PCDHA1 Gene
protein-coding GIFtS: 45
GCID: GC05P140146
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protocadherin alpha 1
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Aliases
for PCDHA1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Protocadherin Alpha 11 2 | | PCDH-Alpha-11 | | PCDH-ALPHA12 | | KIAA0345-Like 132 | | Protocadherin Alpha-12 |
Export aliases for PCDHA1 gene to outside databasesPrevious GC identifers: GC05P139982 GC05P140748 GC05P140150 GC05P140194 GC05P135311 |
Summaries
for PCDHA1 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 PCDHA1:
This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked onchromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor geneclusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes andconsists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons,or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes inthe cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exonsencode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteinsthat most likely play a critical role in the establishment and function of specific cell-cell connections in thebrain. Alternative splicing has been observed and additional variants have been suggested but their full-length naturehas yet to be determined. (provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: PCDA1_HUMAN, Q9Y5I3Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance ofspecific neuronal connections in the brain
Gene Wiki entry for PCDHA1 (Protocadherin alpha 1)
|
Genomic Views
for PCDHA1 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 PCDHA1 gene promoter:
RelA CUTL1 NF-AT NF-AT4 NF-AT2 COMP1 NF-AT3 NF-kappaB1 NF-AT1
Other transcription factors
Search SABiosciences Chromatin IP Primers for PCDHA1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHA1 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 5q31 Ensembl cytogenetic band: 5q31.3 HGNC cytogenetic band: 5q31PCDHA1 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 GC05P140146: view genomic region
(about GC identifiers)
Start:
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140,165,876 bp from pter |
End:
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140,391,929 bp from pter |
Size:
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226,054 bases |
Orientation:
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plus strand |
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Proteins
for PCDHA1 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: PCDA1_HUMAN, Q9Y5I3 (See
protein sequence)Recommended Name: Protocadherin alpha-1 precursor Size: 950 amino acids; 102952 Da
Subcellular location: Isoform 1: Cell membrane; Single-pass type I membrane protein (By similarity)
Subcellular location: Isoform 2: Secreted (Potential)
Secondary accessions: O75288 Q9NRT7Alternative splicing: 3 isoforms: Q9Y5I3-1 Q9Y5I3-2 Q9Y5I3-3 Explore the universe of human proteins at neXtProt for PCDHA1: NX_Q9Y5I3
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9Y5I3
PCDHA1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (3 alternative transcripts):
NP_061723.1 NP_113598.1 NP_113599.1
ENSEMBL proteins: ENSP00000420840 ENSP00000378129 ENSP00000367373
Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table
PCDHA1 for ontologies About GeneDecksing
PCDHA1 Antibody Products:
Assay Products for PCDHA1: |
Protein
Domains /
Families
for PCDHA1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
PCDHA1 for domains About GeneDecksing
4 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9Y5I3ProtoNet protein and cluster: Q9Y5I3 1 Blocks protein family: IPB002126 Cadherin
UniProtKB/Swiss-Prot: PCDA1_HUMAN, Q9Y5I3Similarity: Contains 6 cadherin domains |
Function
for PCDHA1 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: PCDA1_HUMAN, Q9Y5I3Function: 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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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHA1 |
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 | -- |
PCDHA1 for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for PCDHA1:
Animal Models:
1 MGI mutant phenotype (inferred from 1 allele ) (MGI details for Pcdha1):
PCDHA1 for phenotypes About GeneDecksing
|
Pathways & Interactions
for PCDHA1 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 PCDHA1
STRING Interaction
Network Preview (showing 1 interactants - click image to see more details)
1 Interacting protein for PCDHA1 (Q9Y5I33 ENSP000003673734) via UniProtKB, MINT, STRING, and/or I2DAbout this table
Gene Ontology (GO): 3 biological process terms (GO ID links to tree view): About this table
PCDHA1 for ontologies About GeneDecksing
|
Drugs & Compounds
for PCDHA1 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 PCDHA1
1 HMDB Compound for PCDHA1 About this table
Search CenterWatch for drugs/clinical trials and news about PCDHA1 / PCDA1
|
Transcripts
for PCDHA1 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 PCDHA1 gene (3 alternative transcripts): NM_018900.2 NM_031410.1 NM_031411.1 3 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000504120(uc003lhb.2) ENST00000394633(uc003lha.2) ENST00000378133(uc003lgz.3)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHA1 (see all 6)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PCDHA1 (see all 3)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript Custom all cDNA clones Services for PCDHA1 | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for PCDHA1 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PCDHA1 |
24/261 AceView cDNA sequences (see all 261): NM_031883 CA396936 NM_031500 T30761 AF152478 AF152482 AF152483 AF152306 AF152313 CD239823 AI370466 NM_018908 NM_031857 NM_018900 NM_031864 AW572498 AI452508 AF152486 AI161196 NM_018904 NM_031410 NM_031495 AF152312 AI969295
GeneLoc Exon Structure
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Expression
for PCDHA1 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
| PCDHA1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
See PCDHA1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PCDHA1
SABiosciences Custom PCR Arrays for PCDHA1
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for PCDHA1
Browse OriGene validated miRNA SYBR primer pairs
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Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHA1 |
Orthologs
for PCDHA1 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 PCDHA1 gene from 4/13 species (see all 13) About this table
ENSEMBL Gene Tree for PCDHA1 (if available)
TreeFam Gene Tree for PCDHA1 (if available) |
Paralogs
for PCDHA1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for PCDHA1 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 PCDHGB12 PCDHGB42 PCDHGA22 PCDHA112 PCDHA72 PCDHGA112 PCDHGA62
- PCDHB32 PCDHB62 PCDHGC52 PCDHGC42 PCDHA102 PCDHA92 PCDHGA12 PCDHB102
- PCDHB12 PCDHGA32 PCDHGB72
18/61 SIMAP similar genes for PCDHA1 using alignment to 1 protein entry: PCDA1_HUMAN(see all similar genes):PCDHA11 PCDHA2 PCDHA3 PCDHA4 PCDHA5 PCDHA6
PCDHA9 PCDHA8 PCDHA7 PCDHA13 PCDHA10 PCDHA12
PCDHB17 PCDHAC2 PCDHB15 PCDHB16 PCDHGA3 PCDHB10
PCDHA1 for paralogs About GeneDecksing
|
Genomic Variants
for PCDHA1 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 PCDHA1 (140165876 - 140391929 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 23 variations for PCDHA1
15/22 CNVs (see all 22): 93255 32748 1701 64320 53833 59240 3578 31248 31250 81058 31249 64319 6449 62437 51579
1 Indel: 64317 | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDHA1 |
|
Disorders
/ Diseases
for PCDHA1 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
|
PCDHA1 for disorders About GeneDecksing
OMIM gene information: 606307
OMIM disorders: --
3  diseases for PCDHA1: About MalaCardsbipolar disorder schizophrenia neuronitis
1 disease from the University of Copenhagen DISEASES database for PCDHA1:Thyrotoxicosis Human Genome Epidemiology (HuGE) Navigator: PCDHA1 (1 document)
Export disorders for PCDHA1 gene to outside databases
|
Publications
for PCDHA1 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 PCDHA1 gene, integrated from 9 sources (see all 11):
(articles sorted by number of sources associating them with PCDHA1) | |  | 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 DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)1, 2 Schmutz J.... Rubin E.M. (2004)
- Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PubMed id 22589738)1 Fox C.S....Borecki I.B. (2012)
- Analysis of protocadherin alpha gene deletion variant in bipolar disorder and schizophrenia. (PubMed id 18496207)1 Lachman H.M....Stopkova P. (2008)
- Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. (PubMed id 17474147)1 Wu C....Li S.S. (2007)
- 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)
- Genomic organization of the family of CNR cadherin genes in mice and humans. (PubMed id 10662547)1 Sugino H....Yagi T. (2000)
- Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (2000)
- Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. (PubMed id 10737800)1 Dias Neto E....Simpson A.J.G. (2000)
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External Searches for PCDHA1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing PCDHA1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing PCDHA1 gene
(According to HUGE)
About This Section
| |
Specialized Databases showing PCDHA1 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 PCDHA1 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for PCDHA1 gene:
Search GeneIP for patents involving PCDHA1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for PCDHA1 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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variant library, vector shuttling | | | OriGene Custom Antibody Services for PCDHA1 | | OriGene Custom Protein Services for PCDHA1 | | | OriGene Custom Immunoassay Development | | |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat PCDHA1 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PCDHA1 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHA1 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PCDHA1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PCDHA1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PCDHA1 |
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| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PCDHA1 |
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