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PCDHA2 protocadherin alpha 2 [ Homo sapiens (human) ]

Gene ID: 56146, updated on 24-Aug-2014
Official Symbol
PCDHA2provided by HGNC
Official Full Name
protocadherin alpha 2provided by HGNC
Primary source
HGNC:8668
See related
Ensembl:ENSG00000204969; HPRD:07320; MIM:606308; Vega:OTTHUMG00000163363
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PCDH-ALPHA2
Summary
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]
See PCDHA2 in Epigenomics, MapViewer
Location:
5q31
Exon count:
5
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 5 NC_000005.10 (140794859..141012344)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140174444..140391929)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene vault RNA 1-3 Neighboring gene ZFP14 zinc finger protein pseudogene Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha cluster, complex locus Neighboring gene protocadherin alpha 3 Neighboring gene protocadherin alpha 4 Neighboring gene protocadherin alpha 5 Neighboring gene protocadherin alpha 6 Neighboring gene protocadherin alpha 7 Neighboring gene protocadherin alpha 8 Neighboring gene protocadherin alpha 10 Neighboring gene protocadherin alpha 9 Neighboring gene protocadherin alpha 14 pseudogene Neighboring gene protocadherin alpha 11 Neighboring gene protocadherin alpha 12 Neighboring gene protocadherin alpha 13 Neighboring gene protocadherin alpha subfamily C, 1 Neighboring gene protocadherin alpha subfamily C, 2 Neighboring gene protocadherin alpha constant Neighboring gene uncharacterized LOC101926905 Neighboring gene protocadherin beta 1 Neighboring gene protocadherin beta cluster Neighboring gene protocadherin beta 2

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA Catalog

Replication interactions

Interaction Pubs
Knockdown of protocadherin alpha 2 (PCDHA2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Protein Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell adhesion TAS
Traceable Author Statement
more info
PubMed 
homophilic cell adhesion IEA
Inferred from Electronic Annotation
more info
 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
Preferred Names
protocadherin alpha-2
Names
protocadherin alpha-2
KIAA0345-like 12

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_000016.2 

    Range
    60732..278218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018905.2NP_061728.1  protocadherin alpha-2 isoform 1 precursor

    See proteins identical to NP_061728.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
    Source sequence(s)
    AF152310, BC003126
    Consensus CDS
    CCDS54914.1
    UniProtKB/Swiss-Prot
    Q9Y5H9
    Related
    ENSP00000431748, OTTHUMP00000223672, ENST00000526136, OTTHUMT00000372877
    Conserved Domains (1) summary
    cd11304
    Location:246346
    Blast Score: 325
    Cadherin_repeat; Cadherin tandem repeat domain
  2. NM_031495.1NP_113683.1  protocadherin alpha-2 isoform 2 precursor

    See proteins identical to NP_113683.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) utilizes the large, first exon then continues into the downstream intron 1 sequence before terminating. This one-exon transcript encodes a shorter isoform (2), compared to isoform 1. This short variant is represented based on data in PMID:10380929.
    Source sequence(s)
    AF152480, BC003126
    UniProtKB/Swiss-Prot
    Q9Y5H9
    Related
    ENSP00000367372, ENST00000378132
    Conserved Domains (1) summary
    cd11304
    Location:246346
    Blast Score: 322
    Cadherin_repeat; Cadherin tandem repeat domain
  3. NM_031496.1NP_113684.1  protocadherin alpha-2 isoform 3 precursor

    See proteins identical to NP_113684.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) splices the large, first exon into a unique exon contained within the intron between PCDHA3 and PCDHA4. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    BC003126
    Consensus CDS
    CCDS64269.1
    UniProtKB/Swiss-Prot
    Q9Y5H9
    Related
    ENSP00000430584, OTTHUMP00000224327, ENST00000520672, OTTHUMT00000374265
    Conserved Domains (1) summary
    cd11304
    Location:246346
    Blast Score: 323
    Cadherin_repeat; Cadherin tandem repeat domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000005.10 

    Range
    140794859..141012344
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000137.1 

    Range
    135319158..135536628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018916.2 

    Range
    139607636..139825092
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)