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Pcdh17 protocadherin 17 [ Rattus norvegicus (Norway rat) ]

Gene ID: 306055, updated on 10-Oct-2024

Summary

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Official Symbol
Pcdh17provided by RGD
Official Full Name
protocadherin 17provided by RGD
Primary source
RGD:1304753
See related
EnsemblRapid:ENSRNOG00000008970 AllianceGenome:RGD:1304753
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 synaptic membrane adhesion. Predicted to act upstream of or within several processes, including negative regulation of synaptic transmission; presynaptic active zone assembly; and regulation of synaptic vesicle clustering. Predicted to be active in GABA-ergic synapse and glutamatergic synapse. Predicted to be integral component of postsynaptic membrane and integral component of presynaptic membrane. Orthologous to human PCDH17 (protocadherin 17). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Lung (RPKM 99.4), Brain (RPKM 89.2) and 7 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Pcdh17 in Genome Data Viewer
Location:
15q12
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (66631549..66725007)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (60222088..60316172)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (67555835..67647990)

Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA17 Neighboring gene small nucleolar RNA U3 Neighboring gene uncharacterized LOC108352949 Neighboring gene uncharacterized LOC120097053 Neighboring gene U6 spliceosomal RNA

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 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. Protocadherin 17 regulates presynaptic assembly in topographic corticobasal Ganglia circuits. Hoshina N, et al. Neuron, 2013 Jun 5. PMID 23684785
  2. 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
acts_upstream_of_or_within adult behavior ISO
Inferred from Sequence Orthology
more info
  
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
  
acts_upstream_of_or_within negative regulation of synaptic transmission ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within presynaptic active zone assembly ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within regulation of synaptic vesicle clustering ISO
Inferred from Sequence Orthology
more info
  
involved_in synaptic membrane adhesion ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in GABA-ergic synapse ISO
Inferred from Sequence Orthology
more info
  
is_active_in glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in postsynaptic membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in presynaptic membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
protocadherin-17

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_001431447.1 → NP_001418376.1  protocadherin-17 isoform 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000015

  2. NM_001431448.1 → NP_001418377.1  protocadherin-17 isoform 2

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000015

  3. NM_001431449.1 → NP_001418378.1  protocadherin-17 isoform 3

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000015

  4. NM_001431450.1 → NP_001418379.1  protocadherin-17 isoform 4

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000015
    UniProtKB/TrEMBL
    A0A8I5ZPT5

  5. NM_001431451.1 → NP_001418380.1  protocadherin-17 isoform 5

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000015

  6. NM_001431452.1 → NP_001418381.1  protocadherin-17 isoform 6

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000015

  7. NM_001431453.1 → NP_001418382.1  protocadherin-17 isoform 7

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000015
    UniProtKB/TrEMBL
    A0A8I5ZZ04

RNA

  1. NR_197215.1 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
    66631549..66725007
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063274313.1 → XP_063130383.1  protocadherin-17 isoform X10

  2. XM_006252377.5 → XP_006252439.1  protocadherin-17 isoform X1

    Related
    ENSRNOP00000084215.2, ENSRNOT00000103578.2
    Conserved Domains (2) summary
    cd11304
    Location:248 → 348
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:21 → 113
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  3. XM_006252379.4 → XP_006252441.1  protocadherin-17 isoform X3

    Conserved Domains (2) summary
    cd11304
    Location:248 → 348
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:21 → 113
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  4. XM_006252378.5 → XP_006252440.1  protocadherin-17 isoform X2

    UniProtKB/TrEMBL
    A6HU20, D3ZPN0
    Conserved Domains (2) summary
    cd11304
    Location:248 → 348
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:21 → 113
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  5. XM_063274309.1 → XP_063130379.1  protocadherin-17 isoform X4

  6. XM_063274310.1 → XP_063130380.1  protocadherin-17 isoform X5

  7. XM_063274311.1 → XP_063130381.1  protocadherin-17 isoform X6

  8. XM_063274312.1 → XP_063130382.1  protocadherin-17 isoform X8

  9. XM_006252381.5 → XP_006252443.1  protocadherin-17 isoform X7

    Conserved Domains (2) summary
    cd11304
    Location:248 → 348
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:21 → 113
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  10. XM_039093360.2 → XP_038949288.1  protocadherin-17 isoform X9

    UniProtKB/TrEMBL
    A6HU20, D3ZPN0
    Conserved Domains (2) summary
    cd11304
    Location:248 → 348
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:21 → 113
    Cadherin_2; Cadherin-like

  11. XM_063274314.1 → XP_063130384.1  protocadherin-17 isoform X11

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001107279.1: Suppressed sequence

    Description
    NM_001107279.1: This RefSeq was removed because currently there is insufficient support for the transcript.
Nucleotide Protein Strain
Heading Accession and Version

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