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    PCDH1 protocadherin 1 [ Homo sapiens (human) ]

    Gene ID: 5097, updated on 2-Nov-2024

    Summary

    Official Symbol
    PCDH1provided by HGNC
    Official Full Name
    protocadherin 1provided by HGNC
    Primary source
    HGNC:HGNC:8655
    See related
    Ensembl:ENSG00000156453 MIM:603626; AllianceGenome:HGNC:8655
    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
    PC42; PCDH42
    Summary
    This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 10.0), colon (RPKM 8.9) and 22 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PCDH1 in Genome Data Viewer
    Location:
    5q31.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (141853090..141878410, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (142379045..142404656, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (141232655..141257975, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141137138-141137707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141137708-141138276 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141138277-141138846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141141594-141142094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141166068-141166568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141166569-141167069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141174703-141175204 Neighboring gene uncharacterized LOC107986454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141191515-141192163 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141195215-141196206 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:141196207-141197197 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141202604-141203104 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141204908-141205596 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141218303-141219041 Neighboring gene Sharpr-MPRA regulatory region 8612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141226341-141227162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141227919-141228475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23313 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141229034-141229590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141243287-141243787 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:141244239-141244418 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141252448-141253170 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141256273-141256957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141257224-141257973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141262003-141262885 Neighboring gene glycine cleavage system protein H (aminomethyl carrier) pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:141293283-141293820 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:141303317-141303830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:141308886-141309386 Neighboring gene DAP3 binding cell death enhancer 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis identifies two novel loci associated with high myopia in the Han Chinese population.
    EBI GWAS Catalog
    Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ53887, MGC45991

    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 cell-cell signaling TAS
    Traceable Author Statement
    more info
    PubMed 
    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 
    Component Evidence Code Pubs
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
     
    located_in cell-cell junction TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    protocadherin-1
    Names
    cadherin-like 1
    cadherin-like protein 1
    protocadherin 42

    NCBI Reference Sequences (RefSeq)

    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.

    mRNA and Protein(s)

    1. NM_001278613.2NP_001265542.1  protocadherin-1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an alternate 5' exon and lacks two 3' exons. Its transcription extends past a splice site that is used in variant 2, resulting in a novel 3' coding region and 3' UTR compared to variant 2. It encodes isoform 3 which is shorter and has a distinct C-terminus, compared to isoform 2.
      Source sequence(s)
      AK300564, AK304231, BC035812, HO663512
      UniProtKB/TrEMBL
      B4E2D8
      Related
      ENST00000357517.6
      Conserved Domains (3) summary
      cd11304
      Location:528624
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:8311042
      Protocadherin; Protocadherin
      cl09101
      Location:76154
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    2. NM_001278615.1NP_001265544.1  protocadherin-1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two 5' and 3' exons, respectively. It has an alternate 5' exon and its transcription extends past a splice site that is used in variant 2, resulting in a novel 3' coding region and 3' UTR compared to variant 2. It encodes isoform 4 which has a shorter N-terminus and a shorter and distinct C-terminus, compared to isoform 2.
      Source sequence(s)
      AK308338, BC035812
      UniProtKB/TrEMBL
      B4DUA8
      Related
      ENST00000511044.1
      Conserved Domains (2) summary
      cd11304
      Location:133229
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:436647
      Protocadherin; Protocadherin
    3. NM_002587.5NP_002578.2  protocadherin-1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_002578.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks two exons and its transcription extends past a splice site that is used in variant 2, resulting in a novel 3' coding region and 3' UTR compared to variant 2. It encodes isoform 1 which is shorter and has a distinct C-terminus, compared to isoform 2.
      Source sequence(s)
      AK289512, AK304231, BC035812
      Consensus CDS
      CCDS43375.1
      UniProtKB/Swiss-Prot
      Q08174, Q8IUP2
      UniProtKB/TrEMBL
      A8K0E7
      Related
      ENSP00000378043.3, ENST00000394536.4
      Conserved Domains (3) summary
      cd11304
      Location:512608
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:8151026
      Protocadherin; Protocadherin
      cl09101
      Location:60138
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    4. NM_032420.5NP_115796.2  protocadherin-1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_115796.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
      Source sequence(s)
      AC094107, AK304231, BC035812, BM680840, DA096772, L11369
      Consensus CDS
      CCDS4267.1
      UniProtKB/TrEMBL
      A8K0E7
      Related
      ENSP00000287008.3, ENST00000287008.8
      Conserved Domains (3) summary
      cd11304
      Location:512608
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:8151026
      Protocadherin; Protocadherin
      cl09101
      Location:60138
      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
      141853090..141878410 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005268452.4XP_005268509.2  protocadherin-1 isoform X1

      UniProtKB/TrEMBL
      B3KQM8
      Conserved Domains (3) summary
      cd11304
      Location:528624
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:8311042
      Protocadherin
      cl09101
      Location:76154
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    2. XM_005268454.6XP_005268511.2  protocadherin-1 isoform X2

      UniProtKB/TrEMBL
      B4E2D8
      Conserved Domains (3) summary
      cd11304
      Location:528624
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:8311042
      Protocadherin
      cl09101
      Location:76154
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    3. XM_017009517.3XP_016865006.1  protocadherin-1 isoform X3

      UniProtKB/TrEMBL
      B3KQM8
      Conserved Domains (2) summary
      cd11304
      Location:133229
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:436647
      Protocadherin; Protocadherin

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      142379045..142404656 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352706.1XP_054208681.1  protocadherin-1 isoform X4

    2. XM_054352705.1XP_054208680.1  protocadherin-1 isoform X1

    3. XM_054352707.1XP_054208682.1  protocadherin-1 isoform X2

    4. XM_054352708.1XP_054208683.1  protocadherin-1 isoform X3