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    PCDHGA11 protocadherin gamma subfamily A, 11 [ Homo sapiens (human) ]

    Gene ID: 56105, updated on 11-Apr-2024

    Summary

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    Official Symbol
    PCDHGA11provided by HGNC
    Official Full Name
    protocadherin gamma subfamily A, 11provided by HGNC
    Primary source
    HGNC:HGNC:8698
    See related
    Ensembl:ENSG00000253873 MIM:606298; AllianceGenome:HGNC:8698
    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-GAMMA-A11
    Summary
    This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
    Orthologs
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    Genomic context

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    Location:
    5q31.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (141421051..141512975)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141946885..142038959)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140800618..140892542)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23293 Neighboring gene solute carrier family 25 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23294 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140713237-140713466 Neighboring gene protocadherin gamma subfamily A, 1 Neighboring gene TATA-box binding protein associated factor 7 Neighboring gene protocadherin gamma cluster Neighboring gene protocadherin gamma subfamily A, 2 Neighboring gene protocadherin gamma subfamily A, 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140745768-140745946 Neighboring gene protocadherin gamma subfamily B, 1 Neighboring gene protocadherin gamma subfamily A, 4 Neighboring gene protocadherin gamma subfamily B, 2 Neighboring gene protocadherin gamma subfamily A, 5 Neighboring gene protocadherin gamma subfamily B, 3 Neighboring gene protocadherin gamma subfamily A, 6 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23295 Neighboring gene protocadherin gamma subfamily B, 4 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily B, 5 Neighboring gene protocadherin gamma subfamily A, 9 Neighboring gene protocadherin gamma subfamily B, 6 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23296 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140821493-140821993 Neighboring gene protocadherin gamma subfamily B, 8 pseudogene Neighboring gene protocadherin gamma subfamily A, 12 Neighboring gene protocadherin gamma subfamily B, 9 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140855840-140856383 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:140864468-140864695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23299 Neighboring gene RNA, 7SL, cytoplasmic 68, pseudogene Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene protocadherin gamma subfamily C, 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140888408-140888908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23303 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140893101-140893726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140893727-140894352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140894353-140894978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140895605-140896230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140896231-140896856 Neighboring gene uncharacterized LOC124901091 Neighboring gene Sharpr-MPRA regulatory region 13534 Neighboring gene diaphanous related formin 1 Neighboring gene MPRA-validated peak5501 silencer Neighboring gene Sharpr-MPRA regulatory region 13738 Neighboring gene DIAPH1 antisense RNA 1

    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
    • 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. Epigenetic silencing of the protocadherin family member PCDH-gamma-A11 in astrocytomas. Waha A, et al. Neoplasia, 2005 Mar. PMID 15799819, Free PMC Article
    2. [The methylation analysis of EMP3 and PCDH-gamma-A11 gene in human glioma]. Jiang Z, et al. Zhonghua Wai Ke Za Zhi, 2010 Feb 15. PMID 20388442
    3. Mindbomb 1, an E3 ubiquitin ligase, forms a complex with RYK to activate Wnt/β-catenin signaling. Berndt JD, et al. J Cell Biol, 2011 Sep 5. PMID 21875946, Free PMC Article
    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 (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The promoter methylation and mRNA expressions of EMP3 and PCDH-gamma-A11 are closely related with the malignant development of glioma.
      Title: [The methylation analysis of EMP3 and PCDH-gamma-A11 gene in human glioma].
    2. PCDH-gamma-A11 is silenced epigenetically in astrocytic gliomas
      Title: Epigenetic silencing of the protocadherin family member PCDH-gamma-A11 in astrocytomas.
    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)

    Genotypes

    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
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin gamma-A11

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_000012.2 

      Range
      131167..223176
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018914.3 → NP_061737.1  protocadherin gamma-A11 isoform 1 precursor

      See identical proteins and their annotated locations for NP_061737.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
      Source sequence(s)
      AA329824, AF152320, DA503678
      Consensus CDS
      CCDS47294.1
      UniProtKB/Swiss-Prot
      B7ZVY8, Q9Y5D8, Q9Y5D9, Q9Y5H2
      Related
      ENSP00000381589.2, ENST00000398587.7
      Conserved Domains (4) summary
      cd11304
      Location:247 → 344
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:31 → 113
      Cadherin_2; Cadherin-like
      pfam15974
      Location:812 → 908
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
      pfam16492
      Location:689 → 773
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    2. NM_032091.2 → NP_114480.1  protocadherin gamma-A11 isoform 2 precursor

      See identical proteins and their annotated locations for NP_114480.1

      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 an isoform (2) that is shorter than isoform 1 and has a unique C-terminus.
      Source sequence(s)
      AA329824, AC005618, AF152505, BE007760, BF327891, DA503678
      Consensus CDS
      CCDS75345.1
      UniProtKB/Swiss-Prot
      Q9Y5H2
      Related
      ENSP00000480917.1, ENST00000622044.1
      Conserved Domains (3) summary
      cd11304
      Location:247 → 344
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:31 → 113
      Cadherin_2; Cadherin-like
      pfam16492
      Location:689 → 773
      Cadherin_C_2; Cadherin cytoplasmic C-terminal

    3. NM_032092.2 → NP_114481.1  protocadherin gamma-A11 isoform 3 precursor

      See identical proteins and their annotated locations for NP_114481.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) utilizes an alternative splice donor site that truncates exon 1. This shortest isoform (3) lacks the transmembrane region and has five complete and one partial cadherin domain.
      Source sequence(s)
      AA329824, AF152320, AF152504, DA503678
      Consensus CDS
      CCDS54930.1
      UniProtKB/Swiss-Prot
      Q9Y5H2
      Related
      ENSP00000428333.1, ENST00000518882.2
      Conserved Domains (3) summary
      cd11304
      Location:247 → 344
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:31 → 113
      Cadherin_2; Cadherin-like
      pfam15974
      Location:627 → 723
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      141421051..141512975
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      141946885..142038959
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5H2.1 GenPept UniProtKB/Swiss-Prot:Q9Y5H2

    Gene LinkOut

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

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