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    PCDHB12 protocadherin beta 12 [ Homo sapiens (human) ]

    Gene ID: 56124, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PCDHB12provided by HGNC
    Official Full Name
    protocadherin beta 12provided by HGNC
    Primary source
    HGNC:HGNC:8683
    See related
    Ensembl:ENSG00000120328 MIM:606338; AllianceGenome:HGNC:8683
    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-BETA12
    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

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    See PCDHB12 in Genome Data Viewer
    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 (141208719..141212571)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141734032..141737884)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140588291..140592143)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protocadherin beta cluster Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140573789-140574314 Neighboring gene protocadherin beta 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140589723-140590312 Neighboring gene protocadherin beta 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140595068-140595596 Neighboring gene protocadherin beta 13 Neighboring gene protocadherin beta 14

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. Vanhalst K, et al. FEBS Lett, 2001 Apr 20. PMID 11322959
    2. 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
    3. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. Yagi T, et al. Genes Dev, 2000 May 15. PMID 10817752
    4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Wu Q, et al. Genome Res, 2001 Mar. PMID 11230163, Free PMC Article
    5. A striking organization of a large family of human neural cadherin-like cell adhesion genes. Wu Q, et al. Cell, 1999 Jun 11. PMID 10380929

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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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    Markers

    Homology

    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 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 beta-12
    Names
    PCDH-beta-12

    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_000017.2 

      Range
      176844..180251
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018932.4 → NP_061755.1  protocadherin beta-12 precursor

      See identical proteins and their annotated locations for NP_061755.1

      Status: REVIEWED

      Source sequence(s)
      AC244517, AF217746, BC045637
      Consensus CDS
      CCDS4254.1
      UniProtKB/Swiss-Prot
      B4DDU1, Q9Y5F1
      Related
      ENSP00000239450.2, ENST00000239450.4
      Conserved Domains (3) summary
      cd11304
      Location:247 → 343
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:35 → 112
      Cadherin_2; Cadherin-like
      pfam16492
      Location:685 → 768
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    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
      141208719..141212571
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791778.1 Reference GRCh38.p14 PATCHES

      Range
      443895..447747
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      141734032..141737884
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5F1.1 GenPept UniProtKB/Swiss-Prot:Q9Y5F1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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