U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Pcdh1 protocadherin 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 307481, updated on 27-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Pcdh1provided by RGD
    Official Full Name
    protocadherin 1provided by RGD
    Primary source
    RGD:1308490
    See related
    EnsemblRapid:ENSRNOG00000060410 AllianceGenome:RGD:1308490
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. Predicted to be located in cell junction; nucleolus; and nucleoplasm. Predicted to be active in plasma membrane. Orthologous to human PCDH1 (protocadherin 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 106.6), Brain (RPKM 51.9) and 8 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Pcdh1 in Genome Data Viewer
    Location:
    18p11
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (30258154..30290828, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (30011692..30039679, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (31330081..31343147, complement)

    Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108348772 Neighboring gene uncharacterized LOC134482932 Neighboring gene DAP3 binding cell death enhancer 1 Neighboring gene protocadherin 12

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    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
    		  
    Component Evidence Code Pubs
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    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

    Go to the top of the page Help
    Preferred Names
    protocadherin-1
    Names
    protocadherin 1 (cadherin-like 1)

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001100689.2 → NP_001094159.1  protocadherin-1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000018
      UniProtKB/TrEMBL
      A0A8I6AAW9
      Related
      ENSRNOP00000086663.1, ENSRNOT00000113171.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086036.1 Reference GRCr8

      Range
      30258154..30290828 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039097355.2 → XP_038953283.1  protocadherin-1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AAW9
      Conserved Domains (3) summary
      cd11304
      Location:490 → 586
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:37 → 116
      Cadherin_2; Cadherin-like
      pfam08374
      Location:793 → 1007
      Protocadherin

    2. XM_039097353.2 → XP_038953281.1  protocadherin-1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K6T9
      Related
      ENSRNOP00000077172.2, ENSRNOT00000101935.2
      Conserved Domains (3) summary
      cd11304
      Location:505 → 601
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:52 → 131
      Cadherin_2; Cadherin-like
      pfam08374
      Location:808 → 1022
      Protocadherin

    3. XM_039097356.2 → XP_038953284.1  protocadherin-1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AAW9
      Conserved Domains (3) summary
      cd11304
      Location:490 → 586
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:37 → 116
      Cadherin_2; Cadherin-like
      pfam08374
      Location:793 → 1007
      Protocadherin

    4. XM_017601102.3 → XP_017456591.2  protocadherin-1 isoform X3

      Related
      ENSRNOP00000073940.3, ENSRNOT00000081850.3
      Conserved Domains (3) summary
      cd11304
      Location:505 → 601
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:52 → 131
      Cadherin_2; Cadherin-like
      pfam08374
      Location:808 → 1022
      Protocadherin
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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