U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Pcdh9 protocadherin 9 [ Rattus norvegicus (Norway rat) ]

Gene ID: 306091, updated on 4-Jan-2025

Summary

Go to the top of the page Help
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, Jan 2025]
Expression
Biased expression in Brain (RPKM 327.7) and Adrenal (RPKM 17.0) 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 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

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. 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

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 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

Go to the top of the page Help
Preferred Names
protocadherin-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_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

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