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C2orf71 Gene

protein-coding   GIFtS: 43
GCID: GC02M029284

Chromosome 2 Open Reading Frame 71

  See C2orf71-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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Aliases
Chromosome 2 Open Reading Frame 711 2
RP542
Uncharacterized Protein C2orf712

External Ids:    HGNC: 343831   Entrez Gene: 3889392   Ensembl: ENSG000001792707   OMIM: 6134255   UniProtKB: A6NGG83   

Export aliases for C2orf71 gene to outside databases

Previous GC identifers: GC02M029139 GC02M029140 GC02M029025


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for C2orf71 Gene:
The protein encoded by this gene is highly expressed in photoreceptors and may associate with the primary cilium
of the outer segment. The encoded protein appears to undergo post-translational lipid modification. Nonsense and
missense variants of this gene appear to cause a recessive form of retinitis pigmentosa. (provided by RefSeq, Jun
2010)

GeneCards Summary for C2orf71 Gene:
C2orf71 (chromosome 2 open reading frame 71) is a protein-coding gene. Diseases associated with C2orf71 include retinitis pigmentosa 54, and c2orf71-related retinitis pigmentosa.

UniProtKB/Swiss-Prot: CB071_HUMAN, A6NGG8
Function: May play an important role in the development of normal vision




(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_000002.11  NC_018913.2  NT_022184.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the C2orf71 gene promoter:
         Bach1   AhR   GR   AML1a   GR-beta   AP-2gamma   C/EBPalpha   Arnt   CHOP-10   GR-alpha   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C2orf71

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C2orf71


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

Entrez Gene cytogenetic band: 2p23.2   Ensembl cytogenetic band:  2p23.2   HGNC cytogenetic band: 2p23.2

C2orf71 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C2orf71 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M029284:  view genomic region     (about GC identifiers)

Start:
29,283,842 bp from pter      End:
29,297,127 bp from pter
Size:
13,286 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, 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: CB071_HUMAN, A6NGG8 (See protein sequence)
Recommended Name: Uncharacterized protein C2orf71  
Size: 1288 amino acids; 139655 Da

Explore the universe of human proteins at neXtProt for C2orf71: NX_A6NGG8

Explore proteomics data for C2orf71 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See C2orf71 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001025054.1  
    ENSEMBL proteins: 
     ENSP00000332809  

    C2orf71 Human Recombinant Protein Products:

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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: A6NGG8


    (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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CB071_HUMAN, A6NGG8
    Function: May play an important role in the development of normal vision

    Animal Models:

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for C2orf71
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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
    CB071_HUMAN, A6NGG8: Cell projection, cilium, photoreceptor outer segment
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001750photoreceptor outer segment IEA--
    GO:0072372primary cilium IDA--

    Find genes that share ontologies with C2orf71           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for C2orf71
    Interactions:

        Search GeneGlobe Interaction Network for C2orf71

    Gene Ontology (GO): 2 biological process terms:    About this table

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

    Find genes that share ontologies with C2orf71           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 C2orf71 (CB071)



    (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 C2orf71 gene: 
    NM_001029883.2  

    Unigene Cluster for C2orf71:

    Chromosome 2 open reading frame 71
    Hs.354243  [show with all ESTs]
    Unigene Representative Sequence: NM_001029883
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000602958 ENST00000331664(uc002rmt.2)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate C2orf71 (see all 25):
    hsa-miR-217 hsa-miR-3655 hsa-miR-631 hsa-miR-509-5p hsa-miR-4263 hsa-miR-134 hsa-miR-578 hsa-miR-3661
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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      QuantiFast Probe-based Assays in human, mouse, rat C2orf71

    Additional mRNA sequence: AK092250.1 

    2 DOTS entries:

    DT.75154121  DT.97800417 

    Selected AceView cDNA sequences (see all 26):

    BM683942 BM698795 BM717131 BM675245 BU740486 BM714060 CN478537 BM701367 
    BG394633 BU738609 BM680702 CD245267 BM721416 BM669582 BQ636237 BM719306 
    BM718811 BM683239 AK092250 AX747432 BM726732 BQ185778 BM931809 BM685732 

    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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    C2orf71 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TGAATTAGAC
    C2orf71 Expression
    About this image


    C2orf71 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) 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
    C2orf71 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    C2orf71 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.354243

    UniProtKB/Swiss-Prot: CB071_HUMAN, A6NGG8
    Tissue specificity: Specifically expressed in retina

        Custom PCR Arrays for C2orf71
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C2orf71

    (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 C2orf71 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia BC0270721 , 5 cDNA sequence BC0270721, 5 72.57(n)1
    60.14(a)1
      17 (42.67 cM)5
    2250041  NM_146082.31  NP_666194.21 
     717435575 
    chicken
    (Gallus gallus)
    Aves C3H2orf711 chromosome 3 open reading frame, human C2orf71 52.44(n)
    40.37(a)
      101748653  XM_004940188.1  XP_004940245.1 
    lizard
    (Anolis carolinensis)
    Reptilia C2orf716
    chromosome 2 open reading frame 71
    35(a)
    1 ↔ 1
    1(248522056-248525739)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1017326351 chromosome unknown open reading frame, human C2orf71 46.82(n)
    36.81(a)
      101732635  XM_004914927.1  XP_004914984.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1005377931 uncharacterized LOC100537793 44.58(n)
    36.34(a)
      100537793  XM_003200381.2  XP_003200429.2 


    ENSEMBL Gene Tree for C2orf71 (if available)
    TreeFam Gene Tree for C2orf71 (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 C2orf71 (see all 580)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1407768701,2,,4
    CRetinitis pigmentosa 54 (RP54)4 --29217187(+) TCTGGA/TCCCTT 2 D V mis10--------
    rs2007581831,2,,4
    CRetinitis pigmentosa 54 (RP54)4 --29217196(+) TTCGCA/GGCTCC 2 P L mis10--------
    rs2012843501,2,,4
    Retinitis pigmentosa 54 (RP54)4 --29217917(+) AAGGTC/TCCAGC 2 N D mis10--------
    VAR_0633954
    Retinitis pigmentosa 54 (RP54)4--see VAR_0633952 I F mis40--------
    rs2676066911,2
    Cpathogenic129218475(-) ACCAGA/C/TAGGCT 2 Q * stg10--------
    rs1995807201,2
    Cuntested129217746(+) TGCTTC/TGTCCT 2 K E mis10--------
    rs105433991,2
    C--29039768(+) TCTTC-/AAAAAAAA 1 -- us2k10--------
    rs1808769031,2
    --29205999(+) GCATAC/TGATGT 1 -- ds50010--------
    rs116841091,2
    C,F,H--29206002(+) TACGAT/CGTGAG 1 -- ds50014Minor allele frequency- C:0.00NS EA 420
    rs1160608711,2
    C,F--29206023(+) AGATAC/TGGCTT 1 -- ds50011Minor allele frequency- T:0.02NA 120

    HapMap Linkage Disequilibrium report for C2orf71 (29283842 - 29297127 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for C2orf71:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv2657CNV Loss18451855
    esv34904CNV Gain17911159
    dgv1163e1CNV Complex17122850

    Human Gene Mutation Database (HGMD): C2orf71
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing C2orf71
    DNA2.0 Custom Variant and Variant Library Synthesis for C2orf71

    (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: 613425   
    OMIM disorders: 613428  
    UniProtKB/Swiss-Prot: CB071_HUMAN, A6NGG8
  • Retinitis pigmentosa 54 (RP54) [MIM:613428]: 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

  • 3 diseases for C2orf71:    
    About MalaCards
    retinitis pigmentosa 54    c2orf71-related retinitis pigmentosa    leber congenital amaurosis

    1 disease from the University of Copenhagen DISEASES database for C2orf71:
    Retinitis pigmentosa

    Find genes that share disorders with C2orf71           About GenesLikeMe

    Genetic Association Database (GAD): C2orf71
    Human Genome Epidemiology (HuGE) Navigator: C2orf71 (1 document)

    Export disorders for C2orf71 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 C2orf71 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with C2orf71)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Discovery and functional analysis of a retinitis pigmentosa gene, C2orf71. (PubMed id 20398886)1, 2, 3 Nishimura D.Y....Sheffield V.C. (Am. J. Hum. Genet. 2010)
    2. Novel C2orf71 mutations account for approximately 1% of cases in a large French arRP cohort. (PubMed id 21412943)1, 2 Audo I.... Zeitz C. (Hum. Mutat. 2011)
    3. Genome-wide association study of recurrent early-onset major depressive disorder. (PubMed id 20125088)1, 4 Shi J....Levinson D.F. (Mol. Psychiatry 2011)
    4. Mutations in C2orf71 cause autosomal-recessive retinitis pigmentosa. (PubMed id 20398884)1, 2 Collin R.W.J.... Ben-Yosef T. (Am. J. Hum. Genet. 2010)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. A survey of DNA variation of C2ORF71 in probands with progressive autosomal recessive retinal degeneration and controls. (PubMed id 20811058)1 Sergouniotis P.I....Webster A.R. (amp 2011)
    7. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W.... Wilson R.K. (Nature 2005)
    8. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)
    9. Retinitis Pigmentosa Overview (PubMed id 20301590)1 Pagon R.A....Stephens K. (1993)

    (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: 388939 HGNC: 34383 AceView: LOC388939 Ensembl:ENSG00000179270 euGenes: HUgn388939
    ECgene: C2orf71 H-InvDB: C2orf71

    (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 C2orf71 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 C2orf71 gene:
    Search GeneIP for patents involving C2orf71

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    (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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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     Browse OriGene Antibodies   OriGene RNAi products in human, mouse, rat for C2orf71  
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