Human Gene PCDHAC2 (ENST00000289269.7) from GENCODE V44
  Description: Homo sapiens protocadherin alpha subfamily C, 2 (PCDHAC2), transcript variant 1, mRNA. (from RefSeq NM_018899)
RefSeq Summary (NM_018899): This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists 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 in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000289269.7
Gencode Gene: ENSG00000243232.6
Transcript (Including UTRs)
   Position: hg38 chr5:140,966,476-141,012,347 Size: 45,872 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr5:140,966,767-141,009,937 Size: 43,171 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:140,966,476-141,012,347)mRNA (may differ from genome)Protein (1007 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCDC2_HUMAN
DESCRIPTION: RecName: Full=Protocadherin alpha-C2; Short=PCDH-alpha-C2; Flags: Precursor;
FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (By similarity).
SIMILARITY: Contains 6 cadherin domains.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PCDHAC2
Diseases sorted by gene-association score: spherocytosis, type 5 (9)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.55 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 24.37 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -151.00291-0.519 Picture PostScript Text
3' UTR -585.702410-0.243 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002126 - Cadherin
IPR015919 - Cadherin-like
IPR020894 - Cadherin_CS
IPR013164 - Cadherin_N

Pfam Domains:
PF00028 - Cadherin domain
PF08266 - Cadherin-like

ModBase Predicted Comparative 3D Structure on Q9Y5I4
FrontTopSide
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding

Biological Process:
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007267 cell-cell signaling
GO:0007399 nervous system development

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AB384778 - Synthetic construct DNA, clone: pF1KB3294, Homo sapiens PCDHA1 gene for protocadherin alpha 1 precursor, complete cds, without stop codon, in Flexi system.
AF169695 - Homo sapiens protocadherin alpha 1 alternate isoform (PCDH-alpha1) mRNA, complete cds.
AF152305 - Homo sapiens protocadherin alpha 1 (PCDH-alpha1) mRNA, complete cds.
BC166697 - Synthetic construct Homo sapiens clone IMAGE:100066423, MGC:195560 protocadherin alpha 1 (PCDHA1) mRNA, encodes complete protein.
AF152310 - Homo sapiens protocadherin alpha 2 (PCDH-alpha2) mRNA, complete cds.
AF152311 - Homo sapiens protocadherin alpha 3 (PCDH-alpha3) mRNA, complete cds.
AB208925 - Homo sapiens mRNA for protocadherin alpha 4 isoform 1 precursor variant protein.
AF152312 - Homo sapiens protocadherin alpha 4 (PCDH-alpha4) mRNA, complete cds.
BC033735 - Homo sapiens protocadherin alpha 5, mRNA (cDNA clone MGC:44897 IMAGE:5175471), complete cds.
AF152313 - Homo sapiens protocadherin alpha 5 (PCDH-alpha5) mRNA, complete cds.
AB208863 - Homo sapiens mRNA for protocadherin alpha 5 isoform 1 precursor variant protein.
BC036674 - Homo sapiens protocadherin alpha 6, mRNA (cDNA clone MGC:33675 IMAGE:5263226), complete cds.
AF169694 - Homo sapiens protocadherin alpha 6 alternate isoform (PCDH-alpha6) mRNA, complete cds.
KJ901067 - Synthetic construct Homo sapiens clone ccsbBroadEn_10461 PCDHA6-like gene, encodes complete protein.
AF152314 - Homo sapiens protocadherin alpha 6 (PCDH-alpha6) mRNA, complete cds.
AB209205 - Homo sapiens mRNA for protocadherin alpha 6 isoform 2 precursor variant protein.
AB527331 - Synthetic construct DNA, clone: pF1KE0061, Homo sapiens PCDHA7 gene for protocadherin alpha 7, without stop codon, in Flexi system.
BC148656 - Synthetic construct Homo sapiens clone IMAGE:100015585, MGC:183108 protocadherin alpha 7 (PCDHA7) mRNA, encodes complete protein.
BC156820 - Synthetic construct Homo sapiens clone IMAGE:100062561, MGC:190561 protocadherin alpha 7 (PCDHA7) mRNA, encodes complete protein.
BC156893 - Synthetic construct Homo sapiens clone IMAGE:100062695, MGC:190588 protocadherin alpha 7 (PCDHA7) mRNA, encodes complete protein.
AF152315 - Homo sapiens protocadherin alpha 7 (PCDH-alpha7) mRNA, complete cds.
AF152316 - Homo sapiens protocadherin alpha 8 (PCDH-alpha8) mRNA, complete cds.
AJ007610 - Homo sapiens mRNA for protocadherin alpha 9 (PCDHA9 gene).
AK314303 - Homo sapiens cDNA, FLJ95060.
BC104802 - Homo sapiens protocadherin alpha 9, mRNA (cDNA clone MGC:132462 IMAGE:8143805), complete cds.
BC104804 - Homo sapiens protocadherin alpha 9, mRNA (cDNA clone MGC:132464 IMAGE:8143807), complete cds.
AB384773 - Synthetic construct DNA, clone: pF1KB3279, Homo sapiens PCDHA9 gene for protocadherin alpha 9 precursor, complete cds, without stop codon, in Flexi system.
KJ892840 - Synthetic construct Homo sapiens clone ccsbBroadEn_02234 PCDHA9 gene, encodes complete protein.
AF152317 - Homo sapiens protocadherin alpha 9 (PCDH-alpha9) mRNA, complete cds.
BC130447 - Homo sapiens protocadherin alpha 10, mRNA (cDNA clone MGC:163319 IMAGE:40146478), complete cds.
HQ258585 - Synthetic construct Homo sapiens clone IMAGE:100073117 protocadherin alpha 10 (PCDHA10), transcript variant 3 (PCDHA10) gene, encodes complete protein.
KJ894313 - Synthetic construct Homo sapiens clone ccsbBroadEn_03707 PCDHA10 gene, encodes complete protein.
AF169689 - Homo sapiens protocadherin alpha 10 alternate isoform (PCDH-alpha10) mRNA, complete cds.
AF152306 - Homo sapiens protocadherin alpha 10 (PCDH-alpha10) mRNA, complete cds.
AJ007609 - Homo sapiens mRNA for protocadherin alpha 11 (PCDHA11 gene).
AB384789 - Synthetic construct DNA, clone: pF1KB3329, Homo sapiens PCDHA11 gene for protocadherin alpha 11 precursor, complete cds, without stop codon, in Flexi system.
AF152307 - Homo sapiens protocadherin alpha 11 (PCDH-alpha11) mRNA, complete cds.
AB384894 - Synthetic construct DNA, clone: pF1KB4085, Homo sapiens PCDHA12 gene for protocadherin alpha 12 precursor, complete cds, without stop codon, in Flexi system.
AF152308 - Homo sapiens protocadherin alpha 12 (PCDH-alpha12) mRNA, complete cds.
AK075556 - Homo sapiens cDNA PSEC0256 fis, clone NT2RP3003549, highly similar to Homo sapiens protocadherin alpha 12 (PCDH-alpha12) mRNA.
AB208924 - Homo sapiens mRNA for protocadherin alpha 13 isoform 1 precursor variant protein.
AF152309 - Homo sapiens protocadherin alpha 13 (PCDH-alpha13) mRNA, complete cds.
AJ007608 - Homo sapiens mRNA for protocadherin alpha-C1 (PCDHAC1 gene).
AF152303 - Homo sapiens protocadherin alpha C1 (PCDH-alpha-C1) mRNA, complete cds.
AK123867 - Homo sapiens cDNA FLJ41873 fis, clone OCBBF2010871, highly similar to Homo sapiens protocadherin alpha C2 (PCDH-alpha-C2) mRNA.
BC063288 - Homo sapiens protocadherin alpha subfamily C, 2, mRNA (cDNA clone MGC:71598 IMAGE:30343089), complete cds.
BC105111 - Homo sapiens protocadherin alpha subfamily C, 2, transcript variant 2, mRNA (cDNA clone MGC:132771 IMAGE:8144114), complete cds.
BC104776 - Homo sapiens protocadherin alpha subfamily C, 2, transcript variant 2, mRNA (cDNA clone MGC:132436 IMAGE:8143779), complete cds.
KJ899233 - Synthetic construct Homo sapiens clone ccsbBroadEn_08627 PCDHAC2 gene, encodes complete protein.
AF152474 - Homo sapiens protocadherin alpha C2 short form protein (PCDH-alpha-C2) variable region sequence, complete cds.
AF152304 - Homo sapiens protocadherin alpha C2 (PCDH-alpha-C2) mRNA, complete cds.
JD167065 - Sequence 148089 from Patent EP1572962.
JD132468 - Sequence 113492 from Patent EP1572962.
JD268914 - Sequence 249938 from Patent EP1572962.
JD134550 - Sequence 115574 from Patent EP1572962.
JD134878 - Sequence 115902 from Patent EP1572962.
JD352722 - Sequence 333746 from Patent EP1572962.
JD046762 - Sequence 27786 from Patent EP1572962.
JD428758 - Sequence 409782 from Patent EP1572962.
JD083984 - Sequence 65008 from Patent EP1572962.
JD530511 - Sequence 511535 from Patent EP1572962.
JD314730 - Sequence 295754 from Patent EP1572962.
JD499381 - Sequence 480405 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000289269.1, ENST00000289269.2, ENST00000289269.3, ENST00000289269.4, ENST00000289269.5, ENST00000289269.6, NM_018899, PCDC2_HUMAN, Q2M3V1, Q9Y5F4, Q9Y5I4, uc003lii.1, uc003lii.2, uc003lii.3, uc003lii.4, uc003lii.5
UCSC ID: ENST00000289269.7
RefSeq Accession: NM_018899
Protein: Q9Y5I4 (aka PCDC2_HUMAN or CHC2_HUMAN)
CCDS: CCDS4242.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.