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    Pcdh9 protocadherin 9 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 306091, updated on 9-Dec-2024

    Summary

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    Symbol
    Pcdh9provided by RGD
    Full Name
    protocadherin 9provided by RGD
    Primary source
    RGD:1306348
    See related
    EnsemblRapid:ENSRNOG00000038068 AllianceGenome:RGD:1306348
    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. Involved in forebrain development. Is active in glutamatergic synapse and synaptic membrane. Orthologous to human PCDH9 (protocadherin 9). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 327.7) and Adrenal (RPKM 17.0) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pcdh9 in Genome Data Viewer
    Location:
    15q21
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (75748472..76646644, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (69340108..70237531, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (76787108..77738668, complement)

    Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA17 Neighboring gene U2 spliceosomal RNA Neighboring gene U1 spliceosomal RNA Neighboring gene uncharacterized LOC120097140 Neighboring gene voltage-dependent anion channel 1, pseudogene 13 Neighboring gene SNF related kinase, pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Spatiotemporal expression pattern of non-clustered protocadherin family members in the developing rat brain. Kim SY, et al. Neuroscience, 2007 Jul 29. PMID 17614211
    2. Distribution of protocadherin 9 protein in the developing mouse nervous system. Asahina H, et al. Neuroscience, 2012 Dec 6. PMID 22982106
    3. Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. Loh KH, et al. Cell, 2016 Aug 25. PMID 27565350, Free PMC Article
    4. 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

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    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 forebrain development IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell-cell contact zone ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in glutamatergic synapse EXP
    Inferred from Experiment
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in growth cone ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in synaptic membrane EXP
    Inferred from Experiment
    more info
    		 PubMed 
    is_active_in synaptic membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protocadherin-9

    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.

    mRNA and Protein(s)

    1. NM_001191688.2 → NP_001178617.1  protocadherin-9 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A0A8I5ZK96, A6HU40
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 1000
      Protocadherin

    2. NM_001431494.1 → NP_001418423.1  protocadherin-9 isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A0A8I5ZK96, A6HU40

    3. NM_001431495.1 → NP_001418424.1  protocadherin-9 isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A6HU38, A6HU40, F1LS01

    4. NM_001431496.1 → NP_001418425.1  protocadherin-9 isoform 2 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A6HU38, A6HU40, F1LS01

    5. NM_001431497.1 → NP_001418426.1  protocadherin-9 isoform 3 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A6HU40

    6. NM_001431498.1 → NP_001418427.1  protocadherin-9 isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A6HU40

    7. NM_001431499.1 → NP_001418428.1  protocadherin-9 isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A6HU40

    RNA

    1. NR_197223.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015

    2. NR_197224.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015

    3. NR_197225.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015

    4. NR_197226.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015

    5. NR_197227.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015

    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_086033.1 Reference GRCr8

      Range
      75748472..76646644 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    2. NC_086033.1 Reference GRCr8

      Range
      76078024..76127778 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008770867.4 → XP_008769089.2  protocadherin-9 isoform X4

      UniProtKB/TrEMBL
      A6HU40

    2. XM_017599711.3 → XP_017455200.1  protocadherin-9 isoform X2

      UniProtKB/TrEMBL
      A6HU38, A6HU40, F1LS01
      Related
      ENSRNOP00000054733.5, ENSRNOT00000057924.6
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    3. XM_017599712.3 → XP_017455201.1  protocadherin-9 isoform X3

      UniProtKB/TrEMBL
      A6HU40

    4. XM_017599710.3 → XP_017455199.1  protocadherin-9 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZK96, A6HU40
      Related
      ENSRNOP00000077280.1, ENSRNOT00000096830.2
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 1000
      Protocadherin

    5. XM_039093368.2 → XP_038949296.1  protocadherin-9 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZK96, A6HU40
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 1000
      Protocadherin

    6. XM_063274319.1 → XP_063130389.1  protocadherin-9 isoform X4

      UniProtKB/TrEMBL
      A6HU40

    7. XM_063274318.1 → XP_063130388.1  protocadherin-9 isoform X2

      UniProtKB/TrEMBL
      A6HU38, A6HU40, F1LS01

    8. XM_039093373.2 → XP_038949301.1  protocadherin-9 isoform X9

      UniProtKB/TrEMBL
      A6HU40
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 1000
      Protocadherin

    9. XM_039093372.2 → XP_038949300.1  protocadherin-9 isoform X7

      UniProtKB/TrEMBL
      A6HU40
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 1000
      Protocadherin

    10. XM_017599713.3 → XP_017455202.1  protocadherin-9 isoform X5

      UniProtKB/TrEMBL
      A6HU40

    11. XM_039093371.2 → XP_038949299.1  protocadherin-9 isoform X6

      UniProtKB/TrEMBL
      A6HU40
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 1000
      Protocadherin

    12. XM_063274320.1 → XP_063130390.1  protocadherin-9 isoform X8

      UniProtKB/TrEMBL
      A6HU40

    13. XM_039093374.2 → XP_038949302.1  protocadherin-9 isoform X10

      UniProtKB/TrEMBL
      A6HU40
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 1000
      Protocadherin
    Nucleotide Protein Strain
    Heading Accession and Version

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