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PCDHB6 protocadherin beta 6 [ Homo sapiens (human) ]

Gene ID: 56130, updated on 1-Aug-2020

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
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

Genomic context

See PCDHB6 in Genome Data Viewer
Location:
5q31.3
Exon count:
1
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (141150022..141153287)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140529839..140532868)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protocadherin beta cluster Neighboring gene protocadherin beta 4 Neighboring gene protocadherin beta 5 Neighboring gene protocadherin beta 17 pseudogene Neighboring gene protocadherin beta 7

Genomic regions, transcripts, and products

Expression

  • Project title: 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
 
identical protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS
Non-traceable Author Statement
more info
PubMed 
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell recognition ISS
Inferred from Sequence or Structural Similarity
more info
 
chemical synaptic transmission TAS
Traceable Author Statement
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules ISS
Inferred from Sequence or Structural Similarity
more info
 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
synapse assembly TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 

NCBI Reference Sequences (RefSeq)

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_000017.2 

    Range
    118155..121420
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001303145.2NP_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/Swiss-Prot
    Q9Y5E3
    UniProtKB/TrEMBL
    A0A096LNH7, B4DSB6
    Related
    ENSP00000485034.1, ENST00000622991.1
    Conserved Domains (2) summary
    cd11304
    Location:110205
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam16492
    Location:547630
    Cadherin_C_2; Cadherin cytoplasmic C-terminal
  2. NM_018939.4NP_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
    Q9Y5E3
    Related
    ENSP00000231136.1, ENST00000231136.3
    Conserved Domains (3) summary
    cd11304
    Location:246341
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:30111
    Cadherin_2; Cadherin-like
    pfam16492
    Location:683766
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    141150022..141153287
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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