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SYNE4 Gene

protein-coding   GIFtS: 38
GCID: GC19M037065

Spectrin Repeat Containing, Nuclear Envelope Family Member...

(Previous names: chromosome 19 open reading frame 46, deafness, autosomal...)
(Previous symbols: C19orf46, DFNB76)
  See related disease
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
Spectrin Repeat Containing, Nuclear Envelope Family Member 41 2     Chromosome 19 Open Reading Frame 461
C19orf461 2 3 5     Nesp42
DFNB761 2 5     nesprin-42
Deafness, Autosomal Recessive 761 2     NESP45
Nuclear Envelope Spectrin Repeat Protein 42 3     

External Ids:    HGNC: 267031   Entrez Gene: 1631832   Ensembl: ENSG000001813927   OMIM: 6155355   UniProtKB: Q8N2053   

Export aliases for SYNE4 gene to outside databases

Previous GC identifers: GC19M036496 GC19M036602


(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 SYNE4 Gene:
SYNE4 (spectrin repeat containing, nuclear envelope family member 4) is a protein-coding gene. Diseases associated with SYNE4 include deafness, autosomal recessive 76. GO annotations related to this gene include actin binding.

UniProtKB/Swiss-Prot: SYNE4_HUMAN, Q8N205
Function: As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, involved in the
connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the
LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in
nuclear movement and positioning (By similarity). Behaves as a kinesin cargo, providing a functional binding site
for kinesin-1 at the nuclear envelope. Hence may contribute to the establishment of secretory epithelial
morphology by promoting kinesin-dependent apical migration of the centrosome and Golgi apparatus and basal
localization of the nucleus (By similarity)




(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:
NC_000019.10  NT_011109.17  NC_018930.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SYNE4
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SYNE4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SYNE4


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

Entrez Gene cytogenetic band: 19q13.12   Ensembl cytogenetic band:  19q13.12   HGNC cytogenetic band: 19q13.12

SYNE4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SYNE4 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M037065:  view genomic region     (about GC identifiers)

Start:
36,494,002 bp from pter      End:
36,499,695 bp from pter
Size:
5,694 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, 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., 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: SYNE4_HUMAN, Q8N205 (See protein sequence)
Recommended Name: Nesprin-4  
Size: 404 amino acids; 43512 Da
Subunit: Core component of the LINC complex which is composed of inner nuclear membrane SUN domain-containing
proteins coupled to outer nuclear membrane KASH domain-containing nesprins. SUN domain-containing proteins
interact with A-type lamins of the nuclear lamina, while at the other end of the complex, nesprins interact with
unique cytoskeletal components (By similarity). Interacts with kinesins KIF5B and KLC1 (By similarity)
Sequence caution: Sequence=BAC04222.1; Type=Miscellaneous discrepancy; Note=Intron retention;
Secondary accessions: A8MRS0 A8MYE3 Q7Z7L3
Alternative splicing: 2 isoforms:  Q8N205-1   Q8N205-2   

Explore the universe of human proteins at neXtProt for SYNE4: NX_Q8N205

Explore proteomics data for SYNE4 at MOPED


See SYNE4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001034965.1  
ENSEMBL proteins: 
 ENSP00000380572   ENSP00000425550   ENSP00000343152   ENSP00000316130   ENSP00000422716  

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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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1 InterPro protein domain:
 IPR012315 KASH

Graphical View of Domain Structure for InterPro Entry Q8N205

ProtoNet protein and cluster: Q8N205

UniProtKB/Swiss-Prot: SYNE4_HUMAN, Q8N205
Domain: The KASH domain, which contains a transmembrane domain, mediates the nuclear envelope targeting and is
involved in the binding to SUN1 and SUN2 through recognition of their SUN domains (By similarity)
Similarity: Belongs to the nesprin family
Similarity: Contains 1 KASH domain


SYNE4 for domains           About GeneDecksing


(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: SYNE4_HUMAN, Q8N205
Function: As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, involved in the
connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the
LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in
nuclear movement and positioning (By similarity). Behaves as a kinesin cargo, providing a functional binding site
for kinesin-1 at the nuclear envelope. Hence may contribute to the establishment of secretory epithelial
morphology by promoting kinesin-dependent apical migration of the centrosome and Golgi apparatus and basal
localization of the nucleus (By similarity)

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003779actin binding IEA--
GO:0005515protein binding ----
     
SYNE4 for ontologies           About GeneDecksing


Phenotypes:
     2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Syne4):
 hearing/vestibular/ear  nervous system 

SYNE4 for phenotypes           About GeneDecksing

Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SYNE4
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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
SYNE4_HUMAN, Q8N205: Nucleus outer membrane; Single-pass type IV membrane protein. Note=Localization at the
nucleus outer membrane requires the presence of SUN1 (By similarity)

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane ----
GO:0031309integral component of nuclear outer membrane ISS--

SYNE4 for ontologies           About GeneDecksing


(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 SYNE4
Interactions:

    Search GeneGlobe Interaction Network for SYNE4

STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

Selected Interacting proteins for SYNE4 (Q8N2052, 3 ENSP000003161304) via UniProtKB, MINT, STRING, and/or I2D (see all 16)
InteractantInteraction Details
GeneCardExternal ID(s)
CSNK2BP678702, 3MINT-8253077 I2D: score=2 
ENSG00000206406P678702, 3MINT-8253077 I2D: score=2 
ENSG00000224398P678702, 3MINT-8253077 I2D: score=2 
ENSG00000224774P678702, 3MINT-8253077 I2D: score=2 
ENSG00000228875P678702, 3MINT-8253077 I2D: score=2 
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Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0045198establishment of epithelial cell apical/basal polarity ISS--

SYNE4 for ontologies           About GeneDecksing



(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 SYNE4



(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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for SYNE4 gene (2 alternative transcripts): 
NM_153233.1  NM_001039876.1  

Unigene Cluster for SYNE4:

Spectrin repeat containing, nuclear envelope family member 4
Hs.436743  [show with all ESTs]
Unigene Representative Sequence: NM_001039876
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000505054 ENST00000397428 ENST00000503121 ENST00000340477(uc021utd.1 uc002ocs.1)
ENST00000324444(uc002ocq.1 uc010een.1) ENST00000465425 ENST00000490730(uc002ocr.1)

miRNA
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Predesigned siRNA for gene silencing in human, mouse, rat SYNE4
Clone
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Primer
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  QuantiTect SYBR Green Assays in human, mouse, rat SYNE4
  QuantiFast Probe-based Assays in human, mouse, rat SYNE4

Additional mRNA sequence: 

BC038360.1 BC052573.1 

5 DOTS entries:

DT.100752167  DT.86847338  DT.100021380  DT.101981153  DT.121452927 

Selected AceView cDNA sequences (see all 29):

AA827649 BC038360 AX748293 AK093764 AW299369 AI244887 AW016070 NM_153233 
CR595098 CB052141 BM976898 BM980299 AI088309 AL541773 BF434490 CB241656 
AI052236 BX115848 BG740714 BU538399 BC052573 CB052140 AW615387 AV750009 

GeneLoc Exon Structure

4 Alternative Splicing Database (ASD) splice patterns (SP) for SYNE4    About this scheme

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b
SP1:                    -     -     -           -                           
SP2:                                                                        
SP3:                                                                        
SP4:              -     -                                                   


ECgene alternative splicing isoforms for SYNE4

(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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SYNE4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SYNE4 Expression
About this image

SYNE4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SYNE4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.436743
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SYNE4

(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 human and mouse.

Orthologs for SYNE4 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Syne41 , 5 expressed sequence AI4289365
spectrin repeat containing, nuclear envelope family more1
76.72(n)1
68.3(a)1
  7 (17.39 cM)5
2330661  NM_153577.21  NP_705805.11 
 303148075 


ENSEMBL Gene Tree for SYNE4 (if available)
TreeFam Gene Tree for SYNE4 (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 SYNE4 (see all 176)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs777589491,2
C,F--36493930(+) CCTAGG/AGTACA 1 -- ds50011Minor allele frequency- A:0.02WA 118
rs739283791,2
C--36494195(+) CACCTA/GGTATC 1 -- ut312Minor allele frequency- G:0.04WA 120
rs739283801,2
C--36494234(+) ATTACG/ACACAT 1 -- ut311Minor allele frequency- A:0.50WA 2
rs1466492261,2
C--36494246(+) AGACTA/GGGGGA 2 P L mis10--------
rs2008181931,2
C--36494297(+) GTATTC/TGGGCA 2 Q R mis10--------
rs1999389881,2
C--36494327(+) CTGACG/ACGGGC 2 /A /V mis11Minor allele frequency- A:0.00EU 1239
rs3747021341,2
C--36494328(+) TGACGC/TGGGCA 2 T A mis10--------
rs1412025301,2
C--36494352(+) ACCCAC/TCAGGA 2 M V mis10--------
rs1449519041,2
C--36494376(+) GAAGAA/G/TGATAA 3 I L F mis10--------
rs2021075341,2
C--36494424(+) GGCCCA/TGTGAA 1 -- spa10--------

HapMap Linkage Disequilibrium report for SYNE4 (36494002 - 36499695 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SYNE4: --
Human Gene Mutation Database (HGMD): SYNE4
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing SYNE4
DNA2.0 Custom Variant and Variant Library Synthesis for SYNE4

(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: 615535   
OMIM disorders: 615540  
UniProtKB/Swiss-Prot: SYNE4_HUMAN, Q8N205
  • Deafness, autosomal recessive, 76 (DFNB76) [MIM:615540]: A form of non-syndromic sensorineural deafness,
    a disorder resulting from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or
    the area of the brain that receives sound information. DFNB76 affected individuals have onset of progressive high
    frequency hearing impairment between birth and 6 years of age. The hearing loss is severe at high frequencies by
    adulthood. Note=The disease is caused by mutations affecting the gene represented in this entry

  • 1 disease for SYNE4:    
    About MalaCards
    deafness, autosomal recessive 76


    SYNE4 for disorders           About GeneDecksing


    Export disorders for SYNE4 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 SYNE4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SYNE4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The LINC complex is essential for hearing. (PubMed id 23348741)1, 2, 3 Horn H.F....Avraham K.B. (J. Clin. Invest. 2013)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. A directed protein interaction network for investigating intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (Sci Signal 2011)
    4. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    6. 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: 163183 HGNC: 26703 AceView: FLJ36445 Ensembl:ENSG00000181392 euGenes: HUgn163183
    ECgene: SYNE4 H-InvDB: SYNE4

    (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 SYNE4 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 SYNE4 gene:
    Search GeneIP for patents involving SYNE4

    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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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