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    Pcdh11x protocadherin 11 X-linked [ Rattus norvegicus (Norway rat) ]

    Gene ID: 317204, updated on 30-Mar-2024

    Summary

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    Symbol
    Pcdh11xprovided by RGD
    Full Name
    protocadherin 11 X-linkedprovided by RGD
    Primary source
    RGD:1562864
    See related
    Ensembl:ENSRNOG00000069840 AllianceGenome:RGD:1562864
    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
    Also known as
    RGD1562864
    Summary
    Orthologous to human PCDH11X (protocadherin 11 X-linked). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 86.9), Testes (RPKM 33.5) and 5 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    Xq31
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) X NC_086039.1 (90279191..90974671)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) X NC_051356.1 (86058348..86751078)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) X NC_005120.4 (92596355..93341412)

    Chromosome X - NC_086039.1Genomic Context describing neighboring genes Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene uncharacterized LOC108349237 Neighboring gene uncharacterized LOC134484094 Neighboring gene VENT homeobox Neighboring gene U6 spliceosomal RNA Neighboring gene 60 kDa heat shock protein, mitochondrial pseudogene Neighboring gene ribosomal protein L27, pseudogene 9

    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. Docking motif-guided mapping of the interactome of protein phosphatase-1. Hendrickx A, et al. Chem Biol, 2009 Apr 24. PMID 19389623
    2. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. Prunotto M, et al. J Proteomics, 2013 Apr 26. PMID 23376485
    3. 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 homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin-11 X-linked
    Names
    protocadherin-11 X-linked-like

    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_001271228.1 → NP_001258157.1  protocadherin-11 X-linked precursor

      See identical proteins and their annotated locations for NP_001258157.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000021
      UniProtKB/TrEMBL
      A0A8I6AKA9
      Related
      ENSRNOP00000093805.1, ENSRNOT00000106182.1
      Conserved Domains (4) summary
      cd11304
      Location:253 → 351
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:384 → 464
      CA; Cadherin repeats
      pfam08374
      Location:775 → 977
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 114
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086039.1 Reference GRCr8

      Range
      90279191..90974671
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039099733.2 → XP_038955661.1  protocadherin-11 X-linked isoform X1

      Conserved Domains (5) summary
      cd11304
      Location:253 → 351
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:384 → 464
      CA; Cadherin repeats
      pfam08266
      Location:28 → 99
      Cadherin_2; Cadherin-like
      pfam08374
      Location:775 → 977
      Protocadherin
      pfam14642
      Location:1148 → 1223
      FAM47; FAM47 family

    2. XM_039099735.2 → XP_038955663.1  protocadherin-11 X-linked isoform X3

      UniProtKB/TrEMBL
      A0A8I6AEP1
      Related
      ENSRNOP00000091088.1
      Conserved Domains (5) summary
      cd11304
      Location:253 → 351
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:384 → 464
      CA; Cadherin repeats
      pfam08266
      Location:28 → 99
      Cadherin_2; Cadherin-like
      pfam08374
      Location:775 → 977
      Protocadherin
      pfam14642
      Location:1138 → 1213
      FAM47; FAM47 family

    3. XM_039099734.2 → XP_038955662.1  protocadherin-11 X-linked isoform X2

      Conserved Domains (5) summary
      cd11304
      Location:253 → 351
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:384 → 464
      CA; Cadherin repeats
      pfam08266
      Location:28 → 99
      Cadherin_2; Cadherin-like
      pfam08374
      Location:775 → 977
      Protocadherin
      pfam14642
      Location:1146 → 1221
      FAM47; FAM47 family
    Nucleotide Protein Strain
    Heading Accession and Version

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