA1
H-InvDB: SPATA1

(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 SPATA1 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 SPATA1 gene:
Search GeneIP for patents involving SPATA1

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
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 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPATA1
 SwitchGear 3'UTR luciferase reporter plasmids for SPATA1
 SwitchGear Promoter luciferase reporter plasmids for SPATA1
 Search ThermoFisher Antibodies for SPATA1
 Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat SPATA1
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SPATA1
 inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SPATA1
 LSBio Antibodies in human, mouse, rat for SPATA1
Customized transgenic rodents for:
 Humanization
 Biomarker expression
 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
 Time-controlled gene expresssion
 Browse compounds at ApexBio
 Search Addgene for plasmids for SPATA1
  Search eBioscience for proteins for SPATA1
  Search eBioscience for elisas for SPATA1
  eBioscience FlowRNA Probe Sets
       
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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