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    PCDHAC2 protocadherin alpha subfamily C, 2 [ Homo sapiens (human) ]

    Gene ID: 56134, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PCDHAC2provided by HGNC
    Official Full Name
    protocadherin alpha subfamily C, 2provided by HGNC
    Primary source
    HGNC:HGNC:8677
    See related
    Ensembl:ENSG00000243232 MIM:606321; AllianceGenome:HGNC:8677
    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-ALPHA-C2
    Summary
    This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. 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 connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
    Orthologs
    mouse all
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    Genomic context

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    See PCDHAC2 in Genome Data Viewer
    Location:
    5q31.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (140966476..141012347)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141491769..141537634)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140346061..140391932)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha cluster, complex locus Neighboring gene protocadherin alpha 2 Neighboring gene protocadherin alpha 3 Neighboring gene protocadherin alpha 4 Neighboring gene protocadherin alpha 5 Neighboring gene protocadherin alpha 6 Neighboring gene uncharacterized LOC112267934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140249655-140250330 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140250331-140251004 Neighboring gene protocadherin alpha 7 Neighboring gene protocadherin alpha 8 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140263344-140263928 Neighboring gene protocadherin alpha 9 Neighboring gene protocadherin alpha 10 Neighboring gene protocadherin alpha 14 (pseudogene) Neighboring gene protocadherin alpha 11 Neighboring gene protocadherin alpha 12 Neighboring gene protocadherin alpha 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140306467-140307024 Neighboring gene NANOG hESC enhancer GRCh37_chr5:140307586-140308097 Neighboring gene protocadherin alpha subfamily C, 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140380918-140381512 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140381513-140382106 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140382107-140382700 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:140383889-140384481 Neighboring gene protocadherin alpha constant Neighboring gene uncharacterized LOC124901090 Neighboring gene VISTA enhancer hs2610 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:140430540-140431368 Neighboring gene PCDHB1 antisense RNA 1 Neighboring gene protocadherin beta 1 Neighboring gene protocadherin beta cluster

    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 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. Genomic organization of the family of CNR cadherin genes in mice and humans. Sugino H, et al. Genomics, 2000 Jan 1. PMID 10662547
    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. A Genome-Wide CRISPR Screen Identifies Genes Critical for Resistance to FLT3 Inhibitor AC220. Hou P, et al. Cancer Res, 2017 Aug 15. PMID 28625976, Free PMC Article
    5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Wu Q, et al. Genome Res, 2001 Mar. PMID 11230163, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    EBI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog

    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

    Clone Names

    • MGC71598

    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 TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in serotonergic neuron axon guidance 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 alpha-C2

    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_000016.2 

      Range
      232036..278218
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018899.6 → NP_061722.1  protocadherin alpha-C2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_061722.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
      Source sequence(s)
      AC010223, AF152304
      Consensus CDS
      CCDS4242.1
      UniProtKB/Swiss-Prot
      Q2M3V1, Q9Y5F4, Q9Y5I4
      UniProtKB/TrEMBL
      Q6P4R2
      Related
      ENSP00000289269.5, ENST00000289269.7
      Conserved Domains (4) summary
      cd11304
      Location:261 → 361
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam15974
      Location:856 → 999
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
      pfam16492
      Location:703 → 808
      Cadherin_C_2; Cadherin cytoplasmic C-terminal
      cl09101
      Location:43 → 127
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    2. NM_031883.2 → NP_114089.1  protocadherin alpha-C2 isoform 2 precursor

      See identical proteins and their annotated locations for NP_114089.1

      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 a shorter isoform (2), compared to variant 1. This short variant is represented based on data in PMID:10380929.
      Source sequence(s)
      AF152474
      UniProtKB/TrEMBL
      Q6P4R2
      Related
      ENSP00000478629.1, ENST00000615316.1
      Conserved Domains (3) summary
      cd11304
      Location:261 → 361
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam16492
      Location:703 → 810
      Cadherin_C_2; Cadherin cytoplasmic C-terminal
      cl09101
      Location:43 → 127
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    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
      140966476..141012347
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791778.1 Reference GRCh38.p14 PATCHES

      Range
      201652..247523
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      141491769..141537634
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y5I4.1 GenPept UniProtKB/Swiss-Prot:Q9Y5I4

    Gene LinkOut

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

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