PCDHB5 protocadherin beta 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDHB5provided by HGNC
Official Full Name: protocadherin beta 5provided by HGNC
Primary source: HGNC:HGNC:8690
See related: Ensembl:ENSG00000113209 MIM:606331; AllianceGenome:HGNC:8690
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-BETA5
Summary: This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]
Orthologs: all
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Genomic context

Location:: 5q31.3

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (141135206..141138615)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (141660524..141663933)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (140514788..140518197)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Weighted genes associated with the progression of retinoblastoma: Evidence from bioinformatic analysis.
Title: Weighted genes associated with the progression of retinoblastoma: Evidence from bioinformatic analysis.

Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-21048 (e-PCR)
- UniSTS:64362

RH80479 (e-PCR)
- UniSTS:85415

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	NAS Non-traceable Author Statement more info	PubMed
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in chemical synaptic transmission	TAS Traceable Author Statement more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in synapse assembly	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protocadherin beta-5

Names: PCDH-beta-5

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

NG_000017.2

Range

103340..106261

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_015669.5 → NP_056484.2 protocadherin beta-5 precursor

See identical proteins and their annotated locations for NP_056484.2

Status: REVIEWED

Source sequence(s)

AA481828, AB209393, AC244517, AF217753, BP310685

Consensus CDS

CCDS4247.1

UniProtKB/Swiss-Prot

Q549F4, Q9UFU9, Q9Y5E4

UniProtKB/TrEMBL

Q59FR6

Related

ENSP00000231134.5, ENST00000231134.8

Conserved Domains (3) summary

cd11304
Location:247 → 342

Cadherin_repeat; Cadherin tandem repeat domain

pfam08266
Location:30 → 112

Cadherin_2; Cadherin-like

pfam16492
Location:684 → 767

Cadherin_C_2; Cadherin cytoplasmic C-terminal