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    Pogk pogo transposable element derived with KRAB domain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304941, updated on 30-Mar-2024

    Summary

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    Official Symbol
    Pogkprovided by RGD
    Official Full Name
    pogo transposable element derived with KRAB domainprovided by RGD
    Primary source
    RGD:1308951
    See related
    Ensembl:ENSRNOG00000032058 AllianceGenome:RGD:1308951
    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 DNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Orthologous to human POGK (pogo transposable element derived with KRAB domain). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Lung (RPKM 118.1), Adrenal (RPKM 72.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    13q23
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (81180410..81196326, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (78647447..78663363, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (84603126..84619042, complement)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene cold shock domain-containing protein E1-like Neighboring gene maelstrom spermatogenic transposon silencer Neighboring gene immunoglobulin-like domain containing receptor 2 Neighboring gene uncharacterized LOC120096307 Neighboring gene uncharacterized LOC120096308 Neighboring gene transcriptional adaptor 1 Neighboring gene flavin-containing monooxygenase 13 Neighboring gene flavin containing dimethylaniline monoxygenase like

    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. 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 DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    pogo transposable element with KRAB domain

    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_001107194.2 → NP_001100664.2  pogo transposable element with KRAB domain

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      D3ZV46
      Related
      ENSRNOP00000051209.2, ENSRNOT00000045056.4
      Conserved Domains (5) summary
      cd07765
      Location:68 → 105
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      smart00674
      Location:275 → 342
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      smart00349
      Location:68 → 123
      KRAB; krueppel associated box
      pfam03184
      Location:414 → 586
      DDE_1; DDE superfamily endonuclease
      pfam09607
      Location:214 → 266
      BrkDBD; Brinker DNA-binding domain

    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_086031.1 Reference GRCr8

      Range
      81180410..81196326 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017598827.3 → XP_017454316.1  pogo transposable element with KRAB domain isoform X1

      UniProtKB/TrEMBL
      A0A8I6A8F7, A6IDK2
      Related
      ENSRNOP00000088020.1
      Conserved Domains (5) summary
      cd07765
      Location:56 → 93
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      smart00674
      Location:263 → 330
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      smart00349
      Location:56 → 111
      KRAB; krueppel associated box
      pfam03184
      Location:402 → 574
      DDE_1; DDE superfamily endonuclease
      pfam09607
      Location:202 → 254
      BrkDBD; Brinker DNA-binding domain

    2. XM_017598828.3 → XP_017454317.1  pogo transposable element with KRAB domain isoform X2

      Conserved Domains (5) summary
      cd07765
      Location:49 → 86
      KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
      smart00674
      Location:256 → 323
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      smart00349
      Location:49 → 104
      KRAB; krueppel associated box
      pfam03184
      Location:395 → 567
      DDE_1; DDE superfamily endonuclease
      pfam09607
      Location:195 → 247
      BrkDBD; Brinker DNA-binding domain

    3. XM_039090789.2 → XP_038946717.1  pogo transposable element with KRAB domain isoform X3

      UniProtKB/TrEMBL
      A6IDK3
      Conserved Domains (3) summary
      smart00674
      Location:122 → 189
      CENPB; Putative DNA-binding domain in centromere protein B, mouse jerky and transposases
      pfam03184
      Location:261 → 433
      DDE_1; DDE superfamily endonuclease
      pfam09607
      Location:61 → 113
      BrkDBD; Brinker DNA-binding domain
    Nucleotide Protein Strain
    Heading Accession and Version

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