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SSNA1 Gene

protein-coding   GIFtS: 54
GCID: GC09P140083

Sjogren Syndrome Nuclear Autoantigen 1

(Previous name: Sjogren's syndrome nuclear autoantigen 1)
  See SSNA1-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)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Sjogren Syndrome Nuclear Autoantigen 11 2     N142
NA142 3 5     NA-142
Sjogren'S Syndrome Nuclear Autoantigen 11 2     Sjoegren Syndrome Nuclear Autoantigen 12
Nuclear Autoantigen Of 14 KDa2 3     

External Ids:    HGNC: 113211   Entrez Gene: 86362   Ensembl: ENSG000001761017   OMIM: 6108825   UniProtKB: O438053   
ORGUL members:         

Export aliases for SSNA1 gene to outside databases

Previous GC identifers: GC00U990442 GC09P131773 GC09P133524 GC09P135440 GC09P137358 GC09P139202 GC09P109543


(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 SSNA1 Gene:
SSNA1 (Sjogren syndrome nuclear autoantigen 1) is a protein-coding gene. Diseases associated with SSNA1 include paralytic squint, and sjogren's syndrome. GO annotations related to this gene include identical protein binding.


(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_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the SSNA1 gene promoter:
         MyoD   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSSNA1 promoter sequence
   Search Chromatin IP Primers for SSNA1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SSNA1


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

Entrez Gene cytogenetic band: 9q34.3   Ensembl cytogenetic band:  9q34.3   HGNC cytogenetic band: 9q34.3

SSNA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SSNA1 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P140083:  view genomic region     (about GC identifiers)

Start:
140,083,054 bp from pter      End:
140,084,822 bp from pter
Size:
1,769 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: SSNA1_HUMAN, O43805 (See protein sequence)
Recommended Name: Sjoegren syndrome nuclear autoantigen 1  
Size: 119 amino acids; 13596 Da
Secondary accessions: Q5VSG0 Q6FG70 Q9BVW8

Explore the universe of human proteins at neXtProt for SSNA1: NX_O43805

Explore proteomics data for SSNA1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys97
  • Modification sites at PhosphoSitePlus

  • See SSNA1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_003722.2  
    ENSEMBL proteins: 
     ENSP00000313752  
    Reactome Protein details: O43805

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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: O43805

    UniProtKB/Swiss-Prot: SSNA1_HUMAN, O43805
    Similarity: Belongs to the SSNA1 family


    (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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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0042802identical protein binding IEA--
         
    Find genes that share ontologies with SSNA1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SSNA1:
     Synthetic lethal with c-Myc af 

    Animal Models:
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    hsa-mir-1 (MIRT001330), hsa-mir-193b-3p (MIRT041367), hsa-mir-124-3p (MIRT022545)

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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
    SSNA1_HUMAN, O43805: Nucleus. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton5
    nucleus5
    cytosol4
    extracellular1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005813centrosome IDA--
    GO:0005829cytosol TAS--

    Find genes that share ontologies with SSNA1           About GenesLikeMe


    (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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    SuperPaths for SSNA1 About    
    See pathways by source

    SuperPathContained pathways About
    1Regulation of PLK1 Activity at G2/M Transition
    Recruitment of mitotic centrosome proteins and complexes0.86
    Regulation of PLK1 Activity at G2/M Transition0.77
    Loss of Nlp from mitotic centrosomes0.86
    G2/M Transition0.70
    Centrosome maturation0.86
    Mitotic G2-G2/M phases0.69
    Loss of proteins required for interphase microtubule organizationfrom the centrosome0.86
    2Cell Cycle, Mitotic
    Cell Cycle, Mitotic0.90
    Cell Cycle0.90


    Find genes that share SuperPaths with SSNA1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    4 Reactome Pathways for SSNA1
        Recruitment of mitotic centrosome proteins and complexes
    Loss of proteins required for interphase microtubule organization,from the centrosome
    Regulation of PLK1 Activity at G2/M Transition
    Loss of Nlp from mitotic centrosomes


        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SSNA1
    Interactions:

        Search GeneGlobe Interaction Network for SSNA1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SSNA1 (O438053 ENSP000003137524) via UniProtKB, MINT, STRING, and/or I2D (see all 57)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SPASTQ9UBP03, ENSP000003208854I2D: score=1 STRING: ENSP00000320885
    SPATA2Q9UM823, ENSP000002894314I2D: score=2 STRING: ENSP00000289431
    CEP135ENSP000002572874STRING: ENSP00000257287
    CEP70ENSP000002649824STRING: ENSP00000264982
    CETN2ENSP000003593004STRING: ENSP00000359300
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    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000086G2/M transition of mitotic cell cycle TAS--
    GO:0000278mitotic cell cycle TAS--
    GO:0042073intraciliary transport IEA--
    GO:0060830ciliary receptor clustering involved in smoothened signaling pathway IEA--

    Find genes that share ontologies with SSNA1           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 Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SSNA1



    (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 SSNA1 gene: 
    NM_003731.2  

    Unigene Cluster for SSNA1:

    Sjogren syndrome nuclear autoantigen 1
    Hs.530314  [show with all ESTs]
    Unigene Representative Sequence: BM559272
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000322310(uc004cls.2) ENST00000459860 ENST00000463511 ENST00000464553

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    Additional mRNA sequence: 

    BC000864.1 BC004118.2 BC015827.2 BT006766.1 CR542238.1 Z96932.1 

    7 DOTS entries:

    DT.95100744  DT.92433145  DT.100797483  DT.100797481  DT.92433146  DT.100797485  DT.40109073 

    Selected AceView cDNA sequences (see all 226):

    AW328179 BM920119 BM993964 AI288565 BI826238 BU538047 AU098405 BM796730 
    AI745563 AA489649 CA423863 CR620508 BE382943 BC004118 AA360529 BQ776958 
    BM911422 CR611889 BM127556 AI797445 CA433865 BQ672898 BM773159 BG773749 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SSNA1    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b · 3c · 3d
    SP1:                                                            
    SP2:                                -                           
    SP3:                                                            
    SP4:                                -                           


    ECgene alternative splicing isoforms for SSNA1

    (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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    SSNA1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGGCCCCCT
    SSNA1 Expression
    About this image

    SSNA1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SSNA1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.530314

    UniProtKB/Swiss-Prot: SSNA1_HUMAN, O43805
    Tissue specificity: Widely expressed

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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 SSNA1 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ssna11 , 5 Sjogren's syndrome nuclear autoantigen 11, 5 90.2(n)1
    97.48(a)1
      2 (17.12 cM)5
    684751  NM_023464.21  NP_075953.11 
     252710395 
    chicken
    (Gallus gallus)
    Aves LOC7711901 Sjoegren syndrome nuclear autoantigen 1-like 61.95(n)
    51.33(a)
      771190  XM_001234483.3  XP_001234484.1 
    lizard
    (Anolis carolinensis)
    Reptilia SSNA16
    Sjogren syndrome nuclear autoantigen 1
    55(a)
    1 ↔ 1
    6(13883337-13883693)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.80822 Xenopus laevis transcribed sequence with moderate similarity more 78.83(n)    BI477766.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ssna11 Sjogren syndrome nuclear autoantigen 1 73.09(n)
    78.9(a)
      561124  NM_001144793.1  NP_001138265.1 


    ENSEMBL Gene Tree for SSNA1 (if available)
    TreeFam Gene Tree for SSNA1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SSNA1 gene
    1 SIMAP similar gene for SSNA1 using alignment to 1 protein entry:     SSNA1_HUMAN:
    USP4

    Find genes that share paralogs with SSNA1           About GenesLikeMe



    (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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    6 SNPs for SSNA1    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0363434
    A breast cancer sample4--see VAR_0363432 K N mis40--------
    rs600731161,2
    C,F--140085060(+) GCTCAC/ACCTCC 1 -- int16Minor allele frequency- A:0.25WA NA CSA 245
    rs727632891,2
    C,F--140085179(+) TCAGAT/CTCAGG 1 -- int18Minor allele frequency- C:0.19WA NA CSA EA 365
    rs727632901,2
    C,F--140085182(+) GATTCA/GGGTCC 1 -- int13Minor allele frequency- G:0.22NA WA 240
    rs675064371,2
    C,F--140085210(+) GGGGAG/CTTCAC 1 -- int19Minor allele frequency- C:0.24WA NA CSA EA 367
    rs735636721,2
    C--140085269(+) TGACAC/ACACTG 1 -- int12Minor allele frequency- A:0.07WA EA 122

    HapMap Linkage Disequilibrium report for SSNA1 (140083054 - 140084822 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SSNA1 (see all 25):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422220CNV Deletion17116639
    dgv8416n71CNV Loss21882294
    dgv8439n71CNV Loss21882294
    dgv8445n71CNV Loss21882294
    dgv8441n71CNV Loss21882294
    dgv8428n71CNV Loss21882294
    nsv894521CNV Loss21882294
    dgv8450n71CNV Loss21882294
    dgv8423n71CNV Loss21882294
    dgv8451n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SSNA1
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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: 610882    OMIM disorders: --

    2 diseases for SSNA1:    
    About MalaCards
    paralytic squint    sjogren's syndrome

    1 disease from the University of Copenhagen DISEASES database for SSNA1:
    Paralytic squint

    Find genes that share disorders with SSNA1           About GenesLikeMe


    Export disorders for SSNA1 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 SSNA1 gene, integrated from 10 sources (see all 22):
    (articles sorted by number of sources associating them with SSNA1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. NA14 is a novel nuclear autoantigen with a coiled-coil domain. (PubMed id 9430706)1, 2, 3 Ramos-Morales F.... Rios R.M. (J. Biol. Chem. 1998)
    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. Proteomic characterization of the human centrosome by protein correlation profiling. (PubMed id 14654843)1, 2 Andersen J.S....Mann M. (Nature 2003)
    4. 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)
    5. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    6. Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (amp 2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    8. Characterization of the structure and self-recognition of the human centrosomal protein NA14: implications for stability and function. (PubMed id 22008182)1 RodrA-guez-RodrA-guez M....JimAcnez M.A. (amp 2011)
    9. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    10. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 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: 8636 HGNC: 11321 AceView: SSNA1 Ensembl:ENSG00000176101 euGenes: HUgn8636
    ECgene: SSNA1 H-InvDB: SSNA1

    (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 SSNA1 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 SSNA1 gene:
    Search GeneIP for patents involving SSNA1

    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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