PCDHB16 Gene
protein-coding GIFtS: 47
GCID: GC05P140561
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protocadherin beta 16
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Aliases
for PCDHB16 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Protocadherin Beta 161 2 | | Cadherin ME12 | | PCDH3X1 2 3 | | PCDHbeta 162 | | ME11 2 | | Protocadherin Beta 8a2 | | PCDH-BETA161 2 | | Protocadherin Beta-162 | | PCDHB8a1 2 | | Protocadherin-3x1 | | KIAA16211 3 | | Protocadherin-3X3 | | PCDH-Beta-161 | | |
Export aliases for PCDHB16 gene to outside databasesPrevious GC identifers: GC05P140377 GC05P141143 GC05P140544 GC05P140599 GC05P140605 GC05P140542 GC05P135706 |
Summaries
for PCDHB16 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 PCDHB16:
This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked onchromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cellreceptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherindomains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domainsinteract in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters,the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. Theseneural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions areunknown but they most likely play a critical role in the establishment and function of specific cell-cell neuralconnections. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: PCDBG_HUMAN, Q9NRJ7Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance ofspecific neuronal connections in the brain
Gene Wiki entry for PCDHB16
|
Genomic Views
for PCDHB16 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_000005.9 NC_018916.1 NT_029289.11
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the PCDHB16 gene promoter:
AhR AREB6 POU2F1 Egr-1 Pax-2 Pax-2a LCR-F1 Arnt
Other transcription factors
Search SABiosciences Chromatin IP Primers for PCDHB16
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHB16 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 5q31 Ensembl cytogenetic band: 5q31.3 HGNC cytogenetic band: 5q31PCDHB16 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 GC05P140561: view genomic region
(about GC identifiers)
Start:
|
140,560,980 bp from pter |
End:
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140,565,796 bp from pter |
Size:
|
4,817 bases |
Orientation:
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plus strand |
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Proteins
for PCDHB16 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: PCDBG_HUMAN, Q9NRJ7 (See
protein sequence)Recommended Name: Protocadherin beta-16 precursor Size: 776 amino acids; 84983 Da
Subcellular location: Membrane; Single-pass type I membrane protein (By similarity)
Sequence caution: Sequence=BAB13447.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: B3KPK5 Q8IYD5 Q96SE9 Q9HCF1Explore the universe of human proteins at neXtProt for PCDHB16: NX_Q9NRJ7
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9NRJ7
PCDHB16 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_066008.1
ENSEMBL proteins: ENSP00000354293
Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
PCDHB16 for ontologies About GeneDecksing
PCDHB16 Antibody Products:
Assay Products for PCDHB16: |
Protein
Domains /
Families
for PCDHB16 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
PCDHB16 for domains About GeneDecksing
4 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9NRJ7ProtoNet protein and cluster: Q9NRJ7 1 Blocks protein family: IPB002126 Cadherin
UniProtKB/Swiss-Prot: PCDBG_HUMAN, Q9NRJ7Similarity: Contains 6 cadherin domains |
Function
for PCDHB16 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: PCDBG_HUMAN, Q9NRJ7Function: 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 PCDHB16
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHB16 |
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 | -- |
PCDHB16 for ontologies About GeneDecksing
|
Pathways & Interactions
for PCDHB16 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 PCDHB16
Gene Ontology (GO): 4 biological process terms (GO ID links to tree view): About this table
PCDHB16 for ontologies About GeneDecksing
|
Drugs & Compounds
for PCDHB16 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 PCDHB16
1 HMDB Compound for PCDHB16 About this table
Search CenterWatch for drugs/clinical trials and news about PCDHB16 / PCDBG
|
Transcripts
for PCDHB16 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 PCDHB16 gene: NM_020957.1 Unigene Cluster for PCDHB16: Protocadherin beta 16 Hs.147674 [show with all ESTs]Unigene Representative Sequence: AB0468411 Ensembl transcript including schematic representation, and UCSC links where relevant: ENST00000361016(uc003liv.3)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHB16 (see all 2)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHB16
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: PCDHB16 (NM_020957) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PCDHB16 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PCDHB16 |
Additional cDNA sequence: AB046841.1 AF217757.1 AK056460.1 AK308125.1 AY013878.1 BC036062.1 D88794.1 3 DOTS entries: DT.308530 DT.120879768 DT.120879782 24/38 AceView cDNA sequences (see all 38): AY013878 CA438727 NM_020957 CR614455 BX114902 CK902223 AA505356 AA428592 BX369763 AL526744 AK056460 AI381876 BC036062 AF217757 AI926355 AI684744 D88794 AB046841 BQ778648 BQ942987 AA453283 BQ778431 CA335337 AI376824
GeneLoc Exon Structure
|
Expression
for PCDHB16 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
| PCDHB16 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CTCACCACCA
About this image
See PCDHB16 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PCDHB16
SOURCE GeneReport for Unigene cluster: Hs.147674
SABiosciences Custom PCR Arrays for PCDHB16
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PCDHB16
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat PCDHB16 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PCDHB16 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PCDHB16 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHB16 |
Orthologs
for PCDHB16 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 PCDHB16 gene from 3/8 species (see all 8) About this table
ENSEMBL Gene Tree for PCDHB16 (if available)
TreeFam Gene Tree for PCDHB16 (if available) |
Paralogs
for PCDHB16 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for PCDHB16 gene
- PCDHAC12 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
- PCDHGB12 PCDHGB42 PCDHA12 PCDHGA22 PCDHA112 PCDHA72 PCDHGA112 PCDHGA62
- PCDHB32 PCDHB62 PCDHGC52 PCDHGC42 PCDHA102 PCDHA92 PCDHGA12 PCDHB102
- PCDHB12 PCDHGA32 PCDHGB72
18/66 SIMAP similar genes for PCDHB16 using alignment to 2 protein entries: PCDBG_HUMAN (see all proteins)
(see all similar genes):PCDHB11 PCDHB12 PCDHB14 PCDHB15 PCDHB3 PCDHB6
PCDHB13 PCDHB8 DKFZp586I1919 PCDHB18 PCDHB2 PCDHB4
PCDHB5 PCDHB9 PCDHB10 PCDHB17 PCDHB7 PCDHB1
PCDHB16 for paralogs About GeneDecksing
1 Pseudogenes.org Pseudogene for PCDHB16
PGOHUM00000258203
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Genomic Variants
for PCDHB16 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 PCDHB16 (140560980 - 140565796 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 5 variations for PCDHB16
5 CNVs: 0714 3578 31251 36352 36351
Human Gene Mutation Database (HGMD): PCDHB16
| SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDHB16 |
|
Disorders
/ Diseases
for PCDHB16 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
|
PCDHB16 for disorders About GeneDecksing
OMIM gene information: 606345
OMIM disorders: --
2  diseases for PCDHB16: About MalaCardsmelanoma neuronitis
Export disorders for PCDHB16 gene to outside databases
|
Publications
for PCDHB16 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 PCDHB16 gene, integrated from 9 sources (see all 15):
(articles sorted by number of sources associating them with PCDHB16) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1, 2, 3 Wu Q.... Maniatis T. (2001)
- The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (PubMed id 11322959)1, 2, 3 Vanhalst K.... van Roy F. (2001)
- 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)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. (PubMed id 12665801)1, 2 Gevaert K.... Vandekerckhove J. (2003)
- Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10997877)1, 2 Nagase T.... Ohara O. (2000)
- The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (2004)
- Protocadherins. (PubMed id 12231349)1 Frank M. and Kemler R. (2002)
- 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)
- 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)
|
External Searches for PCDHB16 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing PCDHB16 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing PCDHB16 gene
(According to HUGE)
About This Section
| |
Specialized Databases showing PCDHB16 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 PCDHB16 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for PCDHB16 gene:
Search GeneIP for patents involving PCDHB16
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for PCDHB16 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
|
 | |
 | |
 |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat PCDHB16 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDHB16 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHB16 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PCDHB16 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PCDHB16 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PCDHB16 |
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| |  |  |  |  | | | | |
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