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OTX2 Gene

protein-coding   GIFtS: 62

GC14M056337
orthodenticle homeobox 2
(Previous name: orthodenticle homolog 2 (Drosophila) )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
MCOPS5 2, 5
MGC45000 2
OTTHUMP00000064776 2
Descriptions
Orthodenticle homolog 2 2, 3
homeobox protein OTX2 2
orthodenticle homeobox 2 2
orthodenticle homolog 2 (Drosophila) 1
External Ids
HGNC: 85221
Entrez Gene: 50152
UniProtKB: P322433
Ensembl: ENSG000001655887
Search outside databases for aliases for OTX2 gene

Previous GC identifers: GC14M054592 GC14M051063 GC14M055257

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for OTX2:
This gene encodes a member of the bicoid sub-family of homeodomain-containing transcription
factors. The encoded protein acts as a transcription factor and may play a role in brain and
sensory organ development. A similar protein in mice is required for proper forebrain development.
Two transcript variants encoding distinct isoforms have been identified for this gene. Other
alternative splice variants may exist, but their full length sequences have not been determined.
[provided by RefSeq]

UniProtKB/Swiss-Prot: OTX2_HUMAN, P32243
Function: Probably plays a role in the development of the brain and the sense organs. Can bind to
the BCD target sequence (BTS): 5'-TCTAATCCC-3'

Gene Wiki entry for OTX2 (Orthodenticle_homeobox_2)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the OTX2 gene  

Entrez Gene cytogenetic band: 14q21-q22   Ensembl cytogenetic band:  14q23.1   HGNC cytogenetic band: 14q22.3

OTX2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M056337:     (about GC identifiers)

Start:
56,337,178 bp from pter
End:
56,346,940 bp from pter
Size:
9,763 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000014.7  NT_026437.11  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: OTX2_HUMAN, P32243 (See protein sequence)
Recommended Name: Homeobox protein OTX2  
Size: 289 amino acids; 31636 Da
Subcellular location: Nucleus (Probable)
Developmental stage: Embryo
Secondary accessions: Q6GTV3 Q9HAW3 Q9P2R1
Alternative splicing: 2 isoforms:  P32243-1   P32243-2   

REFSEQ proteins (2 alternative transcripts): 
NP_068374.1  NP_758840.1  


ENSEMBL proteins: 
ENSP00000386185 ENSP00000343819 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (Otx2)
Browse Abnova for Human Recombinant Proteins
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005634 nucleus IEA--
GO:0030426 growth cone IDA16267555
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Antibodies for OTX2: 
Browse Antibodies Central at Invitrogen
Millipore Mono- and Polyclonal Antibodies for the study of OTX2
Sigma-Aldrich Antibodies for OTX2
R&D Systems Antibodies for OTX2
Antibodies from Abcam (Otx2), each with their AbpromiseSM
Browse Abnova for Monoclonal and Polyclonal Antibodies
Search Novus for antibodies for OTX2

Assays for OTX2: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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5/6 InterPro domains/families (see all 6 ):
 IPR003022 Otx2_TF
 IPR001356 Homeobox
 IPR017970 Homeobox_CS
 IPR003025 Otx_TF
 IPR013851 Otx_TF_C


   GeneDecks  OTX2 for the domains selected above  
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Graphical View of Domain Structure for InterPro Entry P32243

ProtoNet protein and cluster: P32243

2 Blocks protein families:
IPB003022 Otx2 transcription factor signature
IPB003025 Otx transcription factor signature


UniProtKB/Swiss-Prot: OTX2_HUMAN, P32243
Similarity: Belongs to the paired homeobox family. Bicoid subfamily
Similarity: Contains 1 homeobox DNA-binding domain

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (OTX2)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (OTX2)
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_021728

              Applied Biosystems Silencer® siRNAs for OTX2

              Sigma-Aldrich siRNA for OTX2  
                     Sigma-Aldrich shRNA for OTX2  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for OTX2
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_021728
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_021728
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_021728 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_021728

UniProtKB/Swiss-Prot: OTX2_HUMAN, P32243
Function: Probably plays a role in the development of the brain and the sense organs. Can bind to
the BCD target sequence (BTS): 5'-TCTAATCCC-3'

Genatlas biochemistry entry for OTX2:
Drosophila orthodenticle (otd) homolog,paired-like homeo domain encoding gene 2,expressed in the
developing brain of the anterior neural plate,in mouse embryo,playing a major role in
gastrulation,essential for the early specification of neuroectoderm destined to become fore
midbrain

15/20 MGI mutant phenotypes (inferred from 26 alleles(MGI details for Otx2) (see all 20 ):

behavior/neurologicalcraniofacialdigestive/alimentaryembryogenesis
endocrine/exocrine glandgrowth/sizehearing/vestibular/earlethality-postnatallethality-prenatal/perinatal
life span-post-weaning/agingmusclenervous systemnormalpigmentation

3 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0003700 transcription factor activity NAS--
GO:0008190 eukaryotic initiation factor 4E binding TAS15705863
GO:0043565 sequence-specific DNA binding IEA--
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(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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2 Millipore Pathways for OTX2
 Selected targets of Oct-3/4
 Transcription factors in neurogenesis

   GeneDecks  OTX2 for the pathways selected above  
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 Gene Network CentralTM Interacting Genes and Proteins Network for  OTX2 


5/35 Interacting proteins for OTX2 (ENSP000003438193 P322432) via UniProtKB, MINT, and/or STRING (see all 35 )
InteractantInteraction Details
GeneCardExternal ID(s)
ATXN1P542532MINT-2861485
FGF8ENSP000003217973STRING (score=.99)
FOXA2ENSP000003663193STRING (score=.985)
PAX2ENSP000003593173STRING (score=.953)
SOX2ENSP000003235883STRING (score=.934)
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5/7 Gene Ontology (GO) biological process terms (links to tree view) (see all 7 ):

GO IDQualified GO termEvidencePubMed IDs
GO:0006355 regulation of transcription, DNA-dependent NAS--
GO:0007275 multicellular organismal development IEA--
GO:0007411 axon guidance IDA16267555
GO:0008589 regulation of smoothened signaling pathway TAS15705863
GO:0030900 forebrain development TAS15705863
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for OTX2
1 Novoseek chemical compound relationship for OTX2 gene
Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
oligonucleotide 7.17 2 12559959 (1)
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(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (OTX2)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (OTX2)
               OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_021728

              Sigma-Aldrich siRNA for OTX2  
                     Sigma-Aldrich shRNA for OTX2  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_021728  NM_172337  

REFSEQ mRNAs for OTX2 gene (2 alternative transcripts): 

NM_021728.2   NM_172337.1   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_021728  NM_172337  

               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_021728
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_021728
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_021728 

Additional cDNA sequence: 

AF093138.1 AK314271.1 BC032579.1 

6 DOTS entries:

DT.307876  DT.40263755  DT.100025424  DT.100755237  DT.100755238  DT.97842872 

24/59 AceView cDNA sequences (see all 59 ):

BU162097 H08255 BE781530 BQ424035 BE778281 BM564760 BM904035 NM_172337 
BU154244 BQ639181 BM676861 AA364594 BC032579 BU187294 BU176852 BE779765 
BM799551 BM724395 BM903863 BM698799 BU741661 CA397809 BQ432088 AA334301 

highest scoring ESTs for OTX2:

BC032579 BE779002 H08155 AA317337 AA334301 AA364594 AA365227 AF093138 AW953935 BE252764 

Unigene Cluster for OTX2:

Orthodenticle homeobox 2
Hs.288655  [show with all ESTs]
Unigene Representative Sequence: BC032579


GeneLoc Exon Structure

5/8 Alternative Splicing Database (ASD) splice patterns (SP) for OTX2 (see all 8 )

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

About this scheme

ECgene alternative splicing isoforms for OTX2

2 Ensembl transcripts including schematic representations:
ENST00000408990  ENST00000339475  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
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OTX2 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for OTX2

1 / 2 / 3

5 probe-sets matching OTX2 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
53326_at2, 3 U95-B 1 0.81 1.00 1.00 1.00 H08155 0.80 1.00 0.91 1

242128_at2, 3 U133-B 1 1.00 1.00 -- -- BE779765 0.60 1.00 0.82 1

231731_at2, 3 U133-B 1 0.91 1.00 -- -- NM_021728 0.60 1.00 0.82 1

242128_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

231731_at2 U133Plus2 1 0.91 1.00 -- -- -- -- -- -- --
GeneDecks  OTX2 for binary patterns associated with the probe-sets selected above  
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Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: ACCAACTGGT

SOURCE GeneReport for Unigene cluster: Hs.288655

UniProtKB/Swiss-Prot: OTX2_HUMAN, P32243
Tissue specificity: Expressed in brain

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for OTX2 gene from 5/11 species (see all 11 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
OTX21   -- orthodenticle homeobox 2 96.52(n)
99.33(a)
490708  XM_846802.1  XP_851895.1 
chimpanzee
(Pan troglodytes)
OTX21   -- orthodenticle homeobox 2 100(n)
100(a)
452927  XM_001163000.1  XP_001163000.1 
cow
(Bos taurus)
OTX21   -- orthodenticle homeobox 2 96.73(n)
98.99(a)
538953  XM_871744.2  XP_876837.2 
rat
(Rattus norvegicus)
Otx21   -- orthodenticle homolog 2 (Drosophila) 94.35(n)
100(a)
305858  XM_001057814.1  XP_001057814.1 
mouse
(Mus musculus)
Otx21, 5 14 (19.00 cM)5
orthodenticle homolog 2 (Drosophila)1, 5 94.81(n)1
99.31(a)1
184241  NM_144841.21  NP_659090.11 
 AK0537415  AK0815355  (see all 14)
About this table        Species with no ortholog for OTX2

ENSEMBL Gene Tree for OTX2
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for OTX2 gene
GSC2  GSC22  OTX12  CRX2  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
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10/52 NCBI SNPs in OTX2 are shown (see all 52 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 41)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 14 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs1982381,2
A,C,F,H,O56337151(-) ACACCA/GCTATT 2 -- ng5110Minor allele frequency- G:0.10EA NA EU WA 618
rs1719781,2
C,F,H,O56338196(-) CTGTAG/AAACCT 2 -- ut31 ese312Minor allele frequency- A:0.04MN EU EA WA NA 1166
rs1982401,2
A,C,F,O56336681(-) TGATTT/CCTGAA 2 -- ng517Minor allele frequency- C:0.13NA EA 472
rs1982391,2
A,C,H56336776(-) ATTTGG/ATTAAG 2 -- ng511Minor allele frequency- A:0.01EU 120
rs100478461,2
F,H56337088(+) CTCTCT/CGTCCT 2 -- ng514Minor allele frequency- C:0.04EU EA WA 420
rs128873651,2
H56336938(+) GGAAAA/CCAAGA 2 -- ng514Minor allele frequency- C:0.00EU EA WA 418
rs128873411,2
H56336851(+) TCCCTC/TTTAAA 2 -- ng514Minor allele frequency- T:0.00EU EA WA 420
rs37425761,2
H56338165(+) CCCAGT/CATATT 2 -- ut31 ese35Minor allele frequency- C:0.01EA EU WA 1910
rs128884661,2
H56336808(+) TCTTGT/GCATTC 2 -- ng514Minor allele frequency- G:0.00EU EA WA 416
rs345375981,2
F56338641(+) GCACTG/ACTGCT 2 S/S syn11Minor allele frequency- A:0.03NA 64
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HapMap Linkage Disequilibrium images for OTX2 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
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OMIM: 600037   disorders: 610125  

UniProtKB/Swiss-Prot: OTX2_HUMAN, P32243

  • Defects in OTX2 are the cause of microphthalmia syndromic type 5 (MCOPS5) [MIM:610125].
    Microphthalmia is a clinically heterogeneous disorder of eye formation, ranging from small size of
    a single eye to complete bilateral absence of ocular tissues. Up to 80% of cases of microphthalia
    occur in association with syndromes that include non-ocular abnormalities. MCOPS5 patients
    manifest unilateral or bilateral microphthalmia/clinical anophthalmia and variable additional
    features including coloboma, microcornea, cataract, retinal dystrophy, hypoplasia or agenesis of
    the optic nerve, agenesis of the corpus callosum, developmental delay, joint laxity, hypotonia,
    and seizures
  • 4 Novoseek disease relationships for OTX2 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    anophthalmia 83.59 2 18039390 (1), 18385377 (1)
    microphthalmia 75.74 4 17406642 (2), 18039390 (1), 18385377 (1)
    medulloblastoma 62.69 19 16462208 (6), 15705891 (4), 17522332 (2), 11015565 (1)
    tumors 0.00 1 15705891 (1)
    About this table

    GeneTests: OTX2
    Anophthalmia/Microphthalmia

    Human Gene Mutation Database: OTX2
    Human Genome Epidemiology Navigator: OTX2 (3 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/56 PubMed articles for OTX2 gene (see all 56 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Disorders
    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, and/or H-InvDB)
    About This Section

    Entrez Gene: 5015 HGNC: 8522 AceView: OTX2 Ensembl:ENSG00000165588 euGenes: HUgn5015
    ECgene: OTX2 H-InvDB: OTX2
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    GeneReviewshttp://www.genetests.org/query?gene=OTX2
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for OTX2:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
      Invitrogen Antibodies  Invitrogen Assays
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      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for OTX2-related products

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     Millipore Immunoassay Services
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     Predesigned and custom siRNAs for OTX2 Antibodies for OTX2
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for OTX2 Browse small molecules at Sigma-Aldrich
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