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PCDHA13 protocadherin alpha 13 [ Homo sapiens (human) ]

Gene ID: 56136, updated on 2-Nov-2024

Summary

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Official Symbol
PCDHA13provided by HGNC
Official Full Name
protocadherin alpha 13provided by HGNC
Primary source
HGNC:HGNC:8667
See related
Ensembl:ENSG00000239389 MIM:606319; AllianceGenome:HGNC:8667
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
CNR5; CNRN5; CNRS5; CRNR5; PCDH-ALPHA13
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]
Orthologs
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Genomic context

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See PCDHA13 in Genome Data Viewer
Location:
5q31.3
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140882124..141012347)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141407449..141537634)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140261709..140391932)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha cluster, complex locus 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 uncharacterized LOC112267934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140249655-140250330 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140250331-140251004 Neighboring gene protocadherin alpha 7 Neighboring gene protocadherin alpha 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140263344-140263928 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 H3K4me1 hESC enhancer GRCh37_chr5:140306467-140307024 Neighboring gene NANOG hESC enhancer GRCh37_chr5:140307586-140308097 Neighboring gene protocadherin alpha subfamily C, 1 Neighboring gene protocadherin alpha subfamily C, 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140380918-140381512 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140381513-140382106 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140382107-140382700 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:140383889-140384481 Neighboring gene protocadherin alpha constant Neighboring gene uncharacterized LOC124901090 Neighboring gene VISTA enhancer hs2610 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:140430540-140431368 Neighboring gene PCDHB1 antisense RNA 1 Neighboring gene protocadherin beta 1 Neighboring gene protocadherin beta cluster

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Control of epigenetic states by WT1 via regulation of de novo DNA methyltransferase 3A. Szemes M, et al. Hum Mol Genet, 2013 Jan 1. PMID 23042785, Free PMC Article
  2. Genomic organization of the family of CNR cadherin genes in mice and humans. Sugino H, et al. Genomics, 2000 Jan 1. PMID 10662547
  3. The DNA sequence and comparative analysis of human chromosome 5. Schmutz J, et al. Nature, 2004 Sep 16. PMID 15372022
  4. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. Nollet F, et al. J Mol Biol, 2000 Jun 9. PMID 10835267
  5. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. Yagi T, et al. Genes Dev, 2000 May 15. PMID 10817752

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See Variation Viewer (GRCh37.p13)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
  
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protocadherin alpha-13
Names
KIAA0345-like 1
PCDH-alpha-13
ortholog of mouse CNR5

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.

Genomic

  1. NG_000016.2 

    Range
    148142..278218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018904.3 → NP_061727.1  protocadherin alpha-13 isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
    Source sequence(s)
    AC005609, AC010223, AF152309
    Consensus CDS
    CCDS4240.1
    UniProtKB/Swiss-Prot
    O75277, Q9Y5I0
    UniProtKB/TrEMBL
    C9JA99
    Related
    ENSP00000289272.2, ENST00000289272.3
    Conserved Domains (3) summary
    cd11304
    Location:246 → 346
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:30 → 111
    Cadherin_2; Cadherin-like
    pfam15974
    Location:799 → 942
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

  2. NM_031865.1 → NP_114071.1  protocadherin alpha-13 isoform 2 precursor

    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)
    AF152478
    UniProtKB/TrEMBL
    C9JA99
    Related
    ENSP00000479167.1, ENST00000617769.1
    Conserved Domains (2) summary
    cd11304
    Location:246 → 346
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:30 → 111
    Cadherin_2; Cadherin-like

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    140882124..141012347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791778.1 Reference GRCh38.p14 PATCHES

    Range
    117300..247523
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    141407449..141537634
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y5I0.1 GenPept UniProtKB/Swiss-Prot:Q9Y5I0

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