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PCDHA@ protocadherin alpha cluster, complex locus [ Homo sapiens (human) ]

Gene ID: 56117, updated on 4-Sep-2022


Official Symbol
PCDHA@provided by HGNC
Official Full Name
protocadherin alpha cluster, complex locusprovided by HGNC
Primary source
See related
MIM:604966; AllianceGenome:HGNC:8662
Gene type
RefSeq status
Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
The protocadherin alpha gene cluster is one of three related clusters tandemly linked on chromosome five. The clusters have a genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 genes and 1 pseudogene, which are members of the cadherin superfamily and related to the mouse CNR genes. The sequence of the 13 upstream genes and the pseudogene are highly similar to one another, while a subfamily (C) contains two more distantly related coding sequences. The alpha cluster genes are organized in a tandem array of 15 large, variable region exons followed by a constant region, which contains 3 exons shared by all genes in the cluster. Each variable region exon encodes an extracellular domain comprised of 6 cadherin ectodomains and a transmembrane region. The constant region exons encode a common cytoplasmic tail. These neural adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the alpha cluster genes. [provided by RefSeq, Jul 2008]
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Genomic context

See PCDHA@ in Genome Data Viewer
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140786136..141012344)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141311469..141537631)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140165721..140391929)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378198 Neighboring gene Sharpr-MPRA regulatory region 6103 Neighboring gene vault RNA 1-3 Neighboring gene ZFP14 zinc finger protein pseudogene Neighboring gene uncharacterized LOC124901089 Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha 2 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 uncharacterized LOC112267934 Neighboring gene protocadherin alpha 8 Neighboring gene protocadherin alpha 9 Neighboring gene protocadherin alpha 10 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 LOC124901090 Neighboring gene VISTA enhancer hs2610

Genomic regions, transcripts, and products


GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information


Other Names

  • cadherin-related neuronal receptor 1

General protein information

Preferred Names
protocadherin alpha cluster

NCBI Reference Sequences (RefSeq)

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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.


  1. NG_000016.2 

    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly


  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES


  1. NW_025791778.1 Reference GRCh38.p14 PATCHES

    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0


  1. NC_060929.1 Alternate T2T-CHM13v2.0

    GenBank, FASTA, Sequence Viewer (Graphics)