Atlas of Genetics and Cytogenetics in Oncology and Haematology


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PCDHA1 (protocadherin alpha 1)

Identity

Other aliasPCDH-ALPHA1
HGNC (Hugo) PCDHA1
LocusID (NCBI) 56147
Atlas_Id 71704
Location 5q31.3  [Link to chromosome band 5q31]
Location_base_pair Starts at 140786136 and ends at 141012344 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
PCDHA1 (5q31.3) / NRXN1 (2p16.3)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)PCDHA1   8663
Cards
Entrez_Gene (NCBI)PCDHA1  56147  protocadherin alpha 1
AliasesPCDH-ALPHA1
GeneCards (Weizmann)PCDHA1
Ensembl hg19 (Hinxton)ENSG00000204970 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000204970 [Gene_View]  chr5:140786136-141012344 [Contig_View]  PCDHA1 [Vega]
ICGC DataPortalENSG00000204970
TCGA cBioPortalPCDHA1
AceView (NCBI)PCDHA1
Genatlas (Paris)PCDHA1
WikiGenes56147
SOURCE (Princeton)PCDHA1
Genetics Home Reference (NIH)PCDHA1
Genomic and cartography
GoldenPath hg38 (UCSC)PCDHA1  -     chr5:140786136-141012344 +  5q31.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PCDHA1  -     5q31.3   [Description]    (hg19-Feb_2009)
EnsemblPCDHA1 - 5q31.3 [CytoView hg19]  PCDHA1 - 5q31.3 [CytoView hg38]
Mapping of homologs : NCBIPCDHA1 [Mapview hg19]  PCDHA1 [Mapview hg38]
OMIM606307   
Gene and transcription
Genbank (Entrez)AF152305 AF152479 AF169695 BC166697 BF089693
RefSeq transcript (Entrez)NM_018900 NM_031410 NM_031411
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PCDHA1
Cluster EST : UnigeneHs.199343 [ NCBI ]
CGAP (NCI)Hs.199343
Alternative Splicing GalleryENSG00000204970
Gene ExpressionPCDHA1 [ NCBI-GEO ]   PCDHA1 [ EBI - ARRAY_EXPRESS ]   PCDHA1 [ SEEK ]   PCDHA1 [ MEM ]
Gene Expression Viewer (FireBrowse)PCDHA1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)56147
GTEX Portal (Tissue expression)PCDHA1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y5I3   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9Y5I3  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9Y5I3
Splice isoforms : SwissVarQ9Y5I3
PhosPhoSitePlusQ9Y5I3
Domaine pattern : Prosite (Expaxy)CADHERIN_1 (PS00232)    CADHERIN_2 (PS50268)   
Domains : Interpro (EBI)Cadherin    Cadherin-like    Cadherin_CBD    Cadherin_CS    Cadherin_N    PCDHA1   
Domain families : Pfam (Sanger)Cadherin (PF00028)    Cadherin_2 (PF08266)    Cadherin_tail (PF15974)   
Domain families : Pfam (NCBI)pfam00028    pfam08266    pfam15974   
Domain families : Smart (EMBL)CA (SM00112)  
Conserved Domain (NCBI)PCDHA1
DMDM Disease mutations56147
Blocks (Seattle)PCDHA1
SuperfamilyQ9Y5I3
Human Protein AtlasENSG00000204970
Peptide AtlasQ9Y5I3
HPRD07319
IPIIPI00001515   IPI00218712   IPI00218713   
Protein Interaction databases
DIP (DOE-UCLA)Q9Y5I3
IntAct (EBI)Q9Y5I3
FunCoupENSG00000204970
BioGRIDPCDHA1
STRING (EMBL)PCDHA1
ZODIACPCDHA1
Ontologies - Pathways
QuickGOQ9Y5I3
Ontology : AmiGOcalcium ion binding  extracellular region  endoplasmic reticulum  integral component of plasma membrane  cell adhesion  homophilic cell adhesion via plasma membrane adhesion molecules  cell-cell signaling  nervous system development  
Ontology : EGO-EBIcalcium ion binding  extracellular region  endoplasmic reticulum  integral component of plasma membrane  cell adhesion  homophilic cell adhesion via plasma membrane adhesion molecules  cell-cell signaling  nervous system development  
NDEx NetworkPCDHA1
Atlas of Cancer Signalling NetworkPCDHA1
Wikipedia pathwaysPCDHA1
Orthology - Evolution
OrthoDB56147
GeneTree (enSembl)ENSG00000204970
Phylogenetic Trees/Animal Genes : TreeFamPCDHA1
HOVERGENQ9Y5I3
HOGENOMQ9Y5I3
Homologs : HomoloGenePCDHA1
Homology/Alignments : Family Browser (UCSC)PCDHA1
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPCDHA1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PCDHA1
dbVarPCDHA1
ClinVarPCDHA1
1000_GenomesPCDHA1 
Exome Variant ServerPCDHA1
ExAC (Exome Aggregation Consortium)PCDHA1 (select the gene name)
Genetic variants : HAPMAP56147
Genomic Variants (DGV)PCDHA1 [DGVbeta]
DECIPHERPCDHA1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPCDHA1 
Mutations
ICGC Data PortalPCDHA1 
TCGA Data PortalPCDHA1 
Broad Tumor PortalPCDHA1
OASIS PortalPCDHA1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPCDHA1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPCDHA1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PCDHA1
DgiDB (Drug Gene Interaction Database)PCDHA1
DoCM (Curated mutations)PCDHA1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PCDHA1 (select a term)
intoGenPCDHA1
Cancer3DPCDHA1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM606307   
Orphanet
MedgenPCDHA1
Genetic Testing Registry PCDHA1
NextProtQ9Y5I3 [Medical]
TSGene56147
GENETestsPCDHA1
Target ValidationPCDHA1
Huge Navigator PCDHA1 [HugePedia]
snp3D : Map Gene to Disease56147
BioCentury BCIQPCDHA1
ClinGenPCDHA1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD56147
Chemical/Pharm GKB GenePA33009
Clinical trialPCDHA1
Miscellaneous
canSAR (ICR)PCDHA1 (select the gene name)
Probes
Litterature
PubMed13 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePCDHA1
EVEXPCDHA1
GoPubMedPCDHA1
iHOPPCDHA1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 18 13:34:02 CEST 2017

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