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

SPATA7 Gene

protein-coding   GIFtS: 48
GCID: GC14P088852

Spermatogenesis Associated 7

(Previous name: Leber congenital amaurosis 3)
(Previous symbol: LCA3)
  See related diseases
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 71 2     HSD-3.12 3
LCA31 2 5     Leber Congenital Amaurosis 31
HSD32 3 5     Spermatogenesis-Associated Protein 72
Spermatogenesis-Associated Protein HSD32 3     

External Ids:    HGNC: 204231   Entrez Gene: 558122   Ensembl: ENSG000000423177   OMIM: 6098685   UniProtKB: Q9P0W83   

Export aliases for SPATA7 gene to outside databases

Previous GC identifers: GC14P082668 GC14P086842 GC14P087921 GC14P069023


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

Entrez Gene summary for SPATA7 Gene:
This gene, originally isolated from testis, is also expressed in retina. Mutations in this gene are associated
with Leber congenital amaurosis and juvenile retinitis pigmentosa. Alternatively spliced transcript variants
encoding different isoforms have been found for this gene. (provided by RefSeq, May 2010)

GeneCards Summary for SPATA7 Gene: 
SPATA7 (spermatogenesis associated 7) is a protein-coding gene. Diseases associated with SPATA7 include spata7-related retinitis pigmentosa, and leber congenital amaurosis 3.

UniProtKB/Swiss-Prot: SPAT7_HUMAN, Q9P0W8
Function: May be involved in retinal function

Gene Wiki entry for SPATA7 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000014.8  NT_026437.12  NC_018925.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SPATA7 gene promoter:
         Nkx3-1   Nkx3-1 v4   NCX/Ncx   Nkx3-1 v1   Nkx3-1 v2   POU2F1   POU2F1a   Nkx3-1 v3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSPATA7 promoter sequence
   Search SABiosciences Chromatin IP Primers for SPATA7

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SPATA7


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

Entrez Gene cytogenetic band: 14q31.3   Ensembl cytogenetic band:  14q31.3   HGNC cytogenetic band: 14q31.3

SPATA7 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SPATA7 gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14P088852:  view genomic region     (about GC identifiers)

Start:
88,851,268 bp from pter      End:
88,936,694 bp from pter
Size:
85,427 bases      Orientation:
plus 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: SPAT7_HUMAN, Q9P0W8 (See protein sequence)
Recommended Name: Spermatogenesis-associated protein 7  
Size: 599 amino acids; 67719 Da
Secondary accessions: Q5BKY5 Q8WX30 Q96HF3 Q9H0X0 Q9P0W7
Alternative splicing: 3 isoforms:  Q9P0W8-1   Q9P0W8-2   Q9P0W8-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SPATA7: NX_Q9P0W8

Explore proteomics data for SPATA7 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9P0W8

  • SPATA7 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SPATA7 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001035518.1  NP_060888.2  

    ENSEMBL proteins: 
     ENSP00000451128   ENSP00000377176   ENSP00000451663   ENSP00000452359   ENSP00000450515  
     ENSP00000452364   ENSP00000451181   ENSP00000450654   ENSP00000450882   ENSP00000452435  
     ENSP00000450606   ENSP00000451690   ENSP00000452546   ENSP00000045347   ENSP00000450809  
     ENSP00000451019   ENSP00000348991  

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

    ProtoNet protein and cluster: Q9P0W8


    (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: SPAT7_HUMAN, Q9P0W8
    Function: May be involved in retinal function

    Phenotypes:
         2 GenomeRNAi human phenotypes for SPATA7:

     Increased gamma-H2AX phosphory  Increased number of cells in m 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for SPATA7 
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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 SPATA7

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007601visual perception IEA--
    GO:0050896response to stimulus IEA--

    SPATA7 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 SPATA7 (SPAT7)

    Search CenterWatch for drugs/clinical trials and news about SPATA7 / SPAT7

    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    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 SPATA7 gene (2 alternative transcripts): 
    NM_001040428.3  NM_018418.4  

    Unigene Cluster for SPATA7:

    Spermatogenesis associated 7
    Hs.525518  [show with all ESTs]
    Unigene Representative Sequence: BC034635
    18/22 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 22):
    ENST00000556553(uc001xwq.3 uc001xwr.3 uc001xws.3) ENST00000393545
    ENST00000554168 ENST00000556870 ENST00000555534 ENST00000557724 ENST00000555715
    ENST00000555356 ENST00000554102 ENST00000555515 ENST00000555401 ENST00000553626
    ENST00000553885 ENST00000557567 ENST00000557248 ENST00000553908 ENST00000045347(uc001xwu.3)
    ENST00000556666(uc001xwt.3)
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    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SPATA7
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SPATA7

    Additional mRNA sequence: 

    AF144487.3 AF144488.2 AK225746.1 AK290631.1 AK293007.1 AL136604.1 BC008656.1 BC034635.1 
    BC090875.1 CR533563.1 CR936777.1 

    10 DOTS entries:

    DT.40131298  DT.95318954  DT.91662962  DT.95166023  DT.100672705  DT.120763792  DT.100836961  DT.120763808 
    DT.120763848  DT.95166024 

    24/91 AceView cDNA sequences (see all 91):

    BU075591 AA745785 CA395658 BU608666 AI003803 BI828924 BI521313 AK055864 
    BC008656 BU741594 AA999984 CR618045 BI826740 CD556405 BX477865 BU687365 
    AL136604 BM724314 BX497728 BG701445 BE886115 BC037809 AF144487 BX119786 

    GeneLoc Exon Structure

    5/13 Alternative Splicing Database (ASD) splice patterns (SP) for SPATA7 (see all 13)    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g · 2h ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b · 10c · 10d · 10e ^ 11 ^ 12 ^ 13 ^
    SP1:                                                  -           -     -           -     -     -                                                               
    SP2:                                                  -                             -     -     -                                                               
    SP3:                                                                                -     -     -                                                               
    SP4:                                                  -                             -                                                                           
    SP5:                                                  -                             -     -                                                                     

    ExUns: 14a · 14b ^ 15 ^ 16 ^ 17
    SP1:  -                           
    SP2:  -                           
    SP3:  -                           
    SP4:                              
    SP5:                              


    ECgene alternative splicing isoforms for SPATA7

    (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

    SPATA7 expression in normal human tissues (normalized intensities)      SPATA7 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAAATGAGCA
    SPATA7 Expression
    About this image


    SPATA7 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/2 selected tissues (see all 2) fully expand
     
     Pancreas (Endocrine System)
             Posterior foregut-like cells ( A scalable, suspension protocol for derivation of...
     
     Testis (Reproductive System)

    See SPATA7 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SPATA7

    SOURCE GeneReport for Unigene cluster: Hs.525518
        SABiosciences Custom PCR Arrays for SPATA7
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPATA7

    (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 SPATA7 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Spata71 , 5 spermatogenesis associated 71, 5 77.18(n)1
    68.97(a)1
      12 (49.88 cM)5
    1048711  NM_178914.31  NP_849245.21 
     986281575 
    chicken
    (Gallus gallus)
    Aves SPATA71 spermatogenesis associated 7 50.93(n)
    37.29(a)
      423397  XM_421307.3  XP_421307.2 
    lizard
    (Anolis carolinensis)
    Reptilia SPATA76
    Uncharacterized protein
    42(a)
    1 ↔ 1
    1(13668796-13711869)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC7938301 novel protein similar to human and mouse spermatogenesis more 47.81(n)
    42.11(a)
      793830  XM_003200294.1  XP_003200342.1 


    ENSEMBL Gene Tree for SPATA7 (if available)
    TreeFam Gene Tree for SPATA7 (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, 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

    10/1235 SNPs in SPATA7 are shown (see all 1235)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs800442811,2
    Cpathogenic169864933(+) CAATGC/TGAGCC 4 R * stg11Minor allele frequency- A:0.00NA 4030
    rs758959251,2
    Cpathogenic169885545(+) TCGAGC/TGACAT 4 R * stg10--------
    VAR_0671914
    ----see VAR_0671912 I T mis40--------
    rs802300121,2
    C,F--69049196(+) GGCCAG/ACCTCA 2 -- int13Minor allele frequency- A:0.15WA 122
    rs1117192751,2
    C--69053920(+) TTTTTC/TCCCTT 2 -- int10--------
    rs101518821,2
    C--69054017(+) GTGGGG/Tttttt 2 -- int11Minor allele frequency- T:0.00NA 2
    rs1508412391,2
    --69831958(+) AAGCTC/GTCAGT 2 -- us2k10--------
    rs1393098111,2
    C--69832182(+) TTTTGA/TTTTTT 2 -- us2k10--------
    rs1820891281,2
    --69832239(+) GTCATC/GGTATA 2 -- us2k10--------
    rs733198401,2
    C--69832608(+) TTTTGG/CGTAAG 2 -- us2k11Minor allele frequency- C:0.50WA 2

    HapMap Linkage Disequilibrium report for SPATA7 (88851268 - 88936694 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/12 variations for SPATA7 (see all 12):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2276274CNV Deletion18987734
    esv2568808CNV Deletion19546169
    esv2748992CNV Deletion23290073
    esv2619552CNV Deletion19546169
    esv994338CNV Deletion20482838
    esv3753CNV Deletion18987735
    esv2748993CNV Deletion23290073
    esv268022CNV Insertion20981092
    esv273157CNV Insertion20981092
    esv273099CNV Insertion20981092


    Human Gene Mutation Database (HGMD): SPATA7
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing SPATA7
    DNA2.0 Custom Variant and Variant Library Synthesis for SPATA7

    (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
    OMIM gene information: 609868   
    OMIM disorders: 604232  268000  
    UniProtKB/Swiss-Prot: SPAT7_HUMAN, Q9P0W8
  • Leber congenital amaurosis 3 (LCA3) [MIM:604232]: A severe dystrophy of the retina, typically becoming
    evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish
    or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. Note=The disease is caused by
    mutations affecting the gene represented in this entry
  • Retinitis pigmentosa autosomal recessive (ARRP) [MIM:268000]: A retinal dystrophy belonging to the group
    of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus
    examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors.
    Patients typically have night vision blindness and loss of midperipheral visual field. As their condition
    progresses, they lose their far peripheral visual field and eventually central vision as well. Note=The disease
    is caused by mutations affecting the gene represented in this entry

  • 16 diseases for SPATA7:    About MalaCards
    spata7-related retinitis pigmentosa    leber congenital amaurosis 3    spata7-related leber congenital amaurosis    retinitis pigmentosa, juvenile, autosomal recessive
    leber congenital amaurosis    retinitis pigmentosa, juvenile    mixed gonadal dysgenesis    rhyns syndrome
    retinitis pigmentosa    gonadal dysgenesis    pigmentary retinopathy    fundus dystrophy
    hypospadias    retinitis    retinal degeneration    blindness

    2 diseases from the University of Copenhagen DISEASES database for SPATA7:
    Leber congenital amaurosis     Mixed gonadal dysgenesis

    SPATA7 for disorders           About GeneDecksing

    GeneTests: SPATA7
    GeneReviews: SPATA7

    Export disorders for SPATA7 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 SPATA7 gene, integrated from 9 sources (see all 21):
    (articles sorted by number of sources associating them with SPATA7)
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    1. Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. (PubMed id 19268277)1, 2, 3 Wang H.... Chen R. (2009)
    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. A novel gene, RSD-3/HSD-3.1, encodes a meiotic-related protein expressed in rat and human testis. (PubMed id 12736779)1, 2 Zhang X.... Koide S.S. (2003)
    4. The DNA sequence and analysis of human chromosome 14. (PubMed id 12508121)1, 2 Heilig R.... Weissenbach J. (2003)
    5. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (2001)
    6. A novel locus for Leber congenital amaurosis on chromosome 14q24. (PubMed id 9799089)1, 3 Stockton D.W....Lupski J.R. (1998)
    7. Late onset retinitis pigmentosa. (PubMed id 22136677)1 Avila-FernA!ndez A....Cremers F.P. (2011)
    8. Lack of phenotypic effect of triallelic variation in S PATA7 in a family with Leber congenital amaurosis resulting from CRB1 mutations. (PubMed id 22219627)1 Li L....Zhang Q. (2011)
    9. Detection of variants in 15 genes in 87 unrelated Chinese patients with Leber congenital amaurosis. (PubMed id 21602930)2 Li L....Hejtmancik J.F. (2011)
    10. Screening of SPATA7 in patients with Leber congenital amaurosis and severe childhood-onset retinal dystrophy reveals disease-causing mutations. (PubMed id 21310915)1 Mackay D.S....Moore A.T. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 55812 HGNC: 20423 AceView: SPATA7 Ensembl:ENSG00000042317 euGenes: HUgn55812
    ECgene: SPATA7 H-InvDB: SPATA7

    (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 SPATA7 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SPATA7 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SPATA7 gene:
    Search GeneIP for patents involving SPATA7

    GeneCards and IP:
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