PCDHGB1 Gene
protein-coding GIFtS: 37
GCID: GC05P141250
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protocadherin gamma subfamily B, 1
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Aliases
for PCDHGB1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Protocadherin Gamma Subfamily B, 11 2 | | PCDH-GAMMA-B11 2 | | Protocadherin Gamma-B12 | | PCDH-Gamma-B11 |
Export aliases for PCDHGB1 gene to outside databasesPrevious GC identifers: GC05P140546 GC05P141303 GC05P140709 GC05P140768 GC05P140788 GC05P140727 GC05P140813 GC05P140824 GC05P140853 GC05P140859 GC05P140885 GC05P140907 GC05P140922 GC05P140944 GC05P140965 GC05P140987 GC05P141014 GC05P141037 GC05P141081 GC05P135874 GC05P141102 GC05P141141 GC05P141180 GC05P141211 |
Summaries
for PCDHGB1 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 PCDHGB1:
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked onchromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism maybe involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies.Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly relatedsubfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region,containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region,which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the commoncytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in theestablishment and function of specific cell-cell connections in the brain. Alternative splicing has been described forthe gamma cluster genes. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: PCDGD_HUMAN, Q9Y5G3Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance ofspecific neuronal connections in the brain
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Genomic Views
for PCDHGB1 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
| Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the PCDHGB1 gene promoter:
Max1 AREB6 Sp1 AP-1 ATF-2 c-Jun
Other transcription factors
Search SABiosciences Chromatin IP Primers for PCDHGB1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHGB1 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 5q31 Ensembl cytogenetic band: 5q31.3 HGNC cytogenetic band: 5q31PCDHGB1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 5 GeneLoc Exon Structure GeneLoc location for GC05P141250: view genomic region
(about GC identifiers)
Start:
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140,729,828 bp from pter |
End:
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140,892,546 bp from pter |
Size:
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162,719 bases |
Orientation:
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plus strand |
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Proteins
for PCDHGB1 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: PCDGD_HUMAN, Q9Y5G3 (See
protein sequence)Recommended Name: Protocadherin gamma-B1 precursor Size: 927 amino acids; 100360 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Secondary accessions: Q3SY75 Q9Y5C8Alternative splicing: 2 isoforms: Q9Y5G3-1 Q9Y5G3-2 Explore the universe of human proteins at neXtProt for PCDHGB1: NX_Q9Y5G3
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9Y5G3
PCDHGB1 Protein expression data from MOPED and PaxDb: --
REFSEQ proteins (2 alternative transcripts):
NP_061745.1 NP_115266.1
ENSEMBL proteins: ENSP00000429273
Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005886 | plasma membrane |
IEA | -- | | GO:0016021 | integral to membrane |
IEA | -- |
PCDHGB1 for ontologies About GeneDecksing
PCDHGB1 Antibody Products:
Assay Products for PCDHGB1: |
Protein
Domains /
Families
for PCDHGB1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
PCDHGB1 for domains About GeneDecksing
4 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9Y5G3ProtoNet protein and cluster: Q9Y5G3 1 Blocks protein family: IPB002126 Cadherin
UniProtKB/Swiss-Prot: PCDGD_HUMAN, Q9Y5G3Similarity: Contains 6 cadherin domains |
Function
for PCDHGB1 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: PCDGD_HUMAN, Q9Y5G3Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance ofspecific neuronal connections in the brain
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHGB1 (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHGB1 |
Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005509 | calcium ion binding |
IEA | -- |
PCDHGB1 for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for PCDHGB1:
|
Pathways & Interactions
for PCDHGB1 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 PCDHGB1
Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0007156 | homophilic cell adhesion |
IEA | -- |
PCDHGB1 for ontologies About GeneDecksing
|
Drugs & Compounds
for PCDHGB1 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 PCDHGB1
1 HMDB Compound for PCDHGB1 About this table
Search CenterWatch for drugs/clinical trials and news about PCDHGB1 / PCDGD
|
Transcripts
for PCDHGB1 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 PCDHGB1 gene (2 alternative transcripts): NM_018922.2 NM_032095.1 1 Ensembl transcript including schematic representation, and UCSC links where relevant: ENST00000523390(uc003ljo.2)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHGB1 (see all 4)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHGB1 (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector (see all 2): PCDHGB1 (NM_032095) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PCDHGB1 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PCDHGB1 |
24/737 AceView cDNA sequences (see all 737): NM_032403 AF152504 NM_018929 AL832028 BE843380 NM_032086 AF152507 NM_031993 BQ716279 AF152517 NM_032009 BQ018446 BC006439 AF152322 BG818666 BQ689381 CD678805 AL526792 CA442860 BU627870 BU839246 BC019299 AF152526 AW089227
GeneLoc Exon Structure
|
Expression
for PCDHGB1 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
| PCDHGB1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
Genevestigator expression for PCDHGB1
SABiosciences Custom PCR Arrays for PCDHGB1
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PCDHGB1
Browse OriGene validated miRNA SYBR primer pairs
| | | Search SABiosciences RT2 qPCR
Primer Assays in human, mouse, rat PCDHGB1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PCDHGB1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PCDHGB1 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHGB1 |
Orthologs
for PCDHGB1 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 PCDHGB1 gene from 2/8 species (see all 8) About this table
ENSEMBL Gene Tree for PCDHGB1 (if available)
TreeFam Gene Tree for PCDHGB1 (if available) |
Paralogs
for PCDHGB1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for PCDHGB1 gene
- PCDHAC12 PCDHB162 PCDHB22 PCDHAC22 PCDHB72 PCDHB152 PCDHGA102 PCDHGA122
- PCDHGB22 PCDHGA82 PCDHGA92 PCDHGB32 PCDHGC32 PCDHGB62 PCDHA62 PCDHGA52
- PCDHA82 PCDHA132 PCDHB52 PCDHB132 PCDHA32 PCDHGA42 PCDHGA72 PCDHA42
- PCDHB42 PCDHB112 PCDHA22 ENSG000002556222 PCDHB142 PCDHB122 PCDHA122 PCDHB82
- PCDHA52 PCDHGB42 PCDHA12 PCDHGA22 PCDHA112 PCDHA72 PCDHGA112 PCDHGA62
- PCDHB32 PCDHB62 PCDHGC52 PCDHGC42 PCDHA102 PCDHA92 PCDHGA12 PCDHB102
- PCDHB12 PCDHGA32 PCDHGB72
18/74 SIMAP similar genes for PCDHGB1 using alignment to 2 protein entries: PCDGD_HUMAN (see all proteins)
(see all similar genes):PCDHGB4 PCDHGB2 PCDHGB5 PCDHGB6 PCDHGB7 PCDHGB3
ME6 PCDHGC3 PCDHGA3 PCDHGA2 PCDHGA4 PCDHGA8
PCDHGA12 PCDHGA5 PCDHGA6 PCDHGA9 ME3 PCDHGA1
PCDHGB1 for paralogs About GeneDecksing
|
Genomic Variants
for PCDHGB1 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 5 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for PCDHGB1 (140729828 - 140892546 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 3 variations for PCDHGB1
3 CNVs: 3578 69211 6450 | SABiosciences Cancer Mutation PCR Assays |
|
Disorders
/ Diseases
for PCDHGB1 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
|
PCDHGB1 for disorders About GeneDecksing
OMIM gene information: 606299
OMIM disorders: --
1  disease for PCDHGB1: About MalaCardsneuronitis
Export disorders for PCDHGB1 gene to outside databases
|
Publications
for PCDHGB1 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 PCDHGB1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with PCDHGB1) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)1, 2, 3 Wu Q. and Maniatis T. (1999)
- 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. (2004)
- 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)
- Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)
- Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PubMed id 10835267)1 Nollet F....van Roy F. (2000)
- Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (2000)
- Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (2000)
|
External Searches for PCDHGB1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
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|
Genome Databases showing PCDHGB1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing PCDHGB1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing PCDHGB1 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 PCDHGB1 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for PCDHGB1 gene:
Search GeneIP for patents involving PCDHGB1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for PCDHGB1 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 PCDHGB1 | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PCDHGB1 | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PCDHGB1 | | | Browse OriGene Protein Over-expression Lysates | | Browse OriGene Fluorogenic Cell Assay Kits | | | OriGene siRNA for PCDHGB1 | | OriGene 3'-UTR Clone for PCDHGB1 | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHGB1 | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHGB1 | | | 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,
variant library, vector shuttling | | | OriGene Custom Antibody Services for PCDHGB1 | | OriGene Custom Protein Services for PCDHGB1 | | | OriGene Custom Immunoassay Development | | |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat PCDHGB1 | | | Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDHGB1 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHGB1 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PCDHGB1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PCDHGB1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PCDHGB1 |
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 |  |  |  | |
| | | | Search Tocris compounds for PCDHGB1 |
| |  |  |  |  | | | | |
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 | | | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHGB1 |
|  |  |  | | | | Search ThermoFisher Antibodies for PCDHGB1 |
| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PCDHGB1 |
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