U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Pcdha9 protocadherin alpha 9 [ Mus musculus (house mouse) ]

    Gene ID: 192161, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Pcdha9provided by MGI
    Official Full Name
    protocadherin alpha 9provided by MGI
    Primary source
    MGI:MGI:2447322
    See related
    Ensembl:ENSMUSG00000103770 AllianceGenome:MGI:2447322
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Summary
    Predicted to enable calcium ion binding activity. Acts upstream of or within aorta development; aortic valve development; and gene expression. Located in membrane. Is active in cell-cell contact zone. Is expressed in brain and gut. Orthologous to human PCDHA10 (protocadherin alpha 10). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in CNS E18 (RPKM 19.3), cortex adult (RPKM 12.0) and 7 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Pcdha9 in Genome Data Viewer
    Location:
    18 B2- B3; 18 19.46 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (37130933..37320710)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (36997880..37187657)

    Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_44305 Neighboring gene 3-phosphoglycerate dehydrogenase pseudogene Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha 2 Neighboring gene protocadherin alpha 4B Neighboring gene protocadherin alpha 3 Neighboring gene protocadherin alpha 4 Neighboring gene predicted gene, 38666 Neighboring gene protocadherin alpha 5 Neighboring gene predicted gene, 38667 Neighboring gene predicted gene, 36858 Neighboring gene protocadherin alpha 6 Neighboring gene protocadherin alpha 7 Neighboring gene protocadherin alpha 8 Neighboring gene protocadherin alpha 10 Neighboring gene protocadherin alpha 11 Neighboring gene predicted gene 10545 Neighboring gene protocadherin alpha 5 pseudogene Neighboring gene protocadherin alpha 12 Neighboring gene heat shock transcription factor 2 binding protein pseudogene Neighboring gene protocadherin alpha subfamily C, 1 Neighboring gene protocadherin alpha subfamily C, 2 Neighboring gene predicted gene 10544 Neighboring gene STARR-seq mESC enhancer starr_44309 Neighboring gene protocadherin beta 1 Neighboring gene protocadherin beta 2

    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: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. PCDHA9 as a candidate gene for amyotrophic lateral sclerosis. Zhong J, et al. Nat Commun, 2024 Mar 11. PMID 38467605, Free PMC Article
    2. The Genetic Landscape of Hypoplastic Left Heart Syndrome. Yagi H, et al. Pediatr Cardiol, 2018 Aug. PMID 29569026, Free PMC Article
    3. Identification of two novel PCDHA9 mutations associated with Hirschsprung's disease. Shen Q, et al. Gene, 2018 Jun 5. PMID 29477871
    4. Common deletion variants causing protocadherin-α deficiency contribute to the complex genetics of BAV and left-sided congenital heart disease. Teekakirikul P, et al. HGG Adv, 2021 Jul 8. PMID 34888534, Free PMC Article
    5. The complex genetics of hypoplastic left heart syndrome. Liu X, et al. Nat Genet, 2017 Jul. PMID 28530678, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PCDHA9 as a candidate gene for amyotrophic lateral sclerosis.
      Title: PCDHA9 as a candidate gene for amyotrophic lateral sclerosis.
    Submit: New GeneRIF Correction

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within aorta development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within aortic valve development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within aortic valve development ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    acts_upstream_of_or_within apoptotic process ISA
    Inferred from Sequence Alignment
    more info
    		 PubMed 
    acts_upstream_of_or_within apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    acts_upstream_of_or_within cardiac left ventricle formation ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cell migration ISA
    Inferred from Sequence Alignment
    more info
    		 PubMed 
    acts_upstream_of_or_within cell migration ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    acts_upstream_of_or_within cell population proliferation ISA
    Inferred from Sequence Alignment
    more info
    		 PubMed 
    acts_upstream_of_or_within cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    acts_upstream_of_or_within gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within heart development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    acts_upstream_of_or_within heart valve development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cell-cell contact zone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cell-cell contact zone ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 alpha-9
    Names
    PCDH-alpha-9

    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_138661.1 → NP_619602.1  protocadherin alpha-9 precursor

      See identical proteins and their annotated locations for NP_619602.1

      Status: VALIDATED

      Source sequence(s)
      AY013767
      Consensus CDS
      CCDS37777.1
      UniProtKB/Swiss-Prot
      Q91Y11
      UniProtKB/TrEMBL
      O88195
      Related
      ENSMUSP00000111323.4, ENSMUST00000115659.6
      Conserved Domains (3) summary
      cd11304
      Location:276 → 376
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08266
      Location:60 → 141
      Cadherin_2; Cadherin-like
      pfam15974
      Location:828 → 971
      Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000084.7 Reference GRCm39 C57BL/6J

      Range
      37130933..37320710
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q91Y11.1 GenPept UniProtKB/Swiss-Prot:Q91Y11

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools