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

C9orf9 Gene

protein-coding   GIFtS: 44
GCID: GC09P135753

chromosome 9 open reading frame 9
 Explore 6 diseases affiliated with
C9orf9 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for C9orf9    

Aliases
for C9orf9 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Chromosome 9 Open Reading Frame 91 2
Rsb66 Homolog2
Uncharacterized Protein C9orf92

External Ids:    HGNC: 13671   Entrez Gene: 110922   Ensembl: ENSG000001656987   UniProtKB: Q96E403   

Export aliases for C9orf9 gene to outside databases

Previous GC identifers: GC09P126778 GC09P127310 GC09P129107 GC09P131029 GC09P131030 GC09P132783 GC09P134743 GC09P105248


Summaries
for C9orf9 gene

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

Genomic Views
for C9orf9 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000009.11  NC_018920.1  NT_035014.4  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the C9orf9 gene promoter:
         TBP   AP-1   RREB-1   FOXO3   POU3F2   FOXO3b   AREB6   POU2F1   POU2F1a   FOXO3a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for C9orf9

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat C9orf9


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

Entrez Gene cytogenetic band: 9q34   Ensembl cytogenetic band:  9q34.13   HGNC cytogenetic band: 9q34.13

C9orf9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C9orf9 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P135753:  view genomic region     (about GC identifiers)

Start:
 135,753,414 bp from pter      End:
 135,765,588 bp from pter
Size:
 12,175 bases      Orientation:
 plus strand

Proteins
for C9orf9 gene

(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: CI009_HUMAN, Q96E40 (See protein sequence)
Recommended Name: Uncharacterized protein C9orf9  
Size: 222 amino acids; 25166 Da
Secondary accessions: Q9UGQ0
Alternative splicing: 2 isoforms:  Q96E40-1   Q96E40-2   

Explore the universe of human proteins at neXtProt for C9orf9: NX_Q96E40

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96E40

    • C9orf9 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_061829.3  
    ENSEMBL proteins: 
     ENSP00000361209   ENSP00000348659   ENSP00000298546  

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    Uscn Proteins for C9orf9


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    Uscn Antibodies for C9orf9
    ThermoFisher Antibodies for C9orf9

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    Uscn ELISAs and CLIAs for C9orf9

    Protein Domains /
    Families
    for C9orf9 gene

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

    ProtoNet protein and cluster: Q96E40


    Function
    for C9orf9 gene

    (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
    miRNA
    Products:            		 OriGene 3'-UTR Clone: C9orf9
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    Inhib. RNA
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    OriGene shRNA RFP: C9orf9
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    Gene Editing
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    Clone
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    Cell Line
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    Search LifeMap BioReagents cell lines for C9orf9

    In Situ Assay
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         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C9orf9


    Pathways & Interactions
    for C9orf9 gene

    (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 CentralTM Interacting Genes and Proteins Networks for C9orf9

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    5/6 Interacting proteins for C9orf9 (Q96E402, 3 ENSP000002985464) via UniProtKB, MINT, STRING, and/or I2D (see all 6)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DDX24Q9GZR72, 3MINT-65420 I2D: score=4 
    TSC22D1Q157142, 3, ENSP000003974354MINT-8275259 I2D: score=2 STRING: ENSP00000397435
    SEPHS1P499033, ENSP000003678934I2D: score=4 STRING: ENSP00000367893
    SMSENSP000003857464STRING: ENSP00000385746
    --Q5T5U93, 2MINT-64482 I2D: score=1 
    About this table

    Drugs & Compounds
    for C9orf9 gene

    (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
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for C9orf9
    Search CenterWatch for drugs/clinical trials and news about C9orf9 / CI009 

    Transcripts
    for C9orf9 gene

    (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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for C9orf9 gene: 
    NM_018956.3  

    Unigene Cluster for C9orf9:

    Chromosome 9 open reading frame 9
    Hs.62595  [show with all ESTs]
    Unigene Representative Sequence: AK130389
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372136(uc004cbx.1) ENST00000356311(uc004cbz.1) ENST00000350499(uc004cby.1)


    miRNA
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    Inhib. RNA
    Products:             		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for C9orf9 (see all 4)
    OriGene shRNA RFP: C9orf9
    OriGene siRNA: C9orf9
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat C9orf9
    Clone
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    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat C9orf9
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat C9orf9

    Additional cDNA sequence: 

    AJ011375.1 AK075259.1 AK130389.1 BC012940.1 CR457210.1 

    11 DOTS entries:

    DT.91911739  DT.75180161  DT.95266761  DT.75162472  DT.121631466  DT.100000376  DT.121161534  DT.40240484 
    DT.86848944  DT.92420312  DT.121161578 

    10 AceView cDNA sequences:

    AK075259 AA634902 NM_018956 BC012940 AJ011375 CR457210 AK130389 BE067393 
    BE067389 BE067387 

    GeneLoc Exon Structure

    5/6 Alternative Splicing Database (ASD) splice patterns (SP) for C9orf9 (see all 6)    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d · 7e ^ 8
    SP1:                          -                                   -     -         
    SP2:        -     -     -     -                                                   
    SP3:                    -     -                                                   
    SP4:                    -                                                         
    SP5:                          -                                                   


    ECgene alternative splicing isoforms for C9orf9

    Expression
    for C9orf9 gene

    (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

    C9orf9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ACAGAAGCCA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    C9orf9 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Posterior foregut-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See C9orf9 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for C9orf9

    SOURCE GeneReport for Unigene cluster: Hs.62595
        SABiosciences Custom PCR Arrays for C9orf9
    Primer
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat C9orf9
    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C9orf9

    Orthologs
    for C9orf9 gene

    (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 C9orf9 gene from 4/12 species (see all 12)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia 1700026L06Rik1 , 5 RIKEN cDNA 1700026L06 gene1, 5 86.9(n)1
    91.07(a)1    		   2 (19.38 cM)5
    699871  NM_027283.11  NP_081559.11 
     286920805 
    chicken
    (Gallus gallus)    		 Aves C17H9orf91 chromosome 17 open reading frame, human C9orf9 69.33(n)
    65.64(a)    		   772069  XM_001233954.2  XP_001233955.1 
    lizard
    (Anolis carolinensis)    		 Reptilia C9orf96
    		 --
    		 66(a)
    		 1 ↔ 1
    		 GL343448.1(290152-290643)
    zebrafish
    (Danio rerio)    		 Actinopterygii zgc:1537401 zgc:153740 55.63(n)
    50.96(a)    		   791588  NM_001045430.1  NP_001038895.1 


    ENSEMBL Gene Tree for C9orf9 (if available)
    TreeFam Gene Tree for C9orf9 (if available) 

    Paralogs
    for C9orf9 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for C9orf9 gene

    (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

    10/270 NCBI SNPs in C9orf9 are shown (see all 270)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 9 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1999186531,2
    		--135752300(+) AAAAA-/CATTAG 2 -- int1 us2k10--------
    rs125531641,2
    		C,H,--135752335(+) agtctC/Tggcta 2 -- int1 us2k10--------
    rs1494494521,2
    		--135752366(+) AAGGAC/TTGCTT 2 -- int1 us2k10--------
    rs1430891061,2
    		--135752429(+) GCCTGC/GGCAGC 2 -- us2k1 int10--------
    rs1922712221,2
    		--135752460(+) AATCAA/GTAAAA 2 -- us2k1 int10--------
    rs1399044451,2
    		C,--135752575(+) CTTCT-/CAACCC 2 -- us2k1 int10--------
    rs1482102331,2
    		--135752643(+) TCCCTC/TTATCA 2 -- int1 us2k10--------
    rs1830272181,2
    		--135752734(+) AGGGCA/GGAACC 2 -- us2k1 int10--------
    rs1415241841,2
    		--135752812(+) GCAGAC/TAAATG 2 -- us2k1 int10--------
    rs1463790391,2
    		--135752869(+) AGTGGC/GTGAGA 2 -- us2k1 int10--------

    HapMap Linkage Disequilibrium report for C9orf9 (135753414 - 135765588 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for C9orf9: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing C9orf9
    DNA2.0 Custom Variant and Variant Library Synthesis for C9orf9

    Disorders / Diseases
    for C9orf9 gene

    (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
    C9orf9 for disorders           About GeneDecksing

    6 diseases for C9orf9:    About MalaCards
    bladder transitional cell carcinoma    transitional cell carcinoma    chronic lymphocytic leukemia    lymphocytic leukemia
    leukemia    carcinoma

    1 disease from the University of Copenhagen DISEASES database for C9orf9:
    Bladder transitional cell carcinoma
    Human Genome Epidemiology (HuGE) Navigator: C9orf9 (1 document)

    Export disorders for C9orf9 gene to outside databases

    Publications
    for C9orf9 gene

    (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 C9orf9 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with C9orf9)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (2004)
    4. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    5. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)
    6. Single nucleotide polymorphisms of matrix metalloprot einase 9 (MMP-9) and tumour protein 73 (TP73) interact with Epstein Barr virus in chronic lymphocytic leukemia: results from the European case-control study E piLymph. (PubMed id 21048031)1 Casabonne D....de Sanjose S. (2010)
    7. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (2005)
    8. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1 Otsuki T....Isogai T. (2005)
    9. 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)
    10. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

    External Searches for C9orf9 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing C9orf9 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 11092 HGNC: 1367 AceView: C9orf9 Ensembl:ENSG00000165698 euGenes: HUgn11092
    ECgene: C9orf9 H-InvDB: C9orf9

    Other Databases showing C9orf9 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing C9orf9 gene

    (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 C9orf9 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for C9orf9 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for C9orf9 gene:
    Search GeneIP for patents involving C9orf9

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for C9orf9 gene

    (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),
    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
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     Browse OriGene Antibodies   OriGene shRNA RFP for C9orf9  
     OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for C9orf9   OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for C9orf9  
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     QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat C9orf9
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     GenScript Custom Purified and Recombinant Proteins Services for C9orf9 GenScript cDNA clones with any tag delivered in your preferred vector for C9orf9
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     Regulatory tfbs in C9orf9 promoter
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     Browse Sino Biological Proteins and Antibodies
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     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies
     Novus Tissue Slides
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     Search for Antibodies for C9orf9 at Abcam
     See all of Abcam's Antibodies, Kits and Proteins for C9orf9
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     C9orf9 Proteins, Antibodies, CLIAs, and ELISAs
     Search LifeMap BioReagents cell lines for C9orf9
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     Browse SwitchGear 3'UTR luciferase reporter plasmids for C9orf9
     Browse SwitchGear Promoter luciferase reporter plasmids for C9orf9
     ThermoFisher Antibodies for C9orf9
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat C9orf9
           
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