Aliases &
Descriptions
for PCDHAC1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase)
About This Section
|
| Aliases & Descriptions |
|---|
| protocadherin alpha subfamily C, 11 2 | | OTTHUMP000002055792 | | PCDH-ALPHA-C12 | | protocadherin alpha-C12 | | PCDH-alpha-C13 |
Export aliases for PCDHAC1 gene to outside databasesPrevious GC identifers: GC05U990126 GC05P140149 GC05P140214 GC05P140221 GC05P140176 GC05P140178 GC05P140286 GC05P140252 GC05P140261 GC05P140271 GC05P140280 GC05P140291 GC05P140301 GC05P140310 GC05P140313 GC05P140320 GC05P140343 |
Summaries
for PCDHAC1 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for PCDHAC1:
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)
UniProtKB/Swiss-Prot: PCDC1_HUMAN, Q9H158Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance ofspecific neuronal connections in the brain
|
Genomic Views
for PCDHAC1 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 60),
Regulatory elements and Epigenetics data according to
Qiagen and/or
SABiosciences)
About This Section
|
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the PCDHAC1 gene promoter:
HOXA9B Meis-1 NRSF form 2 NRSF form 1 FOXJ2 (long isoform) SRY HSF1 (long) IRF-7A E47 Sox9
Other transcription factors
Search SABiosciences Chromatin IP Primers for PCDHAC1
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for PCDHAC1  |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 5q31 Ensembl cytogenetic band: 5q31.3 HGNC cytogenetic band: 5q31PCDHAC1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc gene densities for chromosome 5 GeneLoc Exon Structure GeneLoc location for GC05P135451: view genomic region
(about GC identifiers)
Start:
|
135,451,037 bp from pter |
End:
|
135,536,628 bp from pter |
Size:
|
85,592 bases |
Orientation:
|
plus strand |
1 alternative location:
| Chr5+ 140,306,457-140,391,929 |
|
Proteins
for PCDHAC1 gene
(According to
1UniProtKB,
neXtProt,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological, and/or
ProSpec,
Biochemical Assays by
Millipore,
Sigma-Aldrich,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Dec 2010 and
Entrez Gene,
Antibodies by
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals, and/or
Epitomics)
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|
UniProtKB/Swiss-Prot: PCDC1_HUMAN, Q9H158 (See
protein sequence)Recommended Name: Protocadherin alpha-C1 precursor Size: 963 amino acids; 103942 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Secondary accessions: Q9Y5F5 Q9Y5I5Alternative splicing: 2 isoforms: Q9H158-1 Q9H158-2 Explore the universe of human proteins at neXtProt for PCDHAC1: NX_Q9H158
Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins (2 alternative transcripts):
NP_061721.2 NP_114088.2
ENSEMBL proteins: ENSP00000253807 ENSP00000386356
Human Recombinant Proteins
3 Gene Ontology (GO) cellular component terms (GO ID links to tree view): About this table
PCDHAC1 for ontologies About GeneDecksing
Antibodies for PCDHAC1:
Assays for PCDHAC1: |
Protein
Domains/
Families
for PCDHAC1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
PCDHAC1 for domains About GeneDecksing
4 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9H158ProtoNet protein and cluster: Q9H158 1 Blocks protein family: IPB002126 Cadherin
UniProtKB/Swiss-Prot: PCDC1_HUMAN, Q9H158Similarity: Contains 6 cadherin domains |
Gene Function
for PCDHAC1 gene
(According to UniProtKB,
IUBMB,and/or
Genatlas, Animal models from MGI Dec 24 2010,
shRNA from
OriGene,
Sigma-Aldrich,
RNAi from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Clones from Millipore,
Sigma-Aldrich,
OriGene,
GenScript,
Sino Biological,
Cell Lines from GenScript,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene.)
About This Section
|
UniProtKB/Swiss-Prot: PCDC1_HUMAN, Q9H158Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance ofspecific neuronal connections in the brain
1 Gene Ontology (GO) molecular function term (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005509 | calcium ion binding |
IEA | -- |
About this table
PCDHAC1 for ontologies About GeneDecksing
Animal Models: 1 MGI mutant phenotype (inferred from 1 allele ) (MGI details for Pcdhac1):
PCDHAC1 for phenotypes About GeneDecksing
|
Pathways & Interactions
for PCDHAC1 gene
(Pathways according to
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
PCR Arrays from
SABiosciences,
Proteins Network according to
SABiosciences,
Sigma-Aldrich,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene).
About This Section
|
SABiosciences Custom Pathway-Focused PCR Arrays for PCDHAC1
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PCDHAC1
3 Gene Ontology (GO) biological process terms (GO ID links to tree view): About this table
PCDHAC1 for ontologies About GeneDecksing
|
Drugs & Compounds
for PCDHAC1 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
|
 Browse Tocris compounds for PCDHAC1
|
Transcripts
for PCDHAC1 gene(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Tagged/untagged cDNA clones from
OriGene,
Sigma-Aldrich,
GenScript,
Primers from
OriGene and/or
SABiosciences)
About This Section
|
REFSEQ mRNAs for PCDHAC1 gene (2 alternative transcripts): NM_018898.3 NM_031882.2 24/261 AceView cDNA sequences (see all 261): NM_031848 AF152479 AF152307 NM_031410 NM_031857 AA973493 NM_031860 BM970705 AF152305 R53055 AW470523 CA396936 AF169695 BM684041 NM_031882 BM682903 NM_031883 CA488079 AA384862 AA757839 AL133883 AI969295 NM_031859 BC033735
 highest scoring ESTs for PCDHAC1:W32224 NM_031882 AA594565 AF152303 AI161196 AI672463 AJ007608 BU071607 BU071903 AF152473
GeneLoc Exon Structure
2 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000253807(uc003lih.2) ENST00000409700(uc003lig.1)
|
Expression
for PCDHAC1 gene
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 228 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Primers from
OriGene and/or
SABiosciences
)
About This Section
| PCDHAC1 expression in normal and diseased human tissues
1 / 2 / 3 2 probe-sets matching PCDHAC1 gene
Affymetrix
probe-set |
Array |
GeneAnnot data |
GeneNote data |
GeneTide data |
| # genes |
Sensitivity |
Specificity |
Correlation |
Length |
Gb_Accession |
Consensus |
Uniqueness |
Score |
Rank |
| 1553237_x_at2
|
U133Plus2 |
1 |
0.73 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 1553235_at2
|
U133Plus2 |
1 |
0.46 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
About this table
Data from
Genenote
(Publications) and GNF BioGPS
About these images
About these images
CGAP SAGE TAG: --
SABiosciences Custom PCR Arrays for PCDHAC1
|
Orthologs
for PCDHAC1 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Dec 24 2010,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for PCDHAC1 gene from 4 species
About this table Species with no ortholog for PCDHAC1
ENSEMBL Gene Tree for PCDHAC1 (if available) |
Paralogs
for PCDHAC1 gene(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
| Paralogs for PCDHAC1 gene
- PCDHAC22 PCDHA22 PCDHA122 PCDHGB42 PCDHA52 PCDHGB12 PCDHA12 PCDHA112
- PCDHGB22 PCDHGC32 PCDHA72 ENSG000002537882 PCDHGB62 PCDHA62 PCDHGC52 PCDHA82
- PCDHGC42 PCDHA132 PCDHA102 PCDHA92 PCDHA32 PCDHGB72 PCDHA42
PCDHAC1 for paralogs About GeneDecksing
|
Genomic Variants
for PCDHAC1 gene(SNPs according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section
|
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for PCDHAC1
2 CNVs: 99310 3578 | | QIAGEN SeqTarget long-range PCR primers for resequencing PCDHAC1 |
|
Disorders & Mutations
for PCDHAC1 gene
(in which this Gene is Involved, According to
OMIM, UniProtKB,
PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
LSDB, HGMD, GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
PCDHAC1 for disorders About GeneDecksing
OMIM: 606320
Export disorders and mutations for PCDHAC1 gene to outside databases
|
Medical News
for PCDHAC1 gene(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications
for PCDHAC1 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6UniProtKB/TrEMBL, and/or
7Novoseek)
About This Section
|
7 PubMed articles for PCDHAC1 gene integrated from 7 sources:
(articles sorted by number of sources associating them with PCDHAC1)- 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)
- 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)
- 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)
- Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (2000)
|
External Searches for PCDHAC1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing PCDHAC1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing PCDHAC1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing PCDHAC1 gene(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
|
About This Section
| Patent Information for PCDHAC1 gene:
Search GeneIP for patents involving PCDHAC1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for PCDHAC1 gene(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or
Enzo Life Sciences)
About This Section
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