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Pcdh17 protocadherin 17 [ Mus musculus (house mouse) ]

Gene ID: 219228, updated on 5-Mar-2024

Summary

Official Symbol
Pcdh17provided by MGI
Official Full Name
protocadherin 17provided by MGI
Primary source
MGI:MGI:2684924
See related
Ensembl:ENSMUSG00000035566 AllianceGenome:MGI:2684924
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Gm78; C030033F14Rik
Summary
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein contains six extracellular cadherin domains, a transmembrane domain, and a cytoplasmic tail differing from those of the classical cadherins. The encoded protein may play a role in the establishment and function of specific cell-cell connections in the brain. [provided by RefSeq, Sep 2009]
Expression
Broad expression in CNS E18 (RPKM 7.2), whole brain E14.5 (RPKM 5.3) and 18 other tissues See more
Orthologs
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Genomic context

See Pcdh17 in Genome Data Viewer
Location:
14 D3; 14 43.54 cM
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (84680626..84775005)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (84443563..84537565)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 32455 Neighboring gene STARR-seq mESC enhancer starr_37315 Neighboring gene STARR-seq mESC enhancer starr_37316 Neighboring gene predicted gene, 29800 Neighboring gene STARR-seq mESC enhancer starr_37317 Neighboring gene STARR-seq mESC enhancer starr_37318 Neighboring gene predicted gene, 32498 Neighboring gene RIKEN cDNA 9630013A20 gene Neighboring gene STARR-seq mESC enhancer starr_37319 Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_37320 Neighboring gene STARR-seq mESC enhancer starr_37321 Neighboring gene STARR-seq mESC enhancer starr_37322 Neighboring gene ribosomal protein L17 pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (2) 

General gene information

Markers

Gene Ontology Provided by MGI

Component Evidence Code Pubs
located_in GABA-ergic synapse IC
Inferred by Curator
more info
PubMed 
is_active_in GABA-ergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in GABA-ergic synapse IEP
Inferred from Expression Pattern
more info
PubMed 
is_active_in GABA-ergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
is_active_in GABA-ergic synapse IPI
Inferred from Physical Interaction
more info
PubMed 
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in glutamatergic synapse IEP
Inferred from Expression Pattern
more info
PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
is_active_in glutamatergic synapse IPI
Inferred from Physical Interaction
more info
PubMed 
is_active_in postsynaptic membrane IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in postsynaptic membrane IEP
Inferred from Expression Pattern
more info
PubMed 
is_active_in presynaptic membrane IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in presynaptic membrane IEP
Inferred from Expression Pattern
more info
PubMed 

General protein information

Preferred Names
protocadherin-17
Names
protocadherin 68

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_001013753.2NP_001013775.2  protocadherin-17 precursor

    Status: REVIEWED

    Source sequence(s)
    AK045478, AK046505, AK139275, AK142358, AK147265, BC089004
    Consensus CDS
    CCDS27304.1
    UniProtKB/TrEMBL
    E9PXF0, Q5HZI5
    Related
    ENSMUSP00000071325.6, ENSMUST00000071370.7
    Conserved Domains (2) summary
    cd11304
    Location:248348
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:21113
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

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_000080.7 Reference GRCm39 C57BL/6J

    Range
    84680626..84775005
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006518905.3XP_006518968.1  protocadherin-17 isoform X1

    UniProtKB/TrEMBL
    Q5HZI5
    Conserved Domains (2) summary
    cd11304
    Location:248348
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:21112
    Cadherin_2; Cadherin-like
  2. XM_006518906.5XP_006518969.1  protocadherin-17 isoform X2

    UniProtKB/TrEMBL
    Q5HZI5
    Conserved Domains (2) summary
    cd11304
    Location:248348
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:21112
    Cadherin_2; Cadherin-like
  3. XM_017315983.3XP_017171472.1  protocadherin-17 isoform X3

    UniProtKB/TrEMBL
    Q5HZI5
    Conserved Domains (2) summary
    cd11304
    Location:248348
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:21112
    Cadherin_2; Cadherin-like

RNA

  1. XR_001781111.3 RNA Sequence

  2. XR_003950846.2 RNA Sequence

  3. XR_004938388.1 RNA Sequence

  4. XR_003950845.2 RNA Sequence