PCDHB6 protocadherin beta 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDHB6provided by HGNC
Official Full Name: protocadherin beta 6provided by HGNC
Primary source: HGNC:HGNC:8691
See related: Ensembl:ENSG00000113211 MIM:606332; AllianceGenome:HGNC:8691
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-BETA6
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. Unlike the alpha and gamma clusters, the transcripts from these genes do not share common 3' exons. 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 neural connections. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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 (141150057..141153287)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (141675376..141678606)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (140529638..140532868)

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

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

Phenotypes

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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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	ISS Inferred from Sequence or Structural Similarity more info

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 cell-cell recognition	ISS Inferred from Sequence or Structural Similarity more info
involved_in chemical synaptic transmission	TAS Traceable Author Statement more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info
involved_in nervous system development	TAS Traceable Author Statement more info	PubMed
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 plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protocadherin beta-6

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

118155..121420

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001303145.2 → NP_001290074.1 protocadherin beta-6 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks a portion of the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.

Source sequence(s)

AF152499, AF217752, AK299661, DA386733, DA789782

Consensus CDS

CCDS78067.1

UniProtKB/TrEMBL

A0A096LNH7, B4DSB6

Related

ENSP00000485034.1, ENST00000622991.1

Conserved Domains (2) summary

cd11304
Location:110 → 205

Cadherin_repeat; Cadherin tandem repeat domain

pfam16492
Location:547 → 630

Cadherin_C_2; Cadherin cytoplasmic C-terminal
NM_018939.4 → NP_061762.2 protocadherin beta-6 isoform 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC244517

Consensus CDS

CCDS4248.1

UniProtKB/Swiss-Prot

B2R8R9, Q9Y5E3

UniProtKB/TrEMBL

B4DSB6

Related

ENSP00000231136.1, ENST00000231136.4

Conserved Domains (3) summary

cd11304
Location:246 → 341

Cadherin_repeat; Cadherin tandem repeat domain

pfam08266
Location:30 → 111

Cadherin_2; Cadherin-like

pfam16492
Location:683 → 766

Cadherin_C_2; Cadherin cytoplasmic C-terminal