VAX2 Gene
protein-coding GIFtS: 51
GCID: GC02P071127
|
|
ventral anterior homeobox 2
| |
Aliases
for VAX2 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Ventral Anterior Homeobox 21 2 | | DRES931 2 |
Export aliases for VAX2 gene to outside databasesPrevious GC identifers: GC02P071137 GC02P071338 GC02P071085 GC02P071102 GC02P071039 GC02P070981 GC02P070864 |
Summaries
for VAX2 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for VAX2:
This gene encodes a homeobox protein and is almost exclusively expressed in the ventral portion of the retina duringdevelopment. In mouse studies, this gene was found to be required for the correct formation of the optic fissure andother aspects of retinal development. (provided by RefSeq, Sep 2008)
UniProtKB/Swiss-Prot: VAX2_HUMAN, Q9UIW0Function: Transcription factor that may function in dorsoventral specification of the forebrain. Regulates theexpression of Wnt signaling antagonists including the expression of a truncated TCF7L2 isoform that cannot bind CTNNB1and acts therefore as a potent dominant-negative Wnt antagonist. Plays a crucial role in eye development and, inparticular, in the specification of the ventral optic vesicle (By similarity). May be a regulator of axialpolarization in the retina
|
Genomic Views
for VAX2 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_000002.11 NC_018913.1 NT_022184.15
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the VAX2 gene promoter:
GATA-3 Sp1 RREB-1 HNF-4alpha2 POU6F1 (c2) HNF-4alpha1 RORalpha1 PPAR-alpha NF-Y CBF(2)
Other transcription factors
Search SABiosciences Chromatin IP Primers for VAX2
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VAX2 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 2p13 Ensembl cytogenetic band: 2p13.3 HGNC cytogenetic band: 2p13.3VAX2 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 2 GeneLoc Exon Structure GeneLoc location for GC02P071127: view genomic region
(about GC identifiers)
Start:
|
71,127,720 bp from pter |
End:
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71,160,576 bp from pter |
Size:
|
32,857 bases |
Orientation:
|
plus strand |
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Proteins
for VAX2 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: VAX2_HUMAN, Q9UIW0 (See
protein sequence)Recommended Name: Ventral anterior homeobox 2 Size: 290 amino acids; 30874 Da
Subcellular location: Nucleus (Probable)
Developmental stage: Expressed in the ventral part of the optic vesicles at 7 week dpc
Secondary accessions: Q53Y33Explore the universe of human proteins at neXtProt for VAX2: NX_Q9UIW0
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9UIW0
VAX2 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_036608.1
ENSEMBL proteins: ENSP00000234392
Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
VAX2 for ontologies About GeneDecksing
VAX2 Antibody Products:
Assay Products for VAX2: |
Protein
Domains /
Families
for VAX2 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
VAX2 for domains About GeneDecksing
5 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9UIW0ProtoNet protein and cluster: Q9UIW0 1 Blocks protein family: IPB000047 Lambda and other repressor helix-turn-helix signature
UniProtKB/Swiss-Prot: VAX2_HUMAN, Q9UIW0Similarity: Belongs to the EMX homeobox familySimilarity: Contains 1 homeobox DNA-binding domain |
Function
for VAX2 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
|
Function Summary:
UniProtKB/Swiss-Prot: VAX2_HUMAN, Q9UIW0Function: Transcription factor that may function in dorsoventral specification of the forebrain. Regulates theexpression of Wnt signaling antagonists including the expression of a truncated TCF7L2 isoform that cannot bind CTNNB1and acts therefore as a potent dominant-negative Wnt antagonist. Plays a crucial role in eye development and, inparticular, in the specification of the ventral optic vesicle (By similarity). May be a regulator of axialpolarization in the retina Genatlas biochemistry entry for VAX2:ventral anterior homeobox 2,specifically expressed in the developing vertebral eye,controlling the patterning of theeye dorsoventral axis
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for VAX2 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for VAX2
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VAX2 |
Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0000976 | transcription regulatory region sequence-specific DNA binding |
IEA | -- | | GO:0003700 | sequence-specific DNA binding transcription factor activity |
IEA | -- | | GO:0031490 | chromatin DNA binding |
IEA | -- |
VAX2 for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for VAX2:
Animal Models:
Mouse knock-outs for VAX2: Vax2tm1Grl Vax2tm1Sba
8 MGI mutant phenotypes (inferred from 2 alleles ) (MGI details for Vax2):
VAX2 for phenotypes About GeneDecksing
|
Pathways & Interactions
for VAX2 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 VAX2
5 Interacting proteins for VAX2 (Q9UIW03) via UniProtKB, MINT, STRING, and/or I2DAbout this table
Gene Ontology (GO): 5/12 biological process terms (GO ID links to tree view) (see all 12): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0000122 | negative regulation of transcription from RNA polymerase II promoter |
IEA | -- | | GO:0006351 | transcription, DNA-dependent |
IEA | -- | | GO:0006355 | regulation of transcription, DNA-dependent |
-- | -- | | GO:0007398 | ectoderm development |
TAS | 10485894 | | GO:0007409 | axonogenesis |
IEA | -- |
VAX2 for ontologies About GeneDecksing
|
Drugs & Compounds
for VAX2 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 Tocris compounds for VAX2
Search CenterWatch for drugs/clinical trials and news about VAX2
|
Transcripts
for VAX2 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 VAX2 gene: NM_012476.2 Unigene Cluster for VAX2: Ventral anterior homeobox 2 Hs.249170 [show with all ESTs]Unigene Representative Sequence: Y177911 Ensembl transcript including schematic representation, and UCSC links where relevant: ENST00000234392(uc002shh.3)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for VAX2 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for VAX2
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: VAX2 (NM_012476) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for VAX2 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VAX2 |
Additional cDNA sequence: AB593145.1 BC006336.2 BT007035.1 Y17791.1 1 DOTS entry: DT.75152909 13 AceView cDNA sequences: NM_012476 BM710832 Y17791 BG601065 BC006336 BQ637322 H92142 BF037978 BF685044 BT007035 H92143 BF684283 BQ957193
GeneLoc Exon Structure
2 Alternative Splicing Database (ASD) splice patterns (SP) for VAX2 About this scheme
| ExUns: | 1 | ^ | 2a | · | 2b | ^ | 3 | ^ | 4a | · | 4b |
|---|
|
| SP1: | | | | | | | | | | | | | |
| SP2: | | | | | | | - | | | | | |
ECgene alternative splicing isoforms for VAX2
|
Expression
for VAX2 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
| VAX2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GGCGATGGGG
About this image
See VAX2 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for VAX2
SOURCE GeneReport for Unigene cluster: Hs.249170
SABiosciences Expression via Pathway-Focused PCR Array including VAX2:
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for VAX2
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat VAX2 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat VAX2 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat VAX2 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VAX2 |
Orthologs
for VAX2 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 animals.
Orthologs for VAX2 gene from 4/11 species (see all 11) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
lizard
(Anolis carolinensis) |
Reptilia |
VAX26 |
-- |
64(a) |
1 ↔ 1 |
AAWZ02036934(4216-19659) |
African clawed frog
(Xenopus laevis) |
Amphibia |
AF113517.12 |
-- |
74.81(n) |
|
AF113517.1 |
zebrafish
(Danio rerio) |
Actinopterygii |
vax22 |
ventral anterior homeobox 2 |
74.21(n) |
|
373869 AY183363.1 |
worm
(Caenorhabditis elegans) |
Secernentea |
ceh-56 |
Homeobox protein ceh-5 |
40(a) |
1 → many |
I(9727195-9728012) |
ENSEMBL Gene Tree for VAX2 (if available)
TreeFam Gene Tree for VAX2 (if available) |
Paralogs
for VAX2 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for VAX2 gene
- EN12 VAX12 EN22
2 SIMAP similar genes for VAX2 using alignment to 2 protein entries: VAX2_HUMAN (see all proteins):VAX1 POU6F1
VAX2 for paralogs About GeneDecksing
|
Genomic Variants
for VAX2 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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 2 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for VAX2 (71127720 - 71160576 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for VAX2: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing VAX2 |
|
Disorders
/ Diseases
for VAX2 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
|
VAX2 for disorders About GeneDecksing
OMIM gene information: 604295
OMIM disorders: --
6  diseases for VAX2: About MalaCardscoloboma retinitis microphthalmia corpus callosum agenesis
corpus callosum orofacial cleft
2 diseases from the University of Copenhagen DISEASES database for VAX2:Coloboma Cleft lip Human Genome Epidemiology (HuGE) Navigator: VAX2 (4 documents)
Export disorders for VAX2 gene to outside databases
|
Publications
for VAX2 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 VAX2 gene integrated from 9 sources:
(articles sorted by number of sources associating them with VAX2) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- A homeobox gene, vax2, controls the patterning of the eye dorsoventral axis. (PubMed id 10485894)1, 2, 3, 9 Barbieri A.M.... Banfi S. (1999)
- 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)
- VAX1 mutation associated with microphthalmia, corpus callosum agenesis, and orofacial clefting: The first description of a VAX1 phenotype in humans. (PubMed id 22095910)2 Slavotinek A.M.... Schorderet D.F. (2012)
- Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. (PubMed id 21697133)1 Oshikawa M.... Kato S. (2011)
- Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1 Bailey S.D....Anand S. (2010)
- Gene-centric association signals for lipids and apoli poproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (2009)
- Classification and nomenclature of all human homeobox genes. (PubMed id 17963489)1 Holland P.W.H.... Bruford E.A. (2007)
- Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. (PubMed id 16953426)1 Beaty T.H....Scott A.F. (2006)
- 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)
- The level of BMP4 signaling is critical for the regulation of distinct T-box gene expression domains and growth along the dorso-ventral axis of the optic cup. (PubMed id 17173667)9 Behesti H....Sowden J.C. (2006)
|
External Searches for VAX2 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing VAX2 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing VAX2 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing VAX2 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
|
| Name | Description |
| PharmGKB entry for VAX2 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for VAX2 gene:
Search GeneIP for patents involving VAX2
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for VAX2 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
About This Section
|
 | |
 | |
 |
| | |  | Browse OriGene Antibodies | | OriGene shRNA RFP for VAX2 | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for VAX2 | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for VAX2 | | | OriGene Protein Over-expression Lysate for VAX2 | | Browse OriGene Fluorogenic Cell Assay Kits | | | OriGene siRNA for VAX2 | | Browse 3'-UTR reporter clones for miRNA target validation | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for VAX2 | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for VAX2 | | | Browse OriGene GFP tagged cDNA clones in CMV expression vector | | Browse OriGene MicroRNA Expression Plasmids | | | Browse OriGene basic RS shRNAs | | Browse OriGene validated miRNA SYBR primer pairs | | | Browse OriGene full length recombinant human proteins expressed in human HEK293 cells | | OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat VAX2 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing VAX2 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VAX2 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat VAX2 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat VAX2 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat VAX2 |
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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VAX2 |
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