PCDHB13 Gene
protein-coding GIFtS: 44
GCID: GC05P140694
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protocadherin beta 13
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Aliases
for PCDHB13 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 131 2 | | PCDH-BETA131 2 | | PCDH-Beta-131 | | Protocadherin Beta-132 |
Export aliases for PCDHB13 gene to outside databasesPrevious GC identifers: GC05P140409 GC05P141176 GC05P140576 GC05P140623 GC05P140624 GC05P140573 GC05P140657 GC05P140662 GC05P135738 GC05P140668 GC05P140673 GC05P140678 GC05P140684 |
Summaries
for PCDHB13 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 PCDHB13:
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: PCDBD_HUMAN, Q9Y5F0Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance ofspecific neuronal connections in the brain
Gene Wiki entry for PCDHB13
|
Genomic Views
for PCDHB13 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 PCDHB13 gene promoter:
AhR GR GR-beta LUN-1 E47 Arnt HEN1 PPAR-alpha GR-alpha
Other transcription factors
Search SABiosciences Chromatin IP Primers for PCDHB13
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHB13 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 5q31 Ensembl cytogenetic band: 5q31.3 HGNC cytogenetic band: 5q31PCDHB13 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 GC05P140694: view genomic region
(about GC identifiers)
Start:
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140,593,509 bp from pter |
End:
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140,596,993 bp from pter |
Size:
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3,485 bases |
Orientation:
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plus strand |
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Proteins
for PCDHB13 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: PCDBD_HUMAN, Q9Y5F0 (See
protein sequence)Recommended Name: Protocadherin beta-13 precursor Size: 798 amino acids; 87552 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)Explore the universe of human proteins at neXtProt for PCDHB13: NX_Q9Y5F0
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9Y5F0
PCDHB13 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_061756.1
ENSEMBL proteins: ENSP00000345491
Human Recombinant Protein Products for PCDHB13:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
PCDHB13 for ontologies About GeneDecksing
PCDHB13 Antibody Products:
Assay Products for PCDHB13: |
Protein
Domains /
Families
for PCDHB13 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
PCDHB13 for domains About GeneDecksing
4 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9Y5F0ProtoNet protein and cluster: Q9Y5F0 1 Blocks protein family: IPB002126 Cadherin
UniProtKB/Swiss-Prot: PCDBD_HUMAN, Q9Y5F0Similarity: Contains 6 cadherin domains |
Function
for PCDHB13 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
inGenious Targeting Laboratory,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase,
shRNA from
OriGene,
Sirion Biotech,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Sirion Biotech,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
Sirion Biotech,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Molecular Function:
UniProtKB/Swiss-Prot Summary: PCDBD_HUMAN, Q9Y5F0Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance ofspecific neuronal connections in the brain 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 | -- |
PCDHB13 for ontologies About GeneDecksing
Phenotypes:
2 GenomeRNAi human phenotypes for PCDHB13:
Animal Models:
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHB13
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHB13 |
|
Pathways & Interactions
for PCDHB13 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 PCDHB13
Gene Ontology (GO): 4 biological process terms (GO ID links to tree view): About this table
PCDHB13 for ontologies About GeneDecksing
|
Drugs & Compounds
for PCDHB13 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 PCDHB13
1 HMDB Compound for PCDHB13 About this table
Search CenterWatch for drugs/clinical trials and news about PCDHB13 / PCDBD
|
Transcripts
for PCDHB13 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,
Sirion Biotech,
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 PCDHB13 gene: NM_018933.2 Unigene Cluster for PCDHB13: Protocadherin beta 13 Hs.283803 [show with all ESTs]Unigene Representative Sequence: AF2177451 Ensembl transcript including schematic representation, and UCSC links where relevant: ENST00000341948(uc003lja.1)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHB13
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHB13
OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: PCDHB13 (NM_018933) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PCDHB13 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PCDHB13 |
Additional cDNA sequence: AF152492.1 AF217745.1 AK021915.1 AK292821.1 AK296151.1 AY358427.1 BC033068.1 BC051348.1 BC071934.1 2 DOTS entries: DT.95210419 DT.97834597 24/30 AceView cDNA sequences (see all 30): BE856564 BC071934 BX117042 AF152492 NM_018933 AA489646 AF217745 BU552555 AI363933 BC051348 AY358427 BQ927385 BC033068 BG697250 AA489751 AK021915 AU119840 BQ958557 BQ887350 BM047725 BM921141 BE677909 BM046493 BE934257
GeneLoc Exon Structure
|
Expression
for PCDHB13 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
| PCDHB13 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
See PCDHB13 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PCDHB13
SOURCE GeneReport for Unigene cluster: Hs.283803
SABiosciences Custom PCR Arrays for PCDHB13
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PCDHB13
Browse OriGene validated miRNA SYBR primer pairs
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Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHB13 |
Orthologs
for PCDHB13 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 PCDHB13 gene from 3/7 species (see all 7) About this table
ENSEMBL Gene Tree for PCDHB13 (if available)
TreeFam Gene Tree for PCDHB13 (if available) |
Paralogs
for PCDHB13 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for PCDHB13 gene
- PCDHAC12 PCDHB162 PCDHB22 PCDHAC22 PCDHB72 PCDHB152 PCDHGA102 PCDHGA122
- PCDHGB22 PCDHGA82 PCDHGA92 PCDHGB32 PCDHGC32 PCDHGB62 PCDHA62 PCDHGA52
- PCDHA82 PCDHA132 PCDHB52 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 PCDHB13 using alignment to 1 protein entry: PCDBD_HUMAN(see all similar genes):PCDHB8 PCDHB16 PCDHB3 PCDHB11 PCDHB12 PCDHB15
PCDHB18 PCDHB6 DKFZp586I1919 PCDHB14 PCDHB2 PCDHB10
PCDHB17 PCDHB4 PCDHB5 PCDHB9 PCDHB7 PCDHB1
PCDHB13 for paralogs About GeneDecksing
|
Genomic Variants
for PCDHB13 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 PCDHB13 (140593509 - 140596993 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 3 variations for PCDHB13
2 CNVs: 3578 69210
1 Indel: 33412 | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDHB13 |
|
Disorders
/ Diseases
for PCDHB13 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
|
PCDHB13 for disorders About GeneDecksing
OMIM gene information: 606339
OMIM disorders: --
1  disease for PCDHB13: About MalaCardsneuronitis
Export disorders for PCDHB13 gene to outside databases
|
Publications
for PCDHB13 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 PCDHB13 gene, integrated from 9 sources (see all 11):
(articles sorted by number of sources associating them with PCDHB13) | |  | 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)1, 2 Gerhard D.S....Malek J. (2004)
- The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
- 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 Vanhalst K.... van Roy F. (2001)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (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)
- 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)
|
External Searches for PCDHB13 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing PCDHB13 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing PCDHB13 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing PCDHB13 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 PCDHB13 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for PCDHB13 gene:
Search GeneIP for patents involving PCDHB13
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for PCDHB13 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 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, 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, Animal models from inGenious Targeting Laboratory)
About This Section
|
 | |
 | |
 |
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